| Geant4 Cross Reference |
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 *
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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 // Phys. Med. Biol. 63(10) (2018) 105014-12pp << 31 // Phys. Med. Biol. 63(10) (2018) 105014-12pp
32 // The Geant4-DNA web site is available at htt 32 // The Geant4-DNA web site is available at http://geant4-dna.org
33 // 33 //
34 // 34 //
35 /// \file chem5.cc 35 /// \file chem5.cc
36 /// \brief Chem5 example 36 /// \brief Chem5 example
37 37
38 #include "ActionInitialization.hh" <<
39 #include "CommandLineParser.hh" <<
40 #include "DetectorConstruction.hh" 38 #include "DetectorConstruction.hh"
41 #include "PhysicsList.hh" 39 #include "PhysicsList.hh"
>> 40 #include "ActionInitialization.hh"
>> 41
>> 42 #ifdef G4MULTITHREADED
>> 43 #include "G4MTRunManager.hh"
>> 44 #else
>> 45 #include "G4RunManager.hh"
>> 46 #endif
42 47
43 #include "G4DNAChemistryManager.hh" 48 #include "G4DNAChemistryManager.hh"
44 #include "G4RunManagerFactory.hh" <<
45 #include "G4UIExecutive.hh" <<
46 #include "G4UImanager.hh" 49 #include "G4UImanager.hh"
>> 50 #include "G4UIExecutive.hh"
47 #include "G4VisExecutive.hh" 51 #include "G4VisExecutive.hh"
48 52
>> 53 #include "CommandLineParser.hh"
>> 54
49 /* 55 /*
50 * WARNING : Geant4 was initially not intended 56 * WARNING : Geant4 was initially not intended for this kind of application
51 * This code is delivered as a prototype 57 * This code is delivered as a prototype
52 * We will be happy to hear from you, do not h 58 * We will be happy to hear from you, do not hesitate to send your feedback and
53 * communicate on the difficulties you may enc 59 * communicate on the difficulties you may encounter
54 * The user interface may change in the next r 60 * The user interface may change in the next releases since a reiteration of the
55 * code has started 61 * code has started
56 */ 62 */
57 63
58 //....oooOO0OOooo........oooOO0OOooo........oo 64 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
59 65
60 using namespace G4DNAPARSER; 66 using namespace G4DNAPARSER;
61 CommandLineParser* parser(0); 67 CommandLineParser* parser(0);
62 long seed = 0; 68 long seed = 0;
63 69
64 unsigned int noise(); 70 unsigned int noise();
65 void SetSeed(); 71 void SetSeed();
66 72
67 void Parse(int& argc, char** argv); 73 void Parse(int& argc, char** argv);
68 74
69 //....oooOO0OOooo........oooOO0OOooo........oo 75 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
70 76
71 int main(int argc, char** argv) 77 int main(int argc, char** argv)
72 { 78 {
73 // Parse options given in commandLine 79 // Parse options given in commandLine
74 Parse(argc, argv); 80 Parse(argc, argv);
75 Command* commandLine(0); 81 Command* commandLine(0);
76 SetSeed(); 82 SetSeed();
77 << 83
78 // Construct the run manager according to wh 84 // Construct the run manager according to whether MT is activated or not
79 // 85 //
80 auto* runManager = G4RunManagerFactory::Crea << 86 #ifdef G4MULTITHREADED
81 << 87 G4MTRunManager* runManager= new G4MTRunManager();
82 if ((commandLine = parser->GetCommandIfActiv << 88
>> 89 if((commandLine = parser->GetCommandIfActive("-mt")))
>> 90 {
83 int nThreads = 2; 91 int nThreads = 2;
84 if (commandLine->GetOption() == "NMAX") { << 92 if(commandLine->GetOption() == "NMAX")
>> 93 {
85 nThreads = G4Threading::G4GetNumberOfCor 94 nThreads = G4Threading::G4GetNumberOfCores();
86 } 95 }
87 else { << 96 else
>> 97 {
88 nThreads = G4UIcommand::ConvertToInt(com 98 nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
89 } 99 }
90 << 100
91 runManager->SetNumberOfThreads(nThreads); 101 runManager->SetNumberOfThreads(nThreads);
92 } 102 }
93 << 103
94 G4cout << "********************************* 104 G4cout << "**************************************************************"
95 << "******\n===== Chem5 is started wi << 105 << "******\n===== Chem5 is started with "
>> 106 << runManager->GetNumberOfThreads() << " of "
96 << G4Threading::G4GetNumberOfCores() 107 << G4Threading::G4GetNumberOfCores()
97 << " available threads =====\n\n***** 108 << " available threads =====\n\n*************************************"
98 << "*******************************" << 109 <<"*******************************"
99 << 110 << G4endl;
>> 111 #else
>> 112 G4RunManager* runManager = new G4RunManager();
>> 113 #endif
>> 114
100 // Set mandatory initialization classes 115 // Set mandatory initialization classes
101 runManager->SetUserInitialization(new Physic 116 runManager->SetUserInitialization(new PhysicsList());
102 runManager->SetUserInitialization(new Detect 117 runManager->SetUserInitialization(new DetectorConstruction());
103 runManager->SetUserInitialization(new Action 118 runManager->SetUserInitialization(new ActionInitialization());
104 << 119
105 // Initialize G4 kernel 120 // Initialize G4 kernel
106 runManager->Initialize(); 121 runManager->Initialize();
107 << 122
108 // Initialize visualization 123 // Initialize visualization
109 G4VisManager* visManager = new G4VisExecutiv 124 G4VisManager* visManager = new G4VisExecutive();
110 // G4VisExecutive can take a verbosity argum 125 // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
111 // G4VisManager* visManager = new G4VisExecu 126 // G4VisManager* visManager = new G4VisExecutive("Quiet");
112 visManager->Initialize(); 127 visManager->Initialize();
113 128
114 // Get the pointer to the User Interface man 129 // Get the pointer to the User Interface manager
115 G4UImanager* UImanager = G4UImanager::GetUIp 130 G4UImanager* UImanager = G4UImanager::GetUIpointer();
116 G4UIExecutive* ui(0); 131 G4UIExecutive* ui(0);
117 << 132
118 // interactive mode : define UI session 133 // interactive mode : define UI session
119 if ((commandLine = parser->GetCommandIfActiv << 134 if((commandLine = parser->GetCommandIfActive("-gui")))
>> 135 {
120 ui = new G4UIExecutive(argc, argv, command 136 ui = new G4UIExecutive(argc, argv, commandLine->GetOption());
121 << 137
122 if (ui->IsGUI()) UImanager->ApplyCommand(" 138 if (ui->IsGUI()) UImanager->ApplyCommand("/control/execute gui.mac");
123 << 139
124 if (parser->GetCommandIfActive("-novis") = << 140 if (parser->GetCommandIfActive("-novis") == 0)
>> 141 {
125 // visualization is used by default 142 // visualization is used by default
126 if ((commandLine = parser->GetCommandIfA << 143 if ((commandLine = parser->GetCommandIfActive("-vis")))
>> 144 {
127 // select a visualization driver if ne 145 // select a visualization driver if needed (e.g. HepFile)
128 UImanager->ApplyCommand(G4String("/vis << 146 UImanager->ApplyCommand
>> 147 (G4String("/vis/open ") + commandLine->GetOption());
129 } 148 }
130 else { << 149 else
>> 150 {
131 // by default OGL is used 151 // by default OGL is used
132 UImanager->ApplyCommand("/vis/open OGL 152 UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
133 } 153 }
134 UImanager->ApplyCommand("/control/execut 154 UImanager->ApplyCommand("/control/execute vis.mac");
135 } 155 }
136 } 156 }
137 else { << 157 else
>> 158 {
138 // to be use visualization file (= store t 159 // to be use visualization file (= store the visualization into
139 // an external file: 160 // an external file:
140 // ASCIITree ; DAWNFILE ; HepRepFile ; VR 161 // ASCIITree ; DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
141 if ((commandLine = parser->GetCommandIfAct << 162 if((commandLine = parser->GetCommandIfActive("-vis")))
142 UImanager->ApplyCommand(G4String("/vis/o << 163 {
>> 164 UImanager->ApplyCommand(G4String("/vis/open ")
>> 165 + commandLine->GetOption());
143 UImanager->ApplyCommand("/control/execut 166 UImanager->ApplyCommand("/control/execute vis.mac");
144 } 167 }
145 } 168 }
146 << 169
147 if ((commandLine = parser->GetCommandIfActiv << 170 if((commandLine = parser->GetCommandIfActive("-mac")))
>> 171 {
148 G4String command = "/control/execute "; 172 G4String command = "/control/execute ";
149 UImanager->ApplyCommand(command + commandL 173 UImanager->ApplyCommand(command + commandLine->GetOption());
150 } 174 }
151 else { << 175 else
>> 176 {
152 UImanager->ApplyCommand("/control/execute 177 UImanager->ApplyCommand("/control/execute beam.in");
153 } 178 }
154 179
155 if ((commandLine = parser->GetCommandIfActiv << 180 if((commandLine = parser->GetCommandIfActive("-gui")))
>> 181 {
156 ui->SessionStart(); 182 ui->SessionStart();
157 delete ui; 183 delete ui;
158 } 184 }
159 << 185
160 // Job termination 186 // Job termination
161 // Free the store: user actions, physics_lis 187 // Free the store: user actions, physics_list and detector_description are
162 // owned and deleted by the run manager, so 188 // owned and deleted by the run manager, so they should not be deleted
163 // in the main() program ! 189 // in the main() program !
164 delete visManager; 190 delete visManager;
165 delete runManager; 191 delete runManager;
166 CommandLineParser::DeleteInstance(); 192 CommandLineParser::DeleteInstance();
167 return 0; 193 return 0;
168 } 194 }
169 195
170 //....oooOO0OOooo........oooOO0OOooo........oo 196 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
171 197
172 bool IsBracket(char c) 198 bool IsBracket(char c)
173 { 199 {
174 switch (c) { << 200 switch(c)
>> 201 {
175 case '[': 202 case '[':
176 case ']': 203 case ']':
177 return true; 204 return true;
178 default: 205 default:
179 return false; 206 return false;
180 } 207 }
181 } 208 }
182 209
183 //....oooOO0OOooo........oooOO0OOooo........oo 210 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
184 211
185 void SetSeed() 212 void SetSeed()
186 { << 213 {
187 Command* commandLine(0); 214 Command* commandLine(0);
188 << 215
189 if ((commandLine = parser->GetCommandIfActiv << 216 if((commandLine = parser->GetCommandIfActive("-seed")))
>> 217 {
190 seed = atoi(commandLine->GetOption().c_str 218 seed = atoi(commandLine->GetOption().c_str());
191 } 219 }
192 << 220
193 if (seed == 0) // If no seed given in argum << 221 if(seed == 0) // If no seed given in argument, setup the seed
194 { 222 {
195 long jobID_int = 0; 223 long jobID_int = 0;
196 long noice = 0; 224 long noice = 0;
197 << 225
198 //____________________________________ 226 //____________________________________
199 // In case on cluster 227 // In case on cluster
200 if ((commandLine = parser->GetCommandIfAct << 228 if((commandLine = parser->GetCommandIfActive("-cluster")))
201 noice = labs((long)noise()); << 229 {
202 << 230 noice = labs((long) noise());
203 const char* env = std::getenv("PBS_JOBID << 231
>> 232 const char * env = std::getenv("PBS_JOBID");
204 233
205 if (env) { << 234 if(env)
>> 235 {
206 G4String buffer(env); 236 G4String buffer(env);
207 G4String jobID_string = buffer.substr( << 237 G4String jobID_string = buffer.substr(0, buffer.find("."));
208 jobID_string.erase(std::remove_if(jobI << 238 jobID_string.erase(std::remove_if(jobID_string.begin(),
209 jobID_string.end()) << 239 jobID_string.end(),
>> 240 &IsBracket),
>> 241 jobID_string.end());
210 jobID_int = atoi(jobID_string.c_str()) 242 jobID_int = atoi(jobID_string.c_str());
211 } 243 }
212 else { << 244 else
>> 245 {
213 env = std::getenv("SGE_TASK_ID"); 246 env = std::getenv("SGE_TASK_ID");
214 if (env) jobID_int = atoi(env); << 247 if(env) jobID_int = atoi(env);
215 } 248 }
216 } // end cluster << 249 } // end cluster
217 << 250
218 //____________________________________ 251 //____________________________________
219 seed = ((long)time(NULL)) + jobID_int + no << 252 seed = ((long) time(NULL)) + jobID_int + noice;
220 } 253 }
221 << 254
222 G4cout << "Seed used : " << seed << G4endl; 255 G4cout << "Seed used : " << seed << G4endl;
223 G4Random::setTheEngine(new CLHEP::MixMaxRng( 256 G4Random::setTheEngine(new CLHEP::MixMaxRng());
224 G4Random::setTheSeed(seed); 257 G4Random::setTheSeed(seed);
225 258
226 // Choose the Random engine 259 // Choose the Random engine
227 // CLHEP::HepRandom::setTheEngine(new CLHEP: 260 // CLHEP::HepRandom::setTheEngine(new CLHEP::RanecuEngine);
228 } 261 }
229 262
230 //....oooOO0OOooo........oooOO0OOooo........oo 263 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
231 264
232 unsigned int noise() 265 unsigned int noise()
233 { 266 {
234 #if defined(WIN32) || defined(_WIN32) || defin << 267 #if defined(WIN32)|| defined(_WIN32)|| defined(__WIN32)&&!defined(__CYGWIN__)
235 // TODO: MS Win 268 // TODO: MS Win
236 return std::time(0); 269 return std::time(0);
237 #else 270 #else
238 unsigned int random_seed, random_seed_a, ran 271 unsigned int random_seed, random_seed_a, random_seed_b;
239 std::ifstream file("/dev/urandom", std::ios: << 272 std::ifstream file ("/dev/urandom", std::ios::binary);
240 if (file.is_open()) { << 273 if (file.is_open())
241 char* memblock; << 274 {
>> 275 char * memblock;
242 int size = sizeof(int); 276 int size = sizeof(int);
243 memblock = new char[size]; << 277 memblock = new char [size];
244 file.read(memblock, size); << 278 file.read (memblock, size);
245 file.close(); 279 file.close();
246 random_seed_a = *reinterpret_cast<int*>(me 280 random_seed_a = *reinterpret_cast<int*>(memblock);
247 delete[] memblock; 281 delete[] memblock;
248 } // end if << 282 }// end if
249 else { << 283 else
>> 284 {
250 random_seed_a = 0; 285 random_seed_a = 0;
251 } 286 }
252 random_seed_b = std::time(0); 287 random_seed_b = std::time(0);
253 random_seed = random_seed_a xor random_seed_ 288 random_seed = random_seed_a xor random_seed_b;
254 return random_seed; 289 return random_seed;
255 #endif 290 #endif
256 } 291 }
257 292
258 //....oooOO0OOooo........oooOO0OOooo........oo 293 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
259 294
260 void Parse(int& argc, char** argv) 295 void Parse(int& argc, char** argv)
261 { 296 {
262 ////////// 297 //////////
263 // Parse options given in commandLine 298 // Parse options given in commandLine
264 // 299 //
265 parser = CommandLineParser::GetParser(); 300 parser = CommandLineParser::GetParser();
266 << 301
267 parser->AddCommand("-gui", Command::OptionNo 302 parser->AddCommand("-gui", Command::OptionNotCompulsory,
268 "Select geant4 UI or just 303 "Select geant4 UI or just launch a geant4 terminal"
269 "session", 304 "session",
270 "qt"); 305 "qt");
271 << 306
272 parser->AddCommand("-mac", Command::WithOpti << 307 parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute",
273 << 308 "macFile.mac");
274 parser->AddCommand("-seed", Command::WithOpt << 309
275 "seed"); << 310 parser->AddCommand("-seed",
276 << 311 Command::WithOption,
277 parser->AddCommand("-mt", Command::WithOptio << 312 "Give a seed value in argument to be tested", "seed");
>> 313
>> 314 #ifdef G4MULTITHREADED
>> 315 parser->AddCommand("-mt",Command::WithOption,
278 "Launch in MT mode (event 316 "Launch in MT mode (events computed in parallel,"
279 " NOT RECOMMANDED WITH CH << 317 " NOT RECOMMANDED WITH CHEMISTRY)", "2");
280 "2"); << 318 #endif
281 << 319
282 parser->AddCommand("-chemOFF", Command::With << 320 parser->AddCommand("-chemOFF", Command::WithoutOption,
283 << 321 "Deactivate chemistry");
284 parser->AddCommand("-vis", Command::WithOpti << 322
285 "OGL 600x600-0+0"); << 323 parser->AddCommand("-vis", Command::WithOption,
286 << 324 "Select a visualization driver", "OGL 600x600-0+0");
287 parser->AddCommand("-novis", Command::Withou << 325
288 << 326 parser->AddCommand("-novis", Command::WithoutOption,
>> 327 "Deactivate visualization when using GUI");
>> 328
289 parser->AddCommand("-cluster", Command::With 329 parser->AddCommand("-cluster", Command::WithoutOption,
290 "Launch the code on a clu 330 "Launch the code on a cluster, avoid dupplicated seeds");
291 << 331
292 ////////// 332 //////////
293 // If -h or --help is given in option : prin 333 // If -h or --help is given in option : print help and exit
294 // 334 //
295 if (parser->Parse(argc, argv) != 0) // help << 335 if (parser->Parse(argc, argv) != 0) // help is being printed
296 { 336 {
297 // if you are using ROOT, create a TApplic 337 // if you are using ROOT, create a TApplication in this condition in order
298 // to print the help from ROOT as well 338 // to print the help from ROOT as well
299 CommandLineParser::DeleteInstance(); 339 CommandLineParser::DeleteInstance();
300 std::exit(0); 340 std::exit(0);
301 } 341 }
302 << 342
303 /////////// 343 ///////////
304 // Kill application if wrong argument in com 344 // Kill application if wrong argument in command line
305 // 345 //
306 if (parser->CheckIfNotHandledOptionsExists(a << 346 if(parser->CheckIfNotHandledOptionsExists(argc, argv))
>> 347 {
307 // if you are using ROOT, you should initi 348 // if you are using ROOT, you should initialise your TApplication
308 // before this condition 349 // before this condition
309 std::exit(0); 350 std::exit(0);
310 } 351 }
311 } 352 }
312 353