| 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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8 // * LICENSE and available at http://cern.ch/ 8 // * LICENSE and available at http://cern.ch/geant4/license . These *
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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"
42 41
43 #include "G4DNAChemistryManager.hh" <<
44 #include "G4RunManagerFactory.hh" 42 #include "G4RunManagerFactory.hh"
45 #include "G4UIExecutive.hh" << 43
>> 44 #include "G4DNAChemistryManager.hh"
46 #include "G4UImanager.hh" 45 #include "G4UImanager.hh"
>> 46 #include "G4UIExecutive.hh"
47 #include "G4VisExecutive.hh" 47 #include "G4VisExecutive.hh"
48 48
>> 49 #include "CommandLineParser.hh"
>> 50
49 /* 51 /*
50 * WARNING : Geant4 was initially not intended 52 * WARNING : Geant4 was initially not intended for this kind of application
51 * This code is delivered as a prototype 53 * This code is delivered as a prototype
52 * We will be happy to hear from you, do not h 54 * We will be happy to hear from you, do not hesitate to send your feedback and
53 * communicate on the difficulties you may enc 55 * communicate on the difficulties you may encounter
54 * The user interface may change in the next r 56 * The user interface may change in the next releases since a reiteration of the
55 * code has started 57 * code has started
56 */ 58 */
57 59
58 //....oooOO0OOooo........oooOO0OOooo........oo 60 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
59 61
60 using namespace G4DNAPARSER; 62 using namespace G4DNAPARSER;
61 CommandLineParser* parser(0); 63 CommandLineParser* parser(0);
62 long seed = 0; 64 long seed = 0;
63 65
64 unsigned int noise(); 66 unsigned int noise();
65 void SetSeed(); 67 void SetSeed();
66 68
67 void Parse(int& argc, char** argv); 69 void Parse(int& argc, char** argv);
68 70
69 //....oooOO0OOooo........oooOO0OOooo........oo 71 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
70 72
71 int main(int argc, char** argv) 73 int main(int argc, char** argv)
72 { 74 {
73 // Parse options given in commandLine 75 // Parse options given in commandLine
74 Parse(argc, argv); 76 Parse(argc, argv);
75 Command* commandLine(0); 77 Command* commandLine(0);
76 SetSeed(); 78 SetSeed();
77 79
78 // Construct the run manager according to wh 80 // Construct the run manager according to whether MT is activated or not
79 // 81 //
80 auto* runManager = G4RunManagerFactory::Crea << 82 auto* runManager= G4RunManagerFactory::CreateRunManager();
81 83
82 if ((commandLine = parser->GetCommandIfActiv << 84 if((commandLine = parser->GetCommandIfActive("-mt")))
>> 85 {
83 int nThreads = 2; 86 int nThreads = 2;
84 if (commandLine->GetOption() == "NMAX") { << 87 if(commandLine->GetOption() == "NMAX")
>> 88 {
85 nThreads = G4Threading::G4GetNumberOfCor 89 nThreads = G4Threading::G4GetNumberOfCores();
86 } 90 }
87 else { << 91 else
>> 92 {
88 nThreads = G4UIcommand::ConvertToInt(com 93 nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
89 } 94 }
90 95
91 runManager->SetNumberOfThreads(nThreads); 96 runManager->SetNumberOfThreads(nThreads);
92 } 97 }
93 98
94 G4cout << "********************************* 99 G4cout << "**************************************************************"
95 << "******\n===== Chem5 is started wi << 100 << "******\n===== Chem5 is started with "
>> 101 << runManager->GetNumberOfThreads() << " of "
96 << G4Threading::G4GetNumberOfCores() 102 << G4Threading::G4GetNumberOfCores()
97 << " available threads =====\n\n***** 103 << " available threads =====\n\n*************************************"
98 << "*******************************" << 104 <<"*******************************"
>> 105 << G4endl;
99 106
100 // Set mandatory initialization classes 107 // Set mandatory initialization classes
101 runManager->SetUserInitialization(new Physic 108 runManager->SetUserInitialization(new PhysicsList());
102 runManager->SetUserInitialization(new Detect 109 runManager->SetUserInitialization(new DetectorConstruction());
103 runManager->SetUserInitialization(new Action 110 runManager->SetUserInitialization(new ActionInitialization());
104 111
105 // Initialize G4 kernel 112 // Initialize G4 kernel
106 runManager->Initialize(); 113 runManager->Initialize();
107 114
108 // Initialize visualization 115 // Initialize visualization
109 G4VisManager* visManager = new G4VisExecutiv 116 G4VisManager* visManager = new G4VisExecutive();
110 // G4VisExecutive can take a verbosity argum 117 // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
111 // G4VisManager* visManager = new G4VisExecu 118 // G4VisManager* visManager = new G4VisExecutive("Quiet");
112 visManager->Initialize(); 119 visManager->Initialize();
113 120
114 // Get the pointer to the User Interface man 121 // Get the pointer to the User Interface manager
115 G4UImanager* UImanager = G4UImanager::GetUIp 122 G4UImanager* UImanager = G4UImanager::GetUIpointer();
116 G4UIExecutive* ui(0); 123 G4UIExecutive* ui(0);
117 124
118 // interactive mode : define UI session 125 // interactive mode : define UI session
119 if ((commandLine = parser->GetCommandIfActiv << 126 if((commandLine = parser->GetCommandIfActive("-gui")))
>> 127 {
120 ui = new G4UIExecutive(argc, argv, command 128 ui = new G4UIExecutive(argc, argv, commandLine->GetOption());
121 129
122 if (ui->IsGUI()) UImanager->ApplyCommand(" 130 if (ui->IsGUI()) UImanager->ApplyCommand("/control/execute gui.mac");
123 131
124 if (parser->GetCommandIfActive("-novis") = << 132 if (parser->GetCommandIfActive("-novis") == 0)
>> 133 {
125 // visualization is used by default 134 // visualization is used by default
126 if ((commandLine = parser->GetCommandIfA << 135 if ((commandLine = parser->GetCommandIfActive("-vis")))
>> 136 {
127 // select a visualization driver if ne 137 // select a visualization driver if needed (e.g. HepFile)
128 UImanager->ApplyCommand(G4String("/vis << 138 UImanager->ApplyCommand
>> 139 (G4String("/vis/open ") + commandLine->GetOption());
129 } 140 }
130 else { << 141 else
>> 142 {
131 // by default OGL is used 143 // by default OGL is used
132 UImanager->ApplyCommand("/vis/open OGL 144 UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
133 } 145 }
134 UImanager->ApplyCommand("/control/execut 146 UImanager->ApplyCommand("/control/execute vis.mac");
135 } 147 }
136 } 148 }
137 else { << 149 else
>> 150 {
138 // to be use visualization file (= store t 151 // to be use visualization file (= store the visualization into
139 // an external file: 152 // an external file:
140 // ASCIITree ; DAWNFILE ; HepRepFile ; VR 153 // ASCIITree ; DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
141 if ((commandLine = parser->GetCommandIfAct << 154 if((commandLine = parser->GetCommandIfActive("-vis")))
142 UImanager->ApplyCommand(G4String("/vis/o << 155 {
>> 156 UImanager->ApplyCommand(G4String("/vis/open ")
>> 157 + commandLine->GetOption());
143 UImanager->ApplyCommand("/control/execut 158 UImanager->ApplyCommand("/control/execute vis.mac");
144 } 159 }
145 } 160 }
146 161
147 if ((commandLine = parser->GetCommandIfActiv << 162 if((commandLine = parser->GetCommandIfActive("-mac")))
>> 163 {
148 G4String command = "/control/execute "; 164 G4String command = "/control/execute ";
149 UImanager->ApplyCommand(command + commandL 165 UImanager->ApplyCommand(command + commandLine->GetOption());
150 } 166 }
151 else { << 167 else
>> 168 {
152 UImanager->ApplyCommand("/control/execute 169 UImanager->ApplyCommand("/control/execute beam.in");
153 } 170 }
154 171
155 if ((commandLine = parser->GetCommandIfActiv << 172 if((commandLine = parser->GetCommandIfActive("-gui")))
>> 173 {
156 ui->SessionStart(); 174 ui->SessionStart();
157 delete ui; 175 delete ui;
158 } 176 }
159 177
160 // Job termination 178 // Job termination
161 // Free the store: user actions, physics_lis 179 // Free the store: user actions, physics_list and detector_description are
162 // owned and deleted by the run manager, so 180 // owned and deleted by the run manager, so they should not be deleted
163 // in the main() program ! 181 // in the main() program !
164 delete visManager; 182 delete visManager;
165 delete runManager; 183 delete runManager;
166 CommandLineParser::DeleteInstance(); 184 CommandLineParser::DeleteInstance();
167 return 0; 185 return 0;
168 } 186 }
169 187
170 //....oooOO0OOooo........oooOO0OOooo........oo 188 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
171 189
172 bool IsBracket(char c) 190 bool IsBracket(char c)
173 { 191 {
174 switch (c) { << 192 switch(c)
>> 193 {
175 case '[': 194 case '[':
176 case ']': 195 case ']':
177 return true; 196 return true;
178 default: 197 default:
179 return false; 198 return false;
180 } 199 }
181 } 200 }
182 201
183 //....oooOO0OOooo........oooOO0OOooo........oo 202 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
184 203
185 void SetSeed() 204 void SetSeed()
186 { 205 {
187 Command* commandLine(0); 206 Command* commandLine(0);
188 207
189 if ((commandLine = parser->GetCommandIfActiv << 208 if((commandLine = parser->GetCommandIfActive("-seed")))
>> 209 {
190 seed = atoi(commandLine->GetOption().c_str 210 seed = atoi(commandLine->GetOption().c_str());
191 } 211 }
192 212
193 if (seed == 0) // If no seed given in argum << 213 if(seed == 0) // If no seed given in argument, setup the seed
194 { 214 {
195 long jobID_int = 0; 215 long jobID_int = 0;
196 long noice = 0; 216 long noice = 0;
197 217
198 //____________________________________ 218 //____________________________________
199 // In case on cluster 219 // In case on cluster
200 if ((commandLine = parser->GetCommandIfAct << 220 if((commandLine = parser->GetCommandIfActive("-cluster")))
201 noice = labs((long)noise()); << 221 {
>> 222 noice = labs((long) noise());
202 223
203 const char* env = std::getenv("PBS_JOBID << 224 const char * env = std::getenv("PBS_JOBID");
204 225
205 if (env) { << 226 if(env)
>> 227 {
206 G4String buffer(env); 228 G4String buffer(env);
207 G4String jobID_string = buffer.substr( << 229 G4String jobID_string = buffer.substr(0, buffer.find("."));
208 jobID_string.erase(std::remove_if(jobI << 230 jobID_string.erase(std::remove_if(jobID_string.begin(),
209 jobID_string.end()) << 231 jobID_string.end(),
>> 232 &IsBracket),
>> 233 jobID_string.end());
210 jobID_int = atoi(jobID_string.c_str()) 234 jobID_int = atoi(jobID_string.c_str());
211 } 235 }
212 else { << 236 else
>> 237 {
213 env = std::getenv("SGE_TASK_ID"); 238 env = std::getenv("SGE_TASK_ID");
214 if (env) jobID_int = atoi(env); << 239 if(env) jobID_int = atoi(env);
215 } 240 }
216 } // end cluster << 241 } // end cluster
217 242
218 //____________________________________ 243 //____________________________________
219 seed = ((long)time(NULL)) + jobID_int + no << 244 seed = ((long) time(NULL)) + jobID_int + noice;
220 } 245 }
221 246
222 G4cout << "Seed used : " << seed << G4endl; 247 G4cout << "Seed used : " << seed << G4endl;
223 G4Random::setTheEngine(new CLHEP::MixMaxRng( 248 G4Random::setTheEngine(new CLHEP::MixMaxRng());
224 G4Random::setTheSeed(seed); 249 G4Random::setTheSeed(seed);
225 250
226 // Choose the Random engine 251 // Choose the Random engine
227 // CLHEP::HepRandom::setTheEngine(new CLHEP: 252 // CLHEP::HepRandom::setTheEngine(new CLHEP::RanecuEngine);
228 } 253 }
229 254
230 //....oooOO0OOooo........oooOO0OOooo........oo 255 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
231 256
232 unsigned int noise() 257 unsigned int noise()
233 { 258 {
234 #if defined(WIN32) || defined(_WIN32) || defin << 259 #if defined(WIN32)|| defined(_WIN32)|| defined(__WIN32)&&!defined(__CYGWIN__)
235 // TODO: MS Win 260 // TODO: MS Win
236 return std::time(0); 261 return std::time(0);
237 #else 262 #else
238 unsigned int random_seed, random_seed_a, ran 263 unsigned int random_seed, random_seed_a, random_seed_b;
239 std::ifstream file("/dev/urandom", std::ios: << 264 std::ifstream file ("/dev/urandom", std::ios::binary);
240 if (file.is_open()) { << 265 if (file.is_open())
241 char* memblock; << 266 {
>> 267 char * memblock;
242 int size = sizeof(int); 268 int size = sizeof(int);
243 memblock = new char[size]; << 269 memblock = new char [size];
244 file.read(memblock, size); << 270 file.read (memblock, size);
245 file.close(); 271 file.close();
246 random_seed_a = *reinterpret_cast<int*>(me 272 random_seed_a = *reinterpret_cast<int*>(memblock);
247 delete[] memblock; 273 delete[] memblock;
248 } // end if << 274 }// end if
249 else { << 275 else
>> 276 {
250 random_seed_a = 0; 277 random_seed_a = 0;
251 } 278 }
252 random_seed_b = std::time(0); 279 random_seed_b = std::time(0);
253 random_seed = random_seed_a xor random_seed_ 280 random_seed = random_seed_a xor random_seed_b;
254 return random_seed; 281 return random_seed;
255 #endif 282 #endif
256 } 283 }
257 284
258 //....oooOO0OOooo........oooOO0OOooo........oo 285 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
259 286
260 void Parse(int& argc, char** argv) 287 void Parse(int& argc, char** argv)
261 { 288 {
262 ////////// 289 //////////
263 // Parse options given in commandLine 290 // Parse options given in commandLine
264 // 291 //
265 parser = CommandLineParser::GetParser(); 292 parser = CommandLineParser::GetParser();
266 293
267 parser->AddCommand("-gui", Command::OptionNo 294 parser->AddCommand("-gui", Command::OptionNotCompulsory,
268 "Select geant4 UI or just 295 "Select geant4 UI or just launch a geant4 terminal"
269 "session", 296 "session",
270 "qt"); 297 "qt");
271 298
272 parser->AddCommand("-mac", Command::WithOpti << 299 parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute",
>> 300 "macFile.mac");
273 301
274 parser->AddCommand("-seed", Command::WithOpt << 302 parser->AddCommand("-seed",
275 "seed"); << 303 Command::WithOption,
>> 304 "Give a seed value in argument to be tested", "seed");
276 305
277 parser->AddCommand("-mt", Command::WithOptio << 306 parser->AddCommand("-mt",Command::WithOption,
278 "Launch in MT mode (event 307 "Launch in MT mode (events computed in parallel,"
279 " NOT RECOMMANDED WITH CH << 308 " NOT RECOMMANDED WITH CHEMISTRY)", "2");
280 "2"); <<
281 309
282 parser->AddCommand("-chemOFF", Command::With << 310 parser->AddCommand("-chemOFF", Command::WithoutOption,
>> 311 "Deactivate chemistry");
283 312
284 parser->AddCommand("-vis", Command::WithOpti << 313 parser->AddCommand("-vis", Command::WithOption,
285 "OGL 600x600-0+0"); << 314 "Select a visualization driver", "OGL 600x600-0+0");
286 315
287 parser->AddCommand("-novis", Command::Withou << 316 parser->AddCommand("-novis", Command::WithoutOption,
>> 317 "Deactivate visualization when using GUI");
288 318
289 parser->AddCommand("-cluster", Command::With 319 parser->AddCommand("-cluster", Command::WithoutOption,
290 "Launch the code on a clu 320 "Launch the code on a cluster, avoid dupplicated seeds");
291 321
292 ////////// 322 //////////
293 // If -h or --help is given in option : prin 323 // If -h or --help is given in option : print help and exit
294 // 324 //
295 if (parser->Parse(argc, argv) != 0) // help << 325 if (parser->Parse(argc, argv) != 0) // help is being printed
296 { 326 {
297 // if you are using ROOT, create a TApplic 327 // if you are using ROOT, create a TApplication in this condition in order
298 // to print the help from ROOT as well 328 // to print the help from ROOT as well
299 CommandLineParser::DeleteInstance(); 329 CommandLineParser::DeleteInstance();
300 std::exit(0); 330 std::exit(0);
301 } 331 }
302 332
303 /////////// 333 ///////////
304 // Kill application if wrong argument in com 334 // Kill application if wrong argument in command line
305 // 335 //
306 if (parser->CheckIfNotHandledOptionsExists(a << 336 if(parser->CheckIfNotHandledOptionsExists(argc, argv))
>> 337 {
307 // if you are using ROOT, you should initi 338 // if you are using ROOT, you should initialise your TApplication
308 // before this condition 339 // before this condition
309 std::exit(0); 340 std::exit(0);
310 } 341 }
311 } 342 }
312 343