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Geant4/examples/extended/medical/dna/chem1/chem1.cc

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Diff markup

Differences between /examples/extended/medical/dna/chem1/chem1.cc (Version 11.3.0) and /examples/extended/medical/dna/chem1/chem1.cc (Version 11.2)


  1 //                                                  1 //
  2 // *******************************************      2 // ********************************************************************
  3 // * License and Disclaimer                         3 // * License and Disclaimer                                           *
  4 // *                                                4 // *                                                                  *
  5 // * The  Geant4 software  is  copyright of th      5 // * The  Geant4 software  is  copyright of the Copyright Holders  of *
  6 // * the Geant4 Collaboration.  It is provided      6 // * the Geant4 Collaboration.  It is provided  under  the terms  and *
  7 // * conditions of the Geant4 Software License      7 // * conditions of the Geant4 Software License,  included in the file *
  8 // * LICENSE and available at  http://cern.ch/      8 // * LICENSE and available at  http://cern.ch/geant4/license .  These *
  9 // * include a list of copyright holders.           9 // * include a list of copyright holders.                             *
 10 // *                                               10 // *                                                                  *
 11 // * Neither the authors of this software syst     11 // * Neither the authors of this software system, nor their employing *
 12 // * institutes,nor the agencies providing fin     12 // * institutes,nor the agencies providing financial support for this *
 13 // * work  make  any representation or  warran     13 // * work  make  any representation or  warranty, express or implied, *
 14 // * regarding  this  software system or assum     14 // * regarding  this  software system or assume any liability for its *
 15 // * use.  Please see the license in the file      15 // * use.  Please see the license in the file  LICENSE  and URL above *
 16 // * for the full disclaimer and the limitatio     16 // * for the full disclaimer and the limitation of liability.         *
 17 // *                                               17 // *                                                                  *
 18 // * This  code  implementation is the result      18 // * This  code  implementation is the result of  the  scientific and *
 19 // * technical work of the GEANT4 collaboratio     19 // * technical work of the GEANT4 collaboration.                      *
 20 // * By using,  copying,  modifying or  distri     20 // * By using,  copying,  modifying or  distributing the software (or *
 21 // * any work based  on the software)  you  ag     21 // * any work based  on the software)  you  agree  to acknowledge its *
 22 // * use  in  resulting  scientific  publicati     22 // * use  in  resulting  scientific  publications,  and indicate your *
 23 // * acceptance of all terms of the Geant4 Sof     23 // * acceptance of all terms of the Geant4 Software license.          *
 24 // *******************************************     24 // ********************************************************************
 25 //                                                 25 //
 26 // This example is provided by the Geant4-DNA      26 // This example is provided by the Geant4-DNA collaboration
 27 // Any report or published results obtained us     27 // Any report or published results obtained using the Geant4-DNA software
 28 // shall cite the following Geant4-DNA collabo     28 // shall cite the following Geant4-DNA collaboration publication:
 29 // Med. Phys. 37 (2010) 4692-4708                  29 // Med. Phys. 37 (2010) 4692-4708
 30 // J. Comput. Phys. 274 (2014) 841-882             30 // J. Comput. Phys. 274 (2014) 841-882
 31 // The Geant4-DNA web site is available at htt     31 // The Geant4-DNA web site is available at http://geant4-dna.org
 32 //                                                 32 //
 33 //                                                 33 //
 34 /// \file chem1.cc                                 34 /// \file chem1.cc
 35 /// \brief Chem1 example                           35 /// \brief Chem1 example
 36                                                    36 
 37 #include "ActionInitialization.hh"             << 
 38 #include "CommandLineParser.hh"                << 
 39 #include "DetectorConstruction.hh"                 37 #include "DetectorConstruction.hh"
 40 #include "PhysicsList.hh"                          38 #include "PhysicsList.hh"
                                                   >>  39 #include "ActionInitialization.hh"
 41                                                    40 
 42 #include "G4DNAChemistryManager.hh"            << 
 43 #include "G4RunManagerFactory.hh"                  41 #include "G4RunManagerFactory.hh"
 44 #include "G4UIExecutive.hh"                    <<  42 
                                                   >>  43 #include "G4DNAChemistryManager.hh"
 45 #include "G4UImanager.hh"                          44 #include "G4UImanager.hh"
                                                   >>  45 #include "G4UIExecutive.hh"
 46 #include "G4VisExecutive.hh"                       46 #include "G4VisExecutive.hh"
 47                                                    47 
                                                   >>  48 #include "CommandLineParser.hh"
                                                   >>  49 
 48 //....oooOO0OOooo........oooOO0OOooo........oo     50 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 49                                                    51 
 50 /*                                                 52 /*
 51  * WARNING : Geant4 was initially not intended     53  * WARNING : Geant4 was initially not intended for this kind of application
 52  * This code is delivered as a prototype           54  * This code is delivered as a prototype
 53  * We will be happy to hear from you, do not h     55  * We will be happy to hear from you, do not hesitate to send your feedback and
 54  * communicate on the difficulties you may enc     56  * communicate on the difficulties you may encounter
 55  * The user interface may change in the next r     57  * The user interface may change in the next releases since a reiteration of the
 56  * code has started                                58  * code has started
 57  */                                                59  */
 58                                                    60 
 59 using namespace G4DNAPARSER;                       61 using namespace G4DNAPARSER;
 60 CommandLineParser* parser(0);                      62 CommandLineParser* parser(0);
 61                                                    63 
 62 void Parse(int& argc, char** argv);                64 void Parse(int& argc, char** argv);
 63                                                    65 
 64 int main(int argc, char** argv)                    66 int main(int argc, char** argv)
 65 {                                                  67 {
 66   //////////                                       68   //////////
 67   // Parse options given in commandLine            69   // Parse options given in commandLine
 68   //                                               70   //
 69   Parse(argc, argv);                               71   Parse(argc, argv);
 70                                                    72 
 71   //////////                                       73   //////////
 72   // Construct the run manager according to wh     74   // Construct the run manager according to whether MT is activated or not
 73   //                                               75   //
 74   Command* commandLine(nullptr);                   76   Command* commandLine(nullptr);
 75                                                    77 
 76   auto* runManager = G4RunManagerFactory::Crea <<  78   auto* runManager= G4RunManagerFactory::CreateRunManager();
 77   if ((commandLine = parser->GetCommandIfActiv <<  79   if ((commandLine = parser->GetCommandIfActive("-mt")))
                                                   >>  80   {
 78     int nThreads = 2;                              81     int nThreads = 2;
 79     if (commandLine->GetOption() == "NMAX") {  <<  82     if(commandLine->GetOption() == "NMAX")
                                                   >>  83     {
 80       nThreads = G4Threading::G4GetNumberOfCor     84       nThreads = G4Threading::G4GetNumberOfCores();
 81     }                                              85     }
 82     else {                                     <<  86     else
                                                   >>  87     {
 83       nThreads = G4UIcommand::ConvertToInt(com     88       nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
 84     }                                              89     }
 85     runManager->SetNumberOfThreads(nThreads);      90     runManager->SetNumberOfThreads(nThreads);
 86     G4cout << "===== Chem1 is started with " <     91     G4cout << "===== Chem1 is started with " << runManager->GetNumberOfThreads()
 87            << " threads =====" << G4endl;          92            << " threads =====" << G4endl;
 88   }                                                93   }
 89                                                    94 
                                                   >>  95 
 90   //////////                                       96   //////////
 91   // Set mandatory user initialization classes     97   // Set mandatory user initialization classes
 92   //                                               98   //
 93   DetectorConstruction* detector = new Detecto     99   DetectorConstruction* detector = new DetectorConstruction();
 94   runManager->SetUserInitialization(new Physic    100   runManager->SetUserInitialization(new PhysicsList);
 95   runManager->SetUserInitialization(detector);    101   runManager->SetUserInitialization(detector);
 96   runManager->SetUserInitialization(new Action    102   runManager->SetUserInitialization(new ActionInitialization());
 97                                                   103 
 98   // Initialize visualization                     104   // Initialize visualization
 99   G4VisManager* visManager = nullptr;             105   G4VisManager* visManager = nullptr;
100                                                   106 
101   // Get the pointer to the User Interface man    107   // Get the pointer to the User Interface manager
102   G4UImanager* UImanager = G4UImanager::GetUIp    108   G4UImanager* UImanager = G4UImanager::GetUIpointer();
103   G4UIExecutive* ui(nullptr);                     109   G4UIExecutive* ui(nullptr);
104                                                   110 
105   // interactive mode : define UI session         111   // interactive mode : define UI session
106   if ((commandLine = parser->GetCommandIfActiv << 112   if ((commandLine = parser->GetCommandIfActive("-gui")))
                                                   >> 113   {
107     visManager = new G4VisExecutive;              114     visManager = new G4VisExecutive;
108     visManager->Initialize();                     115     visManager->Initialize();
109                                                   116 
110     ui = new G4UIExecutive(argc, argv, command    117     ui = new G4UIExecutive(argc, argv, commandLine->GetOption());
111                                                   118 
112     if (parser->GetCommandIfActive("-novis") = << 119     if(parser->GetCommandIfActive("-novis") == 0)
                                                   >> 120     {
113       // visualization is used by default         121       // visualization is used by default
114       if ((commandLine = parser->GetCommandIfA << 122       if((commandLine = parser->GetCommandIfActive("-vis")))
                                                   >> 123       {
115         // select a visualization driver if ne    124         // select a visualization driver if needed (e.g. HepFile)
116         UImanager->ApplyCommand(G4String("/vis << 125         UImanager->ApplyCommand(G4String("/vis/open ")+
                                                   >> 126                                 commandLine->GetOption());
117       }                                           127       }
118       else {                                   << 128       else
                                                   >> 129       {
119         // by default OGL is used                 130         // by default OGL is used
120         UImanager->ApplyCommand("/vis/open OGL    131         UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
121       }                                           132       }
122       UImanager->ApplyCommand("/control/execut    133       UImanager->ApplyCommand("/control/execute vis.mac");
123     }                                             134     }
124                                                   135 
125     if (ui->IsGUI()) {                         << 136     if(ui->IsGUI())
                                                   >> 137     {
126       UImanager->ApplyCommand("/control/execut    138       UImanager->ApplyCommand("/control/execute gui.mac");
127     }                                             139     }
128   }                                               140   }
129   else if ((commandLine = parser->GetCommandIf << 141   else if ((commandLine = parser->GetCommandIfActive("-vis")))
                                                   >> 142   {
130     // to be use visualization file (= store t    143     // to be use visualization file (= store the visualization into
131     // an external file:                          144     // an external file:
132     // ASCIITree ;  DAWNFILE ; HepRepFile ; VR    145     // ASCIITree ;  DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
133     visManager = new G4VisExecutive;              146     visManager = new G4VisExecutive;
134     visManager->Initialize();                     147     visManager->Initialize();
135                                                   148 
136     ui = new G4UIExecutive(argc, argv, command    149     ui = new G4UIExecutive(argc, argv, commandLine->GetOption());
137     UImanager->ApplyCommand(G4String("/vis/ope << 150     UImanager->ApplyCommand(G4String("/vis/open ")+commandLine->GetOption());
138     UImanager->ApplyCommand("/control/execute     151     UImanager->ApplyCommand("/control/execute vis.mac");
139   }                                               152   }
140                                                   153 
141   if ((commandLine = parser->GetCommandIfActiv << 154   if ((commandLine = parser->GetCommandIfActive("-mac")))
                                                   >> 155   {
142     G4String command = "/control/execute ";       156     G4String command = "/control/execute ";
143     UImanager->ApplyCommand(command + commandL    157     UImanager->ApplyCommand(command + commandLine->GetOption());
144   }                                               158   }
145   else {                                       << 159   else
                                                   >> 160   {
146     UImanager->ApplyCommand("/control/execute     161     UImanager->ApplyCommand("/control/execute beam.in");
147   }                                               162   }
148                                                   163 
149   if (ui) {                                    << 164   if(ui)
                                                   >> 165   {
150     ui->SessionStart();                           166     ui->SessionStart();
151     delete ui;                                    167     delete ui;
152   }                                               168   }
153                                                   169 
154   // Job termination                              170   // Job termination
155   // Free the store: user actions, physics_lis    171   // Free the store: user actions, physics_list and detector_description are
156   // owned and deleted by the run manager, so     172   // owned and deleted by the run manager, so they should not be deleted
157   // in the main() program !                      173   // in the main() program !
158                                                   174 
159   delete visManager;                              175   delete visManager;
160   delete runManager;                              176   delete runManager;
161                                                   177 
162   CommandLineParser::DeleteInstance();            178   CommandLineParser::DeleteInstance();
163                                                   179 
164   return 0;                                       180   return 0;
165 }                                                 181 }
166                                                   182 
167 void Parse(int& argc, char** argv)                183 void Parse(int& argc, char** argv)
168 {                                                 184 {
169   //////////                                      185   //////////
170   // Parse options given in commandLine           186   // Parse options given in commandLine
171   //                                              187   //
172   parser = CommandLineParser::GetParser();        188   parser = CommandLineParser::GetParser();
173                                                   189 
174   parser->AddCommand("-gui", Command::OptionNo << 190   parser->AddCommand(
175                      "Select geant4 UI or just << 191       "-gui", Command::OptionNotCompulsory,
176                                                << 192       "Select geant4 UI or just launch a geant4 terminal session", "qt");
177   parser->AddCommand("-mac", Command::WithOpti << 193 
178                                                << 194   parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute",
179   // You cann your own command, as for instanc << 195                      "macFile.mac");
180   //  parser->AddCommand("-seed",              << 196 
181   //                     Command::WithOption,  << 197 // You cann your own command, as for instance:
182   //                     "Give a seed value in << 198 //  parser->AddCommand("-seed",
183   // it is then up to you to manage this optio << 199 //                     Command::WithOption,
                                                   >> 200 //                     "Give a seed value in argument to be tested", "seed");
                                                   >> 201 // it is then up to you to manage this option
                                                   >> 202 
                                                   >> 203   parser->AddCommand("-mt",
                                                   >> 204       Command::WithOption,
                                                   >> 205       "Launch in MT mode (events computed in parallel,"
                                                   >> 206       " NOT RECOMMANDED WITH CHEMISTRY)", "2");
184                                                   207 
185   parser->AddCommand("-mt", Command::WithOptio << 208   parser->AddCommand("-chemOFF", Command::WithoutOption,
186                      "Launch in MT mode (event << 209                      "Deactivate chemistry");
187                      " NOT RECOMMANDED WITH CH << 
188                      "2");                     << 
189                                                   210 
190   parser->AddCommand("-chemOFF", Command::With << 211   parser->AddCommand("-vis", Command::WithOption,
                                                   >> 212                      "Select a visualization driver", "OGL 600x600-0+0");
191                                                   213 
192   parser->AddCommand("-vis", Command::WithOpti << 214   parser->AddCommand("-novis", Command::WithoutOption,
193                      "OGL 600x600-0+0");       << 215                      "Deactivate visualization when using GUI");
194                                                << 
195   parser->AddCommand("-novis", Command::Withou << 
196                                                   216 
197   //////////                                      217   //////////
198   // If -h or --help is given in option : prin    218   // If -h or --help is given in option : print help and exit
199   //                                              219   //
200   if (parser->Parse(argc, argv) != 0)  // help << 220   if (parser->Parse(argc, argv) != 0) // help is being printed
201   {                                               221   {
202     // if you are using ROOT, create a TApplic    222     // if you are using ROOT, create a TApplication in this condition in order
203     // to print the help from ROOT as well        223     // to print the help from ROOT as well
204     CommandLineParser::DeleteInstance();          224     CommandLineParser::DeleteInstance();
205     std::exit(0);                                 225     std::exit(0);
206   }                                               226   }
207                                                   227 
208   ///////////                                     228   ///////////
209   // Kill application if wrong argument in com    229   // Kill application if wrong argument in command line
210   //                                              230   //
211   if (parser->CheckIfNotHandledOptionsExists(a << 231   if (parser->CheckIfNotHandledOptionsExists(argc, argv))
                                                   >> 232   {
212     // if you are using ROOT, you should initi    233     // if you are using ROOT, you should initialise your TApplication
213     // before this condition                      234     // before this condition
214     abort();                                      235     abort();
215   }                                               236   }
216 }                                                 237 }
217                                                   238