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