Geant4 Cross Reference

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Geant4/examples/extended/medical/dna/chem4/chem4.cc

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  1 //
  2 // ********************************************************************
  3 // * License and Disclaimer                                           *
  4 // *                                                                  *
  5 // * The  Geant4 software  is  copyright of the Copyright Holders  of *
  6 // * the Geant4 Collaboration.  It is provided  under  the terms  and *
  7 // * conditions of the Geant4 Software License,  included in the file *
  8 // * LICENSE and available at  http://cern.ch/geant4/license .  These *
  9 // * include a list of copyright holders.                             *
 10 // *                                                                  *
 11 // * Neither the authors of this software system, nor their employing *
 12 // * institutes,nor the agencies providing financial support for this *
 13 // * work  make  any representation or  warranty, express or implied, *
 14 // * regarding  this  software system or assume any liability for its *
 15 // * use.  Please see the license in the file  LICENSE  and URL above *
 16 // * for the full disclaimer and the limitation of liability.         *
 17 // *                                                                  *
 18 // * This  code  implementation is the result of  the  scientific and *
 19 // * technical work of the GEANT4 collaboration.                      *
 20 // * By using,  copying,  modifying or  distributing the software (or *
 21 // * any work based  on the software)  you  agree  to acknowledge its *
 22 // * use  in  resulting  scientific  publications,  and indicate your *
 23 // * acceptance of all terms of the Geant4 Software license.          *
 24 // ********************************************************************
 25 //
 26 // This example is provided by the Geant4-DNA collaboration
 27 // Any report or published results obtained using the Geant4-DNA software
 28 // shall cite the following Geant4-DNA collaboration publication:
 29 // Med. Phys. 37 (2010) 4692-4708
 30 // J. Comput. Phys. 274 (2014) 841-882
 31 // The Geant4-DNA web site is available at http://geant4-dna.org
 32 //
 33 //
 34 /// \file chem4.cc
 35 /// \brief Chem4 example
 36 
 37 #include "ActionInitialization.hh"
 38 #include "CommandLineParser.hh"
 39 #include "DetectorConstruction.hh"
 40 #include "PhysicsList.hh"
 41 
 42 #include "G4DNAChemistryManager.hh"
 43 #include "G4RunManagerFactory.hh"
 44 #include "G4UIExecutive.hh"
 45 #include "G4UImanager.hh"
 46 #include "G4VisExecutive.hh"
 47 
 48 /*
 49  * WARNING : Geant4 was initially not intended for this kind of application
 50  * This code is delivered as a prototype
 51  * We will be happy to hear from you, do not hesitate to send your feedback and
 52  * communicate on the difficulties you may encounter
 53  * The user interface may change in the next releases since a reiteration of the
 54  * code has started
 55  */
 56 
 57 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 58 
 59 using namespace G4DNAPARSER;
 60 CommandLineParser* parser(0);
 61 long seed = 0;
 62 
 63 unsigned int noise();
 64 void SetSeed();
 65 
 66 void Parse(int& argc, char** argv);
 67 
 68 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 69 
 70 int main(int argc, char** argv)
 71 {
 72   // Parse options given in commandLine
 73   Parse(argc, argv);
 74   Command* commandLine(0);
 75   SetSeed();
 76 
 77   // Construct the run manager according to whether MT is activated or not
 78   //
 79   auto* runManager = G4RunManagerFactory::CreateRunManager();
 80 
 81   if ((commandLine = parser->GetCommandIfActive("-mt"))) {
 82     int nThreads = 2;
 83     if (commandLine->GetOption() == "NMAX") {
 84       nThreads = G4Threading::G4GetNumberOfCores();
 85     }
 86     else {
 87       nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
 88     }
 89 
 90     runManager->SetNumberOfThreads(nThreads);
 91   }
 92 
 93   G4cout << "**************************************************************"
 94          << "******\n===== Chem4 is started with " << runManager->GetNumberOfThreads() << " of "
 95          << G4Threading::G4GetNumberOfCores()
 96          << " available threads =====\n\n*************************************"
 97          << "*******************************" << G4endl;
 98 
 99   // Set mandatory initialization classes
100   runManager->SetUserInitialization(new PhysicsList());
101   runManager->SetUserInitialization(new DetectorConstruction());
102   runManager->SetUserInitialization(new ActionInitialization());
103 
104   // Initialize visualization
105   G4VisManager* visManager = new G4VisExecutive();
106   // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
107   // G4VisManager* visManager = new G4VisExecutive("Quiet");
108   visManager->Initialize();
109 
110   // Get the pointer to the User Interface manager
111   G4UImanager* UImanager = G4UImanager::GetUIpointer();
112   G4UIExecutive* ui(0);
113 
114   // interactive mode : define UI session
115   if ((commandLine = parser->GetCommandIfActive("-gui"))) {
116     ui = new G4UIExecutive(argc, argv, commandLine->GetOption());
117 
118     if (ui->IsGUI()) UImanager->ApplyCommand("/control/execute gui.mac");
119 
120     if (parser->GetCommandIfActive("-novis") == 0) {
121       // visualization is used by default
122       if ((commandLine = parser->GetCommandIfActive("-vis"))) {
123         // select a visualization driver if needed (e.g. HepFile)
124         UImanager->ApplyCommand(G4String("/vis/open ") + commandLine->GetOption());
125       }
126       else {
127         // by default OGL is used
128         UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
129       }
130       UImanager->ApplyCommand("/control/execute vis.mac");
131     }
132   }
133   else {
134     // to be use visualization file (= store the visualization into
135     // an external file:
136     // ASCIITree ;  DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
137     if ((commandLine = parser->GetCommandIfActive("-vis"))) {
138       UImanager->ApplyCommand(G4String("/vis/open ") + commandLine->GetOption());
139       UImanager->ApplyCommand("/control/execute vis.mac");
140     }
141   }
142 
143   if ((commandLine = parser->GetCommandIfActive("-mac"))) {
144     G4String command = "/control/execute ";
145     UImanager->ApplyCommand(command + commandLine->GetOption());
146   }
147   else {
148     UImanager->ApplyCommand("/control/execute beam.in");
149   }
150 
151   if ((commandLine = parser->GetCommandIfActive("-gui"))) {
152     ui->SessionStart();
153     delete ui;
154   }
155 
156   // Job termination
157   // Free the store: user actions, physics_list and detector_description are
158   // owned and deleted by the run manager, so they should not be deleted
159   // in the main() program !
160   delete visManager;
161   delete runManager;
162   CommandLineParser::DeleteInstance();
163   return 0;
164 }
165 
166 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
167 
168 bool IsBracket(char c)
169 {
170   switch (c) {
171     case '[':
172     case ']':
173       return true;
174     default:
175       return false;
176   }
177 }
178 
179 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
180 
181 void SetSeed()
182 {
183   Command* commandLine(0);
184 
185   if ((commandLine = parser->GetCommandIfActive("-seed"))) {
186     seed = atoi(commandLine->GetOption().c_str());
187   }
188 
189   if (seed == 0)  // If no seed given in argument, setup the seed
190   {
191     long jobID_int = 0;
192     long noice = 0;
193 
194     //____________________________________
195     // In case on cluster
196     if ((commandLine = parser->GetCommandIfActive("-cluster"))) {
197       noice = labs((long)noise());
198 
199       const char* env = std::getenv("PBS_JOBID");
200 
201       if (env) {
202         G4String buffer(env);
203         G4String jobID_string = buffer.substr(0, buffer.find("."));
204         jobID_string.erase(std::remove_if(jobID_string.begin(), jobID_string.end(), &IsBracket),
205                            jobID_string.end());
206         jobID_int = atoi(jobID_string.c_str());
207       }
208       else {
209         env = std::getenv("SGE_TASK_ID");
210         if (env) jobID_int = atoi(env);
211       }
212     }  // end cluster
213 
214     //____________________________________
215     seed = ((long)time(NULL)) + jobID_int + noice;
216   }
217 
218   G4cout << "Seed used : " << seed << G4endl;
219   G4Random::setTheEngine(new CLHEP::MixMaxRng());
220   G4Random::setTheSeed(seed);
221 
222   // Choose the Random engine
223   // CLHEP::HepRandom::setTheEngine(new CLHEP::RanecuEngine);
224 }
225 
226 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
227 
228 unsigned int noise()
229 {
230 #if defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)
231   // TODO: MS Win
232   return std::time(0);
233 #else
234   unsigned int random_seed, random_seed_a, random_seed_b;
235   std::ifstream file("/dev/urandom", std::ios::binary);
236   if (file.is_open()) {
237     char* memblock;
238     int size = sizeof(int);
239     memblock = new char[size];
240     file.read(memblock, size);
241     file.close();
242     random_seed_a = *reinterpret_cast<int*>(memblock);
243     delete[] memblock;
244   }  // end if
245   else {
246     random_seed_a = 0;
247   }
248   random_seed_b = std::time(0);
249   random_seed = random_seed_a xor random_seed_b;
250   return random_seed;
251 #endif
252 }
253 
254 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
255 
256 void Parse(int& argc, char** argv)
257 {
258   //////////
259   // Parse options given in commandLine
260   //
261   parser = CommandLineParser::GetParser();
262 
263   parser->AddCommand("-gui", Command::OptionNotCompulsory,
264                      "Select geant4 UI or just launch a geant4 terminal"
265                      "session",
266                      "qt");
267 
268   parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute", "macFile.mac");
269 
270   parser->AddCommand("-seed", Command::WithOption, "Give a seed value in argument to be tested",
271                      "seed");
272 
273   parser->AddCommand("-mt", Command::WithOption,
274                      "Launch in MT mode (events computed in parallel,"
275                      " NOT RECOMMANDED WITH CHEMISTRY)",
276                      "2");
277 
278   parser->AddCommand("-chemOFF", Command::WithoutOption, "Deactivate chemistry");
279 
280   parser->AddCommand("-vis", Command::WithOption, "Select a visualization driver",
281                      "OGL 600x600-0+0");
282 
283   parser->AddCommand("-novis", Command::WithoutOption, "Deactivate visualization when using GUI");
284 
285   parser->AddCommand("-cluster", Command::WithoutOption,
286                      "Launch the code on a cluster, avoid dupplicated seeds");
287 
288   //////////
289   // If -h or --help is given in option : print help and exit
290   //
291   if (parser->Parse(argc, argv) != 0)  // help is being printed
292   {
293     // if you are using ROOT, create a TApplication in this condition in order
294     // to print the help from ROOT as well
295     CommandLineParser::DeleteInstance();
296     std::exit(0);
297   }
298 
299   ///////////
300   // Kill application if wrong argument in command line
301   //
302   if (parser->CheckIfNotHandledOptionsExists(argc, argv)) {
303     // if you are using ROOT, you should initialise your TApplication
304     // before this condition
305     std::exit(0);
306   }
307 }
308