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Geant4/examples/advanced/dna/dsbandrepair/dsbandrepair.cc

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Diff markup

Differences between /examples/advanced/dna/dsbandrepair/dsbandrepair.cc (Version 11.3.0) and /examples/advanced/dna/dsbandrepair/dsbandrepair.cc (Version 11.0.p4)


  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 //  author: Le Tuan Anh, 20/10/2023               
 27 /// \file main.cc                                 
 28 /// \brief Main program of the dsbandrepair       
 29                                                   
 30 #include "G4UImanager.hh"                         
 31 #include "G4UIterminal.hh"                        
 32 #include "G4UItcsh.hh"                            
 33 #include "G4UIExecutive.hh"                       
 34                                                   
 35 #include "G4RunManagerFactory.hh"                 
 36                                                   
 37 #ifdef G4VIS_USE                                  
 38 #include "G4VisExecutive.hh"                      
 39 #endif                                            
 40                                                   
 41 #include "G4Timer.hh"                             
 42 #include "G4ExceptionSeverity.hh"                 
 43 #include "G4DNAChemistryManager.hh"               
 44 #include "G4VisExecutive.hh"                      
 45 #include "G4Filesystem.hh"                        
 46                                                   
 47 #include "ActionInitialization.hh"                
 48 #include "DetectorConstruction.hh"                
 49 #include "PhysicsList.hh"                         
 50                                                   
 51 #include "Analysis.hh"                            
 52                                                   
 53 #ifdef USE_MPI                                    
 54 #include "G4MPImanager.hh"                        
 55 #include "G4MPIsession.hh"                        
 56 #include "G4MPIextraWorker.hh"                    
 57 #endif                                            
 58 #include <ctime>                                  
 59                                                   
 60 //....oooOO0OOooo........oooOO0OOooo........oo    
 61                                                   
 62 G4String ExtractChemListNameFromMacroFile(G4St    
 63                                                   
 64 //....oooOO0OOooo........oooOO0OOooo........oo    
 65                                                   
 66 int main(int argc,char** argv)                    
 67 {                                                 
 68 #ifdef USE_MPI                                    
 69         G4MPImanager* g4MPI = new G4MPImanager    
 70         g4MPI->SetVerbose(1);                     
 71         G4MPIsession* session = g4MPI-> GetMPI    
 72         G4String prompt = "";          
 73         prompt += "G4MPI";                        
 74         prompt += "(%s)[%/][0    
 75         session-> SetPrompt(prompt);              
 76 #else                                             
 77         G4UIExecutive* ui = nullptr;              
 78         if ( argc == 1 ) { ui = new G4UIExecut    
 79 #endif // USE_MPI                                 
 80     if (argc < 2) {                               
 81         G4cerr<<"====>> Wrong input. To run Ph    
 82             <<"To run Chem_geo, type : ./dsban    
 83         #ifdef USE_MPI                            
 84             delete g4MPI;                         
 85         #endif // USE_MPI                         
 86         return EXIT_SUCCESS;                      
 87     }                                             
 88     G4String stgstr = "";                         
 89     G4String macrofileName = argv[1];             
 90     if (argc > 2) {                               
 91         const G4String rmode = argv[2];           
 92         if (rmode == "phys") gRunMode = Runnin    
 93         else if (rmode == "chem") gRunMode = R    
 94         else {                                    
 95             G4cout<<"Undefined Running Mode =     
 96             #ifdef USE_MPI                        
 97                 delete g4MPI;                     
 98             #endif // USE_MPI                     
 99             return  EXIT_SUCCESS;                 
100         }                                         
101     }                                             
102     // Choose the Random engine                   
103     time_t timeStart;                             
104     time(&timeStart);                             
105     unsigned long seed = timeStart;               
106 #ifdef USE_MPI                                    
107     // Le Tuan Anh: add rankID to get differen    
108     seed += g4MPI->GetRank();                     
109 #endif // USE_MPI                                 
110     G4cout<<"Initial Seed for random engine: "    
111     CLHEP::HepRandom::setTheEngine(new CLHEP::    
112     CLHEP::HepRandom::setTheSeed(seed);           
113     G4RunManager* runManager{nullptr};            
114     auto analysis = Analysis::GetAnalysis();      
115     if (gRunMode == RunningMode::Phys) {          
116         stgstr = "physical stage";                
117         runManager = G4RunManagerFactory::Crea    
118 #ifdef G4MULTITHREADED                            
119         G4int threadNumber= 1;                    
120         runManager-> SetNumberOfThreads(thread    
121 #endif  // G4MULTITHREADED                        
122 #ifdef USE_MPI                                    
123         stgstr += " in #rank"+std::to_string(g    
124         if (g4MPI->IsMaster()) analysis->Check    
125 #else                                             
126         analysis->CheckAndCreateNewFolderInPhy    
127 #endif                                            
128     } else if (gRunMode == RunningMode::Chem)     
129         stgstr = "chemical stage";                
130         runManager = G4RunManagerFactory::Crea    
131         G4DNAChemistryManager::Instance()->Set    
132         G4Scheduler::Instance();                  
133     }                                             
134                                                   
135     DetectorConstruction* detector = new Detec    
136     runManager->SetUserInitialization(detector    
137     PhysicsList* physList = new PhysicsList;      
138     ActionInitialization* actionIni = new Acti    
139                                                   
140     if (gRunMode == RunningMode::Phys) {          
141         runManager->SetUserInitialization(phys    
142         runManager->SetUserInitialization(acti    
143 #ifdef USE_MPI                                    
144         session-> SessionStart();                 
145         if (g4MPI->GetRank() == 0 ){              
146             analysis->WritePhysGeo();             
147         }                                         
148 #else                                             
149         // Get the pointer to the User Interfa    
150         G4UImanager* UImanager = G4UImanager::    
151         // Process macro or start UI session      
152         if ( ! ui ) {                             
153             // batch mode                         
154             G4String command = "/control/execu    
155             UImanager->ApplyCommand(command+ma    
156         }                                         
157         analysis->WritePhysGeo();                 
158 #endif // USE_MPI                                 
159     }                                             
160                                                   
161                                                   
162     if (gRunMode == RunningMode::Chem) {          
163         //get the pointer to the User Interfac    
164         G4UImanager* UI = G4UImanager::GetUIpo    
165 #ifdef USE_MPI                                    
166         session->SessionStart();                  
167         stgstr += " in #rank"+std::to_string(g    
168         if (g4MPI->IsMaster()) analysis->Check    
169 #else                                             
170         G4String command = "/control/execute "    
171         UI->ApplyCommand(command+macrofileName    
172         analysis->CheckAndCreateNewFolderInChe    
173 #endif                                            
174         //------------------------------------    
175         // Prepare input file                     
176         //------------------------------------    
177         std::string inputFileorFolder = "chem_    
178         if (argc == 4) inputFileorFolder = arg    
179         G4fs::path p{inputFileorFolder};          
180         G4String outputFileName = "test";         
181         std::vector<G4String> totalNumberofFil    
182         if (G4fs::is_directory(p)) {              
183             for (const auto& entry : G4fs::dir    
184                 if (entry.path().extension() =    
185                     totalNumberofFilesVector.p    
186                 }                                 
187             }                                     
188             std::sort(totalNumberofFilesVector    
189 #ifdef USE_MPI                                    
190             G4int numberofRanks = g4MPI->GetAc    
191             size_t filesTobeProcessedSlave = (    
192                 std::floor(G4double(totalNumbe    
193             // note: should not use "std::ceil    
194             size_t filesTobeProcessedMaster =     
195                 totalNumberofFilesVector.size(    
196             if (g4MPI->IsMaster()) {              
197                 for (size_t ii=0; ii< filesTob    
198                     numberOfFilesTobeProcessed    
199                 }                                 
200             } else {                              
201                 for (size_t ii=0; ii< filesTob    
202                     auto rankID = g4MPI->GetRa    
203                     size_t kk = filesTobeProce    
204                     numberOfFilesTobeProcessed    
205                 }                                 
206             }                                     
207             G4cout<<"-----> "<<numberOfFilesTo    
208                     <<" files will be processe    
209 #else                                             
210             numberOfFilesTobeProcessedVector =    
211 #endif                                            
212             if (totalNumberofFilesVector.size(    
213                 G4cout<<"===>> There is no fil    
214                 <<". You have to run Phys_geo     
215                 #ifdef USE_MPI                    
216                 delete g4MPI;                     
217                 #endif // USE_MPI                 
218                 delete runManager;                
219                 return EXIT_SUCCESS;              
220             } else {                              
221                 G4cout<<"===>> Total files fou    
222                 <<" : "<<totalNumberofFilesVec    
223             }                                     
224         } else if (G4fs::is_regular_file(p)) {    
225             numberOfFilesTobeProcessedVector.p    
226             if (p.has_stem()) {                   
227                 outputFileName = p.stem().stri    
228             } else outputFileName = inputFileo    
229         }                                         
230         else G4cout<<"===>>dsbandrepair: "<<p.    
231         G4String firstFileForInit="";             
232         if (numberOfFilesTobeProcessedVector.s    
233             firstFileForInit=numberOfFilesTobe    
234             detector->ParseGeoFileForChemMode(    
235         }                                         
236         //------------------------------------    
237         // Initialization classes                 
238         //------------------------------------    
239                                                   
240         runManager->SetUserInitialization(phys    
241         runManager->SetUserInitialization(acti    
242         runManager->Initialize();                 
243         if (numberOfFilesTobeProcessedVector.s    
244             size_t nprocessedfiles{0}, ncounts    
245             if (numberOfFilesTobeProcessedVect    
246             if (numberOfFilesTobeProcessedVect    
247             if (numberOfFilesTobeProcessedVect    
248             for (auto const &fileInput : numbe    
249                 G4fs::path aP{std::string(file    
250                 if (aP.has_stem()) {              
251                     outputFileName = aP.stem()    
252                 } else outputFileName = fileIn    
253                 analysis->SetFileName(outputFi    
254                 if (fileInput != firstFileForI    
255                 detector->InsertMoleculeInWorl    
256                 UI->ApplyCommand("/run/beamOn     
257                 nprocessedfiles++;                
258                 if (nprocessedfiles == 1 ||       
259                     nprocessedfiles == numberO    
260                     0 == (nprocessedfiles % nc    
261                     G4cout<<"=====> Processed     
262                           <<numberOfFilesTobeP    
263 #ifdef USE_MPI                                    
264                           <<" in rank #"<<g4MP    
265 #endif                                            
266                           <<"!!!"<<G4endl;        
267                 }                                 
268             }                                     
269         } else {                                  
270             UI->ApplyCommand("/run/beamOn 1");    
271         }                                         
272     }                                             
273                                                   
274 #ifdef USE_MPI                                    
275     delete g4MPI;                                 
276 #endif // USE_MPI                                 
277     delete runManager;                            
278                                                   
279     G4cout  <<"----------------------> Finish     
280     return EXIT_SUCCESS;                          
281 }                                                 
282                                                   
283 //....oooOO0OOooo........oooOO0OOooo........oo    
284