| 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 *
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10 // * 10 // * *
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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 chem4.cc 34 /// \file chem4.cc
35 /// \brief Chem4 example 35 /// \brief Chem4 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"
>> 40
>> 41 #ifdef G4MULTITHREADED
>> 42 #include "G4MTRunManager.hh"
>> 43 #else
>> 44 #include "G4RunManager.hh"
>> 45 #endif
41 46
42 #include "G4DNAChemistryManager.hh" 47 #include "G4DNAChemistryManager.hh"
43 #include "G4RunManagerFactory.hh" <<
44 #include "G4UIExecutive.hh" <<
45 #include "G4UImanager.hh" 48 #include "G4UImanager.hh"
>> 49 #include "G4UIExecutive.hh"
46 #include "G4VisExecutive.hh" 50 #include "G4VisExecutive.hh"
47 51
>> 52 #include "CommandLineParser.hh"
>> 53
48 /* 54 /*
49 * WARNING : Geant4 was initially not intended 55 * WARNING : Geant4 was initially not intended for this kind of application
50 * This code is delivered as a prototype << 56 * This code is delivered as a prototype
51 * We will be happy to hear from you, do not h 57 * We will be happy to hear from you, do not hesitate to send your feedback and
52 * communicate on the difficulties you may enc 58 * communicate on the difficulties you may encounter
53 * The user interface may change in the next r 59 * The user interface may change in the next releases since a reiteration of the
54 * code has started 60 * code has started
55 */ 61 */
56 62
57 //....oooOO0OOooo........oooOO0OOooo........oo 63 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
58 64
59 using namespace G4DNAPARSER; 65 using namespace G4DNAPARSER;
60 CommandLineParser* parser(0); 66 CommandLineParser* parser(0);
61 long seed = 0; 67 long seed = 0;
62 68
63 unsigned int noise(); 69 unsigned int noise();
64 void SetSeed(); 70 void SetSeed();
65 71
66 void Parse(int& argc, char** argv); 72 void Parse(int& argc, char** argv);
67 73
68 //....oooOO0OOooo........oooOO0OOooo........oo 74 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
69 75
70 int main(int argc, char** argv) 76 int main(int argc, char** argv)
71 { 77 {
72 // Parse options given in commandLine 78 // Parse options given in commandLine
73 Parse(argc, argv); 79 Parse(argc, argv);
74 Command* commandLine(0); 80 Command* commandLine(0);
75 SetSeed(); 81 SetSeed();
76 << 82
77 // Construct the run manager according to wh 83 // Construct the run manager according to whether MT is activated or not
78 // 84 //
79 auto* runManager = G4RunManagerFactory::Crea << 85 #ifdef G4MULTITHREADED
80 << 86 G4MTRunManager* runManager= new G4MTRunManager();
81 if ((commandLine = parser->GetCommandIfActiv << 87
>> 88 if((commandLine = parser->GetCommandIfActive("-mt")))
>> 89 {
82 int nThreads = 2; 90 int nThreads = 2;
83 if (commandLine->GetOption() == "NMAX") { << 91 if(commandLine->GetOption() == "NMAX")
>> 92 {
84 nThreads = G4Threading::G4GetNumberOfCor 93 nThreads = G4Threading::G4GetNumberOfCores();
85 } 94 }
86 else { << 95 else
>> 96 {
87 nThreads = G4UIcommand::ConvertToInt(com 97 nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
88 } 98 }
89 << 99
90 runManager->SetNumberOfThreads(nThreads); 100 runManager->SetNumberOfThreads(nThreads);
91 } 101 }
92 << 102
93 G4cout << "********************************* 103 G4cout << "**************************************************************"
94 << "******\n===== Chem4 is started wi << 104 << "******\n===== Chem4 is started with "
>> 105 << runManager->GetNumberOfThreads() << " of "
95 << G4Threading::G4GetNumberOfCores() 106 << G4Threading::G4GetNumberOfCores()
96 << " available threads =====\n\n***** 107 << " available threads =====\n\n*************************************"
97 << "*******************************" << 108 <<"*******************************"
98 << 109 << G4endl;
>> 110 #else
>> 111 G4RunManager* runManager = new G4RunManager();
>> 112 #endif
>> 113
99 // Set mandatory initialization classes 114 // Set mandatory initialization classes
100 runManager->SetUserInitialization(new Physic 115 runManager->SetUserInitialization(new PhysicsList());
101 runManager->SetUserInitialization(new Detect 116 runManager->SetUserInitialization(new DetectorConstruction());
102 runManager->SetUserInitialization(new Action 117 runManager->SetUserInitialization(new ActionInitialization());
103 118
104 // Initialize visualization 119 // Initialize visualization
105 G4VisManager* visManager = new G4VisExecutiv 120 G4VisManager* visManager = new G4VisExecutive();
106 // G4VisExecutive can take a verbosity argum 121 // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
107 // G4VisManager* visManager = new G4VisExecu 122 // G4VisManager* visManager = new G4VisExecutive("Quiet");
108 visManager->Initialize(); 123 visManager->Initialize();
109 124
110 // Get the pointer to the User Interface man 125 // Get the pointer to the User Interface manager
111 G4UImanager* UImanager = G4UImanager::GetUIp 126 G4UImanager* UImanager = G4UImanager::GetUIpointer();
112 G4UIExecutive* ui(0); 127 G4UIExecutive* ui(0);
113 << 128
114 // interactive mode : define UI session 129 // interactive mode : define UI session
115 if ((commandLine = parser->GetCommandIfActiv << 130 if((commandLine = parser->GetCommandIfActive("-gui")))
>> 131 {
116 ui = new G4UIExecutive(argc, argv, command 132 ui = new G4UIExecutive(argc, argv, commandLine->GetOption());
117 << 133
118 if (ui->IsGUI()) UImanager->ApplyCommand(" 134 if (ui->IsGUI()) UImanager->ApplyCommand("/control/execute gui.mac");
119 << 135
120 if (parser->GetCommandIfActive("-novis") = << 136 if (parser->GetCommandIfActive("-novis") == 0)
>> 137 {
121 // visualization is used by default 138 // visualization is used by default
122 if ((commandLine = parser->GetCommandIfA << 139 if ((commandLine = parser->GetCommandIfActive("-vis")))
>> 140 {
123 // select a visualization driver if ne 141 // select a visualization driver if needed (e.g. HepFile)
124 UImanager->ApplyCommand(G4String("/vis << 142 UImanager->ApplyCommand
>> 143 (G4String("/vis/open ") + commandLine->GetOption());
125 } 144 }
126 else { << 145 else
>> 146 {
127 // by default OGL is used 147 // by default OGL is used
128 UImanager->ApplyCommand("/vis/open OGL 148 UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
129 } 149 }
130 UImanager->ApplyCommand("/control/execut 150 UImanager->ApplyCommand("/control/execute vis.mac");
131 } 151 }
132 } 152 }
133 else { << 153 else
>> 154 {
134 // to be use visualization file (= store t 155 // to be use visualization file (= store the visualization into
135 // an external file: 156 // an external file:
136 // ASCIITree ; DAWNFILE ; HepRepFile ; VR 157 // ASCIITree ; DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
137 if ((commandLine = parser->GetCommandIfAct << 158 if((commandLine = parser->GetCommandIfActive("-vis")))
138 UImanager->ApplyCommand(G4String("/vis/o << 159 {
>> 160 UImanager->ApplyCommand(G4String("/vis/open ")
>> 161 + commandLine->GetOption());
139 UImanager->ApplyCommand("/control/execut 162 UImanager->ApplyCommand("/control/execute vis.mac");
140 } 163 }
141 } 164 }
142 << 165
143 if ((commandLine = parser->GetCommandIfActiv << 166 if((commandLine = parser->GetCommandIfActive("-mac")))
>> 167 {
144 G4String command = "/control/execute "; 168 G4String command = "/control/execute ";
145 UImanager->ApplyCommand(command + commandL 169 UImanager->ApplyCommand(command + commandLine->GetOption());
146 } 170 }
147 else { << 171 else
>> 172 {
148 UImanager->ApplyCommand("/control/execute 173 UImanager->ApplyCommand("/control/execute beam.in");
149 } 174 }
150 << 175
151 if ((commandLine = parser->GetCommandIfActiv << 176 if((commandLine = parser->GetCommandIfActive("-gui")))
>> 177 {
152 ui->SessionStart(); 178 ui->SessionStart();
153 delete ui; 179 delete ui;
154 } 180 }
155 << 181
156 // Job termination 182 // Job termination
157 // Free the store: user actions, physics_lis 183 // Free the store: user actions, physics_list and detector_description are
158 // owned and deleted by the run manager, so 184 // owned and deleted by the run manager, so they should not be deleted
159 // in the main() program ! 185 // in the main() program !
160 delete visManager; 186 delete visManager;
161 delete runManager; 187 delete runManager;
162 CommandLineParser::DeleteInstance(); 188 CommandLineParser::DeleteInstance();
163 return 0; 189 return 0;
164 } 190 }
165 191
166 //....oooOO0OOooo........oooOO0OOooo........oo 192 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
167 193
168 bool IsBracket(char c) 194 bool IsBracket(char c)
169 { 195 {
170 switch (c) { << 196 switch(c)
>> 197 {
171 case '[': 198 case '[':
172 case ']': 199 case ']':
173 return true; 200 return true;
174 default: 201 default:
175 return false; 202 return false;
176 } 203 }
177 } 204 }
178 205
179 //....oooOO0OOooo........oooOO0OOooo........oo 206 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
180 207
181 void SetSeed() 208 void SetSeed()
182 { << 209 {
183 Command* commandLine(0); 210 Command* commandLine(0);
184 << 211
185 if ((commandLine = parser->GetCommandIfActiv << 212 if((commandLine = parser->GetCommandIfActive("-seed")))
>> 213 {
186 seed = atoi(commandLine->GetOption().c_str 214 seed = atoi(commandLine->GetOption().c_str());
187 } 215 }
188 << 216
189 if (seed == 0) // If no seed given in argum << 217 if(seed == 0) // If no seed given in argument, setup the seed
190 { 218 {
191 long jobID_int = 0; 219 long jobID_int = 0;
192 long noice = 0; 220 long noice = 0;
193 << 221
194 //____________________________________ 222 //____________________________________
195 // In case on cluster 223 // In case on cluster
196 if ((commandLine = parser->GetCommandIfAct << 224 if((commandLine = parser->GetCommandIfActive("-cluster")))
197 noice = labs((long)noise()); << 225 {
198 << 226 noice = labs((long) noise());
199 const char* env = std::getenv("PBS_JOBID << 227
>> 228 const char * env = std::getenv("PBS_JOBID");
200 229
201 if (env) { << 230 if(env)
>> 231 {
202 G4String buffer(env); 232 G4String buffer(env);
203 G4String jobID_string = buffer.substr( << 233 G4String jobID_string = buffer.substr(0, buffer.find("."));
204 jobID_string.erase(std::remove_if(jobI << 234 jobID_string.erase(std::remove_if(jobID_string.begin(),
205 jobID_string.end()) << 235 jobID_string.end(),
>> 236 &IsBracket),
>> 237 jobID_string.end());
206 jobID_int = atoi(jobID_string.c_str()) 238 jobID_int = atoi(jobID_string.c_str());
207 } 239 }
208 else { << 240 else
>> 241 {
209 env = std::getenv("SGE_TASK_ID"); 242 env = std::getenv("SGE_TASK_ID");
210 if (env) jobID_int = atoi(env); << 243 if(env) jobID_int = atoi(env);
211 } 244 }
212 } // end cluster << 245 } // end cluster
213 << 246
214 //____________________________________ 247 //____________________________________
215 seed = ((long)time(NULL)) + jobID_int + no << 248 seed = ((long) time(NULL)) + jobID_int + noice;
216 } 249 }
217 << 250
218 G4cout << "Seed used : " << seed << G4endl; 251 G4cout << "Seed used : " << seed << G4endl;
219 G4Random::setTheEngine(new CLHEP::MixMaxRng( 252 G4Random::setTheEngine(new CLHEP::MixMaxRng());
220 G4Random::setTheSeed(seed); 253 G4Random::setTheSeed(seed);
221 254
222 // Choose the Random engine 255 // Choose the Random engine
223 // CLHEP::HepRandom::setTheEngine(new CLHEP: 256 // CLHEP::HepRandom::setTheEngine(new CLHEP::RanecuEngine);
224 } 257 }
225 258
226 //....oooOO0OOooo........oooOO0OOooo........oo 259 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
227 260
228 unsigned int noise() 261 unsigned int noise()
229 { 262 {
230 #if defined(WIN32) || defined(_WIN32) || defin << 263 #if defined(WIN32)|| defined(_WIN32)|| defined(__WIN32)&&!defined(__CYGWIN__)
231 // TODO: MS Win 264 // TODO: MS Win
232 return std::time(0); 265 return std::time(0);
233 #else 266 #else
234 unsigned int random_seed, random_seed_a, ran 267 unsigned int random_seed, random_seed_a, random_seed_b;
235 std::ifstream file("/dev/urandom", std::ios: << 268 std::ifstream file ("/dev/urandom", std::ios::binary);
236 if (file.is_open()) { << 269 if (file.is_open())
237 char* memblock; << 270 {
>> 271 char * memblock;
238 int size = sizeof(int); 272 int size = sizeof(int);
239 memblock = new char[size]; << 273 memblock = new char [size];
240 file.read(memblock, size); << 274 file.read (memblock, size);
241 file.close(); 275 file.close();
242 random_seed_a = *reinterpret_cast<int*>(me 276 random_seed_a = *reinterpret_cast<int*>(memblock);
243 delete[] memblock; 277 delete[] memblock;
244 } // end if << 278 }// end if
245 else { << 279 else
>> 280 {
246 random_seed_a = 0; 281 random_seed_a = 0;
247 } 282 }
248 random_seed_b = std::time(0); 283 random_seed_b = std::time(0);
249 random_seed = random_seed_a xor random_seed_ 284 random_seed = random_seed_a xor random_seed_b;
250 return random_seed; 285 return random_seed;
251 #endif 286 #endif
252 } 287 }
253 288
254 //....oooOO0OOooo........oooOO0OOooo........oo 289 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
255 290
256 void Parse(int& argc, char** argv) 291 void Parse(int& argc, char** argv)
257 { 292 {
258 ////////// 293 //////////
259 // Parse options given in commandLine 294 // Parse options given in commandLine
260 // 295 //
261 parser = CommandLineParser::GetParser(); 296 parser = CommandLineParser::GetParser();
262 << 297
263 parser->AddCommand("-gui", Command::OptionNo 298 parser->AddCommand("-gui", Command::OptionNotCompulsory,
264 "Select geant4 UI or just 299 "Select geant4 UI or just launch a geant4 terminal"
265 "session", 300 "session",
266 "qt"); 301 "qt");
267 << 302
268 parser->AddCommand("-mac", Command::WithOpti << 303 parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute",
269 << 304 "macFile.mac");
270 parser->AddCommand("-seed", Command::WithOpt << 305
271 "seed"); << 306 parser->AddCommand("-seed",
272 << 307 Command::WithOption,
273 parser->AddCommand("-mt", Command::WithOptio << 308 "Give a seed value in argument to be tested", "seed");
>> 309
>> 310 #ifdef G4MULTITHREADED
>> 311 parser->AddCommand("-mt",Command::WithOption,
274 "Launch in MT mode (event 312 "Launch in MT mode (events computed in parallel,"
275 " NOT RECOMMANDED WITH CH << 313 " NOT RECOMMANDED WITH CHEMISTRY)", "2");
276 "2"); << 314 #endif
277 << 315
278 parser->AddCommand("-chemOFF", Command::With << 316 parser->AddCommand("-chemOFF", Command::WithoutOption,
279 << 317 "Deactivate chemistry");
280 parser->AddCommand("-vis", Command::WithOpti << 318
281 "OGL 600x600-0+0"); << 319 parser->AddCommand("-vis", Command::WithOption,
282 << 320 "Select a visualization driver", "OGL 600x600-0+0");
283 parser->AddCommand("-novis", Command::Withou << 321
284 << 322 parser->AddCommand("-novis", Command::WithoutOption,
>> 323 "Deactivate visualization when using GUI");
>> 324
285 parser->AddCommand("-cluster", Command::With 325 parser->AddCommand("-cluster", Command::WithoutOption,
286 "Launch the code on a clu 326 "Launch the code on a cluster, avoid dupplicated seeds");
287 << 327
288 ////////// 328 //////////
289 // If -h or --help is given in option : prin 329 // If -h or --help is given in option : print help and exit
290 // 330 //
291 if (parser->Parse(argc, argv) != 0) // help << 331 if (parser->Parse(argc, argv) != 0) // help is being printed
292 { 332 {
293 // if you are using ROOT, create a TApplic 333 // if you are using ROOT, create a TApplication in this condition in order
294 // to print the help from ROOT as well 334 // to print the help from ROOT as well
295 CommandLineParser::DeleteInstance(); 335 CommandLineParser::DeleteInstance();
296 std::exit(0); 336 std::exit(0);
297 } 337 }
298 << 338
299 /////////// 339 ///////////
300 // Kill application if wrong argument in com 340 // Kill application if wrong argument in command line
301 // 341 //
302 if (parser->CheckIfNotHandledOptionsExists(a << 342 if(parser->CheckIfNotHandledOptionsExists(argc, argv))
>> 343 {
303 // if you are using ROOT, you should initi 344 // if you are using ROOT, you should initialise your TApplication
304 // before this condition 345 // before this condition
305 std::exit(0); 346 std::exit(0);
306 } 347 }
307 } 348 }
308 349