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