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