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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 *
7 // * conditions of the Geant4 Software License 7 // * conditions of the Geant4 Software License, included in the file *
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 // and papers 30 // and papers
31 // M. Batmunkh et al. J Radiat Res Appl Sci 8 31 // M. Batmunkh et al. J Radiat Res Appl Sci 8 (2015) 498-507
32 // O. Belov et al. Physica Medica 32 (2016) 15 32 // O. Belov et al. Physica Medica 32 (2016) 1510-1520
33 // The Geant4-DNA web site is available at htt 33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 // << 34 //
35 // ------------------------------------------- 35 // -------------------------------------------------------------------
36 // November 2016 36 // November 2016
37 // ------------------------------------------- 37 // -------------------------------------------------------------------
38 // 38 //
>> 39 // $ID$
39 /// \file neuron.cc 40 /// \file neuron.cc
40 /// \brief Implementation of the neuron exampl 41 /// \brief Implementation of the neuron example
41 // 42 //
42 //....oooOO0OOooo........oooOO0OOooo........oo 43 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
43 #include "ActionInitialization.hh" <<
44 #include "CommandLineParser.hh" <<
45 #include "DetectorConstruction.hh" <<
46 #include "PhysicsList.hh" <<
47 44
>> 45 #ifdef G4MULTITHREADED
>> 46 #include "G4MTRunManager.hh"
>> 47 #else
>> 48 #include "G4RunManager.hh"
>> 49 #endif
48 #include "G4DNAChemistryManager.hh" 50 #include "G4DNAChemistryManager.hh"
49 #include "G4RunManagerFactory.hh" <<
50 #include "G4Timer.hh" 51 #include "G4Timer.hh"
51 #include "G4Types.hh" <<
52 #include "G4UIExecutive.hh" <<
53 #include "G4UImanager.hh" 52 #include "G4UImanager.hh"
>> 53 #include "G4UIExecutive.hh"
54 #include "G4VisExecutive.hh" 54 #include "G4VisExecutive.hh"
>> 55 #include "CommandLineParser.hh"
>> 56 #include "ActionInitialization.hh"
>> 57 #include "DetectorConstruction.hh"
>> 58 #include "PhysicsList.hh"
55 59
56 //....oooOO0OOooo........oooOO0OOooo........oo 60 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
57 61
58 using namespace std; 62 using namespace std;
59 using namespace G4DNAPARSER; 63 using namespace G4DNAPARSER;
60 <<
61 CommandLineParser* parser(0); 64 CommandLineParser* parser(0);
62 65
63 void Parse(int& argc, char** argv); 66 void Parse(int& argc, char** argv);
64 67
65 int main(int argc, char** argv) << 68 int main(int argc,char** argv)
66 { 69 {
>> 70
67 // run time in Geant4 71 // run time in Geant4
68 G4Timer* timer = new G4Timer(); << 72 G4Timer *timer = new G4Timer();
69 timer->Start(); << 73 timer->Start();
>> 74
>> 75 // Choose the Random engine
>> 76 G4Random::setTheEngine(new CLHEP::RanecuEngine);
70 77
71 ////////// 78 //////////
72 // Parse options given in commandLine 79 // Parse options given in commandLine
73 // 80 //
74 Parse(argc, argv); 81 Parse(argc, argv);
75 82
76 ////////// 83 //////////
77 // Construct the run manager according to wh 84 // Construct the run manager according to whether MT is activated or not
78 // 85 //
79 Command* commandLine(0); 86 Command* commandLine(0);
80 << 87
81 auto* runManager = G4RunManagerFactory::Crea << 88 #ifdef G4MULTITHREADED
82 << 89 G4MTRunManager* runManager= new G4MTRunManager;
83 if ((commandLine = parser->GetCommandIfActiv << 90 if ((commandLine = parser->GetCommandIfActive("-mt")))
84 G4int nThreads = 2; << 91 {
85 << 92 int nThreads = 2;
86 if (commandLine->GetOption() == "NMAX") { << 93 if(commandLine->GetOption() == "NMAX")
87 nThreads = G4Threading::G4GetNumberOfCor << 94 {
>> 95 nThreads = G4Threading::G4GetNumberOfCores();
88 } 96 }
89 else { << 97 else
90 nThreads = G4UIcommand::ConvertToInt(com << 98 {
>> 99 nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
91 } 100 }
>> 101 G4cout << "===== neuron is started with "
>> 102 << runManager->GetNumberOfThreads()
>> 103 << " threads of MT MODE =====" << G4endl;
>> 104
92 runManager->SetNumberOfThreads(nThreads); 105 runManager->SetNumberOfThreads(nThreads);
93 <<
94 G4cout << "===== neuron is started with " <<
95 << " threads of MT MODE =====" << G <<
96 } 106 }
>> 107 #else
>> 108 G4RunManager* runManager = new G4RunManager();
>> 109 G4cout << "===== neuron is started with "
>> 110 << " SEQUENTIAL MODE =====" << G4endl;
>> 111 #endif
97 112
98 // Set mandatory user initialization classes 113 // Set mandatory user initialization classes
99 DetectorConstruction* detector = new Detecto 114 DetectorConstruction* detector = new DetectorConstruction;
100 runManager->SetUserInitialization(detector); 115 runManager->SetUserInitialization(detector);
101 runManager->SetUserInitialization(new Physic << 116 runManager->SetUserInitialization(new PhysicsList);
102 117
103 // User action initialization << 118 // User action initialization
104 runManager->SetUserInitialization(new Action 119 runManager->SetUserInitialization(new ActionInitialization(detector));
105 << 120
106 // Initialize G4 kernel << 121 // Initialize G4 kernel
107 runManager->Initialize(); 122 runManager->Initialize();
108 123
109 // Initialize visualization 124 // Initialize visualization
110 G4VisManager* visManager = new G4VisExecutiv 125 G4VisManager* visManager = new G4VisExecutive;
111 visManager->Initialize(); 126 visManager->Initialize();
112 127
113 // Get the pointer to the User Interface man 128 // Get the pointer to the User Interface manager
114 G4UImanager* UImanager = G4UImanager::GetUIp 129 G4UImanager* UImanager = G4UImanager::GetUIpointer();
115 G4UIExecutive* ui(0); 130 G4UIExecutive* ui(0);
116 131
117 // interactive mode : define UI session 132 // interactive mode : define UI session
118 if ((commandLine = parser->GetCommandIfActiv << 133 if ((commandLine = parser->GetCommandIfActive("-gui")))
119 ui = new G4UIExecutive(argc, argv, command << 134 {
>> 135 ui = new G4UIExecutive(argc, argv,
>> 136 commandLine->GetOption());
120 137
121 if (ui->IsGUI()) UImanager->ApplyCommand(" << 138 if(ui->IsGUI())
>> 139 UImanager->ApplyCommand("/control/execute gui.mac");
122 140
123 if (parser->GetCommandIfActive("-novis") = << 141 if(parser->GetCommandIfActive("-novis") == 0)
124 // visualization is used by default 142 // visualization is used by default
125 { 143 {
126 if ((commandLine = parser->GetCommandIfA << 144 if((commandLine = parser->GetCommandIfActive("-vis")))
127 // select a visualization driver if need 145 // select a visualization driver if needed (e.g. HepFile)
128 { 146 {
129 UImanager->ApplyCommand(G4String("/vis << 147 UImanager->ApplyCommand(G4String("/vis/open ")+
>> 148 commandLine->GetOption());
130 } 149 }
131 else 150 else
132 // by default OGL is used 151 // by default OGL is used
133 { 152 {
134 UImanager->ApplyCommand("/vis/open OGL 153 UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
135 } 154 }
136 UImanager->ApplyCommand("/control/execut 155 UImanager->ApplyCommand("/control/execute vis.mac");
137 } 156 }
138 } 157 }
139 else 158 else
140 // to be use visualization file (= store the 159 // to be use visualization file (= store the visualization into
141 // an external file: 160 // an external file:
142 // ASCIITree ; DAWNFILE ; HepRepFile ; VRML 161 // ASCIITree ; DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
143 { 162 {
144 if ((commandLine = parser->GetCommandIfAct << 163 if ((commandLine = parser->GetCommandIfActive("-vis")))
145 UImanager->ApplyCommand(G4String("/vis/o << 164 {
>> 165 UImanager->ApplyCommand(G4String("/vis/open ")+commandLine->GetOption());
146 UImanager->ApplyCommand("/control/execut 166 UImanager->ApplyCommand("/control/execute vis.mac");
147 } 167 }
148 } 168 }
149 169
150 if ((commandLine = parser->GetCommandIfActiv << 170 if ((commandLine = parser->GetCommandIfActive("-mac")))
>> 171 {
151 G4String command = "/control/execute "; 172 G4String command = "/control/execute ";
152 UImanager->ApplyCommand(command + commandL 173 UImanager->ApplyCommand(command + commandLine->GetOption());
153 } 174 }
154 else { << 175 else
155 UImanager->ApplyCommand("/control/execute << 176 {
>> 177 UImanager->ApplyCommand("/control/execute "); //neuron.in
156 } 178 }
157 179
158 if ((commandLine = parser->GetCommandIfActiv << 180 if ((commandLine = parser->GetCommandIfActive("-gui")))
>> 181 {
159 ui->SessionStart(); 182 ui->SessionStart();
160 delete ui; 183 delete ui;
161 } 184 }
162 185
163 // calculation time << 186 // calculation time
164 timer->Stop(); << 187 timer->Stop();
165 G4cout << " Calculation time << 188 G4cout << " Calculation time = "
166 << G4endl; << 189 << timer->GetRealElapsed() << " s \n"<< G4endl;
167 << 190
168 delete visManager; 191 delete visManager;
169 delete runManager; 192 delete runManager;
170 193
171 return 0; 194 return 0;
172 } 195 }
173 196
174 //....oooOO0OOooo........oooOO0OOooo........oo 197 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
175 198
176 void GetNameAndPathOfExecutable(char** argv, G << 199 void GetNameAndPathOfExecutable(char** argv,
>> 200 G4String& executable,
>> 201 G4String& path)
177 { 202 {
178 // Get the last position of '/' 203 // Get the last position of '/'
179 std::string aux(argv[0]); 204 std::string aux(argv[0]);
180 205
181 // get '/' or '\\' depending on unix/mac or 206 // get '/' or '\\' depending on unix/mac or windows.
182 #if defined(_WIN32) || defined(WIN32) 207 #if defined(_WIN32) || defined(WIN32)
183 int pos = aux.rfind('\\'); 208 int pos = aux.rfind('\\');
184 #else 209 #else
185 int pos = aux.rfind('/'); 210 int pos = aux.rfind('/');
186 #endif 211 #endif
187 212
188 // Get the path and the name 213 // Get the path and the name
189 path = aux.substr(0, pos + 1); 214 path = aux.substr(0, pos + 1);
190 executable = aux.substr(pos + 1); 215 executable = aux.substr(pos + 1);
191 } 216 }
192 217
193 //....oooOO0OOooo........oooOO0OOooo........oo 218 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
194 219
195 void Parse(int& argc, char** argv) 220 void Parse(int& argc, char** argv)
196 { 221 {
197 ////////// 222 //////////
198 // Parse options given in commandLine 223 // Parse options given in commandLine
199 // 224 //
200 parser = CommandLineParser::GetParser(); 225 parser = CommandLineParser::GetParser();
201 226
202 parser->AddCommand("-gui", Command::OptionNo << 227 parser->AddCommand("-gui",
203 "Select geant4 UI or just << 228 Command::OptionNotCompulsory,
204 << 229 "Select geant4 UI or just launch a geant4 terminal session",
205 parser->AddCommand("-mac", Command::WithOpti << 230 "qt");
206 << 231
207 // You cann your own command, as for instanc << 232 parser->AddCommand("-mac",
208 // parser->AddCommand("-seed", << 233 Command::WithOption,
209 // Command::WithOption, << 234 "Give a mac file to execute",
210 // "Give a seed value in << 235 "macFile.mac");
211 // it is then up to you to manage this optio << 236
212 << 237 // You cann your own command, as for instance:
213 parser->AddCommand("-mt", Command::WithOptio << 238 // parser->AddCommand("-seed",
214 " NOT RECOMMANDED WITH CH << 239 // Command::WithOption,
>> 240 // "Give a seed value in argument to be tested", "seed");
>> 241 // it is then up to you to manage this option
>> 242
>> 243 #ifdef G4MULTITHREADED
>> 244 parser->AddCommand("-mt",
>> 245 Command::WithOption,
>> 246 "Launch in MT mode (events computed in parallel)",
>> 247 " NOT RECOMMANDED WITH CHEMISTRY)",
>> 248 "2");
>> 249 #endif
215 250
216 parser->AddCommand("-sXY", Command::OptionNo 251 parser->AddCommand("-sXY", Command::OptionNotCompulsory,
217 "Initial beam position un << 252 "Initial beam position uniformly spread on a square!");
218 parser->AddCommand("-dXY", Command::OptionNo 253 parser->AddCommand("-dXY", Command::OptionNotCompulsory,
219 "Initial beam position un << 254 "Initial beam position uniformly spread on a disk!");
220 << 255
221 parser->AddCommand("-dnaliv", Command::Optio << 256 parser->AddCommand("-dnaliv", Command::OptionNotCompulsory,
>> 257 "Activate Livermore + DNAPhysics");
222 parser->AddCommand("-dnachemON", Command::Op 258 parser->AddCommand("-dnachemON", Command::OptionNotCompulsory,
223 "Activate Livermore + DNA << 259 "Activate Livermore + DNAPhysics + DNAChemistry");
224 parser->AddCommand("-dnahad", Command::Optio 260 parser->AddCommand("-dnahad", Command::OptionNotCompulsory,
225 "Activate Hadronic + Live 261 "Activate Hadronic + Livermore + DNAPhysics");
226 262
227 parser->AddCommand("-swc", Command::WithOpti << 263 parser->AddCommand("-swc",
>> 264 Command::WithOption,
>> 265 "Give a SWC file to simulation",
>> 266 "fileName.swc");
228 267
229 parser->AddCommand("-network", 268 parser->AddCommand("-network",
230 Command::WithOption, // << 269 Command::WithOption, //OptionNotCompulsory,
231 "Give a DAT file to simul << 270 "Give a DAT file to simulation",
232 << 271 "fileName.dat");
233 parser->AddCommand("-vis", Command::WithOpti << 272
>> 273 parser->AddCommand("-vis",
>> 274 Command::WithOption,
>> 275 "Select a visualization driver",
234 "OGL 600x600-0+0"); 276 "OGL 600x600-0+0");
235 277
236 parser->AddCommand("-novis", Command::Withou << 278 parser->AddCommand("-novis",
>> 279 Command::WithoutOption,
>> 280 "Deactivate visualization when using GUI");
237 281
238 G4String exec; 282 G4String exec;
239 G4String path; 283 G4String path;
240 GetNameAndPathOfExecutable(argv, exec, path) << 284 GetNameAndPathOfExecutable(argv,exec, path);
241 285
242 parser->AddCommand("-out", Command::OptionNo << 286 parser->AddCommand("-out",
>> 287 Command::OptionNotCompulsory,
>> 288 "Output files",
>> 289 exec);
243 290
244 ////////// 291 //////////
245 // If -h or --help is given in option : prin 292 // If -h or --help is given in option : print help and exit
246 // 293 //
247 if (parser->Parse(argc, argv) != 0) // help << 294 if (parser->Parse(argc, argv) != 0) // help is being printed
248 { 295 {
249 // if you are using ROOT, create a TApplic 296 // if you are using ROOT, create a TApplication in this condition in order
250 // to print the help from ROOT as well 297 // to print the help from ROOT as well
251 CommandLineParser::DeleteInstance(); 298 CommandLineParser::DeleteInstance();
252 std::exit(0); 299 std::exit(0);
253 } 300 }
>> 301
254 /////////// 302 ///////////
255 // Kill application if wrong argument in com 303 // Kill application if wrong argument in command line
256 // 304 //
257 if (parser->CheckIfNotHandledOptionsExists(a << 305 if (parser->CheckIfNotHandledOptionsExists(argc, argv))
>> 306 {
258 // if you are using ROOT, you should initi 307 // if you are using ROOT, you should initialise your TApplication
259 // before this condition 308 // before this condition
260 abort(); 309 abort();
261 } 310 }
262 } 311 }
263 312