| Geant4 Cross Reference |
>> 1 $Id: README 99559 2016-09-27 07:02:21Z gcosmo $
1 ---------------------------------------------- 2 -------------------------------------------------------------------
2 3
3 ========================================= 4 =========================================================
4 Geant4 - an Object-Oriented Toolkit for S 5 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
5 ========================================= 6 =========================================================
6 7
7 Example B3 8 Example B3
8 ---------- 9 ----------
9 10
10 This example simulates schematically a Positr 11 This example simulates schematically a Positron Emitted Tomography system.
11 << 12
12 1- GEOMETRY DEFINITION 13 1- GEOMETRY DEFINITION
13 14
14 The support of gamma detection are scintill 15 The support of gamma detection are scintillating crystals. A small number
15 of such crystals are optically grouped in a 16 of such crystals are optically grouped in a matrix of crystals. In
16 this example, individual crystals are not d 17 this example, individual crystals are not described; only the matrix of
17 crystals is and it is still called 'Crystal 18 crystals is and it is still called 'Crystal' hereafter.
18 19
19 Crystals are circularly arranged to form a 20 Crystals are circularly arranged to form a ring. Few rings make up the full
20 detector (gamma camera). This is done by po << 21 detector (gamma camera). This is done by positionning Crystals in
21 Ring with an appropriate rotation matrix. S << 22 Ring with an appropriate rotation matrix. Several copies of Ring are
22 then placed in the full detector. << 23 then placed in the full detector.
23 24
24 The head of a patient is schematised as a h 25 The head of a patient is schematised as a homogeneous cylinder of brain
25 tissue, placed at the center of full detect 26 tissue, placed at the center of full detector.
26 << 27
27 The Crystal material, Lu2SiO5, is not inclu << 28 The Crystal material, Lu2SiO5, is not included in the G4Nist database.
28 Therefore, it is explicitly built in Define 29 Therefore, it is explicitly built in DefineMaterials().
29 << 30
30 2- PHYSICS LIST 31 2- PHYSICS LIST
31 32
32 The physics list contains standard electrom 33 The physics list contains standard electromagnetic processes and the
33 radioactiveDecay module for GenericIon. It << 34 radioactiveDecay module for GenericIon. It is defined in the B3PhysicsList
34 class as a Geant4 modular physics list with << 35 class as a Geant4 modular physics list with registered physics builders
35 provided in Geant4: 36 provided in Geant4:
36 - G4DecayPhysics - defines all particles an 37 - G4DecayPhysics - defines all particles and their decay processes
37 - G4RadioactiveDecayPhysics - defines radio 38 - G4RadioactiveDecayPhysics - defines radioactiveDecay for GenericIon
38 - G4EmStandardPhysics - defines all EM stan 39 - G4EmStandardPhysics - defines all EM standard processes
39 << 40
40 This physics list requires data files for: 41 This physics list requires data files for:
41 - low energy electromagnetic processes whic << 42 - low energy electromagnetic processes which path is defined via
42 the G4LEDATA envirnoment variable 43 the G4LEDATA envirnoment variable
43 - nuclides properties which path is defined << 44 - nuclides properties which path is defined via
44 the G4ENSDFSTATEDATA envirnoment variable 45 the G4ENSDFSTATEDATA envirnoment variable
45 - radioactive decay hadronic processes whic << 46 - radioactive decay hadronic processes which path is defined via
46 the G4RADIOACTIVEDATA envirnoment variabl 47 the G4RADIOACTIVEDATA envirnoment variable.
47 << 48
48 See more on installation of the datasets in 49 See more on installation of the datasets in Geant4 Installation Guide,
49 Chapter 3.3: Note On Geant4 Datasets: 50 Chapter 3.3: Note On Geant4 Datasets:
50 http://geant4.web.cern.ch/geant4/UserDocume 51 http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides
51 /Ins 52 /InstallationGuide/html/ch03s03.html
52 3- ACTION INITALIZATION 53 3- ACTION INITALIZATION
53 54
54 B3[a,b]::ActionInitialization class instant << 55 B3[a,b]ActionInitialization class instantiates and registers to Geant4 kernel
55 all user action classes. 56 all user action classes.
56 57
57 While in sequential mode the action classes 58 While in sequential mode the action classes are instatiated just once,
58 via invoking the method: 59 via invoking the method:
59 B3[a,b]::ActionInitialization::Build() << 60 B3[a,b]ActionInitialization::Build()
60 in multi-threading mode the same method is 61 in multi-threading mode the same method is invoked for each thread worker
61 and so all user action classes are defined 62 and so all user action classes are defined thread-local.
62 63
63 A run action class is instantiated both thr << 64 A run action class is instantiated both thread-local
64 and global that's why its instance is creat 65 and global that's why its instance is created also in the method
65 B3[a,b]::ActionInitialization::BuildForM << 66 B3[a,b]ActionInitialization::BuildForMaster()
66 which is invoked only in multi-threading mo 67 which is invoked only in multi-threading mode.
67 << 68
68 4- PRIMARY GENERATOR 69 4- PRIMARY GENERATOR
69 << 70
70 The default particle beam is an ion (F18), << 71 The default particle beam is an ion (F18), at rest, randomly distributed
71 within a zone inside a patient and is defin << 72 within a zone inside a patient and is defined in
72 B3::PrimaryGeneratorAction::GeneratePrimari << 73 B3PrimaryGeneratorAction::GeneratePrimaries().
73 The type of a primary particle can be chang << 74 The type of a primary particle can be changed with G4ParticleGun commands
74 (see run2.mac). 75 (see run2.mac).
75 << 76
76 5- DETECTOR RESPONSE: scorers 77 5- DETECTOR RESPONSE: scorers
77 78
78 A 'good' event is an event in which an iden << 79 A 'good' event is an event in which an identical energy of 511 keV is
79 deposited in two separate Crystals. A count << 80 deposited in two separate Crystals. A count of the number of such events
80 corresponds to a measure of the efficiency << 81 corresponds to a measure of the efficiency of the PET system.
81 The total dose deposited in a patient durin << 82 The total dose deposited in a patient during a run is also computed.
82 << 83
83 Scorers are defined in B3::DetectorConstruc << 84 Scorers are defined in B3DetectorConstruction::ConstructSDandField(). There are
84 two G4MultiFunctionalDetector objects: one << 85 two G4MultiFunctionalDetector objects: one for the Crystal (EnergyDeposit),
85 and one for the Patient (DoseDeposit) 86 and one for the Patient (DoseDeposit)
86 87
87 The scorers hits are saved in form of ntupl << 88 Two variants of accumulation event statistics in a run are demonstrated
88 analysis tools. This feature is activated i <<
89 G4TScoreNtupleWriter. <<
90 <<
91 Two variants of accumulation event statisti <<
92 in this example: 89 in this example:
93 90
94 B3a: 91 B3a:
95 << 92
96 At the end of event, the values acummulated << 93 At the end of event, the values acummulated in B3aEventAction are passed
97 in B3a::RunAction and summed over the whole << 94 in B3aRunAction and summed over the whole run (see B3aEventAction::EndOfevent()).
98 In multi-threading mode the data accumulate 95 In multi-threading mode the data accumulated in G4Accumulable objects per
99 workers is merged to the master in B3a::Run << 96 workers is merged to the master in B3aRunAction::EndOfRunAction() and the final
100 result is printed on the screen. 97 result is printed on the screen.
101 << 98
102 G4Accumulable<> type instead of G4double an << 99 G4Accumulable<> type instead of G4double and G4int types is used for the B3aRunAction
103 data members in order to facilitate merging << 100 data members in order to facilitate merging of the values accumulated on workers
104 to the master. Currently the accumulables 101 to the master. Currently the accumulables have to be registered to G4AccumulablesManager
105 and G4AccumulablesManager::Merge() has to b 102 and G4AccumulablesManager::Merge() has to be called from the users code. This is planned
106 to be further simplified with a closer inte 103 to be further simplified with a closer integration of G4Accumulable classes in
107 the Geant4 kernel next year. 104 the Geant4 kernel next year.
108 105
109 B3b: 106 B3b:
110 107
111 B3b::Run::RecordEvent(), called at end of e << 108 B3bRun::RecordEvent(), called at end of event, collects informations
112 event per event from the hits collections, << 109 event per event from the hits collections, and accumulates statistic for
113 B3b::RunAction::EndOfRunAction(). << 110 B3bRunAction::EndOfRunAction().
114 In addition, results for dose are accumulat << 111
115 standard floating-point summation and using << 112 In multi-threading mode the statistics accumulated per workers is merged
116 class called G4StatAnalysis. The G4StatAnal << 113 to the master in B3bRun::Merge().
117 (1) the sum, (2) sum^2, (3) number of entri << 114
118 less than mean * machine-epsilon (the machi <<
119 between 1.0 and the next value representabl <<
120 From these 4 values, G4StatAnalysis provide <<
121 standard deviation, variance, coefficient o <<
122 and r2eff. <<
123 <<
124 In multi-threading mode the statistics accu <<
125 to the master in B3b::Run::Merge(). <<
126 <<
127 6- STACKING ACTION 115 6- STACKING ACTION
128 << 116
129 Beta decay of Fluor generates a neutrino. O 117 Beta decay of Fluor generates a neutrino. One wishes not to track this
130 neutrino; therefore one kills it immediatel 118 neutrino; therefore one kills it immediately, before created particles
131 are put in a stack. 119 are put in a stack.
132 The function B3::StackingAction::ClassifyNe << 120 The function B3StackingAction::ClassifyNewTrack() is invoked by G4 kernel
133 each time a new particle is created. << 121 each time a new particle is created.
134 122
135 The following paragraphs are common to all ba 123 The following paragraphs are common to all basic examples
136 124
137 A- VISUALISATION 125 A- VISUALISATION
138 126
139 The visualization manager is set via the G4 127 The visualization manager is set via the G4VisExecutive class
140 in the main() function in exampleB3.cc. << 128 in the main() function in exampleB3.cc.
141 The initialisation of the drawing is done v 129 The initialisation of the drawing is done via a set of /vis/ commands
142 in the macro vis.mac. This macro is automat 130 in the macro vis.mac. This macro is automatically read from
143 the main function when the example is used 131 the main function when the example is used in interactive running mode.
144 132
145 By default, vis.mac opens an OpenGL viewer 133 By default, vis.mac opens an OpenGL viewer (/vis/open OGL).
146 The user can change the initial viewer by c 134 The user can change the initial viewer by commenting out this line
147 and instead uncommenting one of the other / 135 and instead uncommenting one of the other /vis/open statements, such as
148 HepRepFile or DAWNFILE (which produce files 136 HepRepFile or DAWNFILE (which produce files that can be viewed with the
149 HepRApp and DAWN viewers, respectively). N 137 HepRApp and DAWN viewers, respectively). Note that one can always
150 open new viewers at any time from the comma 138 open new viewers at any time from the command line. For example, if
151 you already have a view in, say, an OpenGL 139 you already have a view in, say, an OpenGL window with a name
152 "viewer-0", then 140 "viewer-0", then
153 /vis/open DAWNFILE 141 /vis/open DAWNFILE
154 then to get the same view 142 then to get the same view
155 /vis/viewer/copyView viewer-0 143 /vis/viewer/copyView viewer-0
156 or to get the same view *plus* scene-modifi 144 or to get the same view *plus* scene-modifications
157 /vis/viewer/set/all viewer-0 145 /vis/viewer/set/all viewer-0
158 then to see the result 146 then to see the result
159 /vis/viewer/flush 147 /vis/viewer/flush
160 148
161 The DAWNFILE, HepRepFile drivers are always 149 The DAWNFILE, HepRepFile drivers are always available
162 (since they require no external libraries), 150 (since they require no external libraries), but the OGL driver requires
163 that the Geant4 libraries have been built w 151 that the Geant4 libraries have been built with the OpenGL option.
164 152
165 Since 11.1, the TSG visualization driver ca <<
166 file output in png, jpeg, gl2ps formats wit <<
167 It can be controlled via UI commands provid <<
168 demonstrated in the tsg_offscreen.mac macro <<
169 <<
170 For more information on visualization, incl 153 For more information on visualization, including information on how to
171 install and run DAWN, OpenGL and HepRApp, s 154 install and run DAWN, OpenGL and HepRApp, see the visualization tutorials,
172 for example, 155 for example,
173 http://geant4.slac.stanford.edu/Presentatio 156 http://geant4.slac.stanford.edu/Presentations/vis/G4[VIS]Tutorial/G4[VIS]Tutorial.html
174 (where [VIS] can be replaced by DAWN, OpenG 157 (where [VIS] can be replaced by DAWN, OpenGL and HepRApp)
175 158
176 The tracks are automatically drawn at the e 159 The tracks are automatically drawn at the end of each event, accumulated
177 for all events and erased at the beginning 160 for all events and erased at the beginning of the next run.
178 161
179 B- USER INTERFACES 162 B- USER INTERFACES
180 << 163
181 The user command interface is set via the G 164 The user command interface is set via the G4UIExecutive class
182 in the main() function in exampleB3.cc << 165 in the main() function in exampleB3.cc
183 << 166 The selection of the user command interface is then done automatically
184 The selection of the user command interface << 167 according to the Geant4 configuration or it can be done explicitly via
185 according to the Geant4 configuration or it << 168 the third argument of the G4UIExecutive constructor (see exampleB4a.cc).
186 the third argument of the G4UIExecutive con << 169
187 <<
188 The gui.mac macros are provided in examples <<
189 is automatically executed if Geant4 is buil <<
190 It is also possible to customise the icons <<
191 demonstrated in the icons.mac macro in exam <<
192 <<
193 C- HOW TO RUN 170 C- HOW TO RUN
194 171
195 - Execute exampleB3a in the 'interactive m 172 - Execute exampleB3a in the 'interactive mode' with visualization
196 % ./exampleB3a << 173 % exampleB3a
197 and type in the commands from run1.mac l << 174 and type in the commands from run1.mac line by line:
198 Idle> /control/verbose 2 175 Idle> /control/verbose 2
199 Idle> /tracking/verbose 2 176 Idle> /tracking/verbose 2
200 Idle> /run/beamOn 1 << 177 Idle> /run/beamOn 1
201 Idle> ... 178 Idle> ...
202 Idle> exit 179 Idle> exit
203 or 180 or
204 Idle> /control/execute run1.mac 181 Idle> /control/execute run1.mac
205 .... 182 ....
206 Idle> exit 183 Idle> exit
207 184
208 - Execute exampleB3a in the 'batch' mode f << 185 - Execute exampleB3a in the 'batch' mode from macro files
209 (without visualization) 186 (without visualization)
210 % ./exampleB3a run2.mac << 187 % exampleB3a run2.mac
211 % ./exampleB3a exampleB3.in > exampleB << 188 % exampleB3a exampleB3.in > exampleB3.out
212 <<
213 189
>> 190