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Diff markup

Differences between /examples/basic/B3/README (Version 11.3.0) and /examples/basic/B3/README (Version 10.2)


                                                   >>   1 $Id: README 94093 2015-11-05 15:16:06Z 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    - radioactive decay hadronic processes which path is defined via 
 44      the G4ENSDFSTATEDATA envirnoment variable << 
 45    - radioactive decay hadronic processes whic << 
 46      the G4RADIOACTIVEDATA envirnoment variabl     45      the G4RADIOACTIVEDATA envirnoment variable.
 47                                                <<  46    
 48    See more on installation of the datasets in     47    See more on installation of the datasets in Geant4 Installation Guide,
 49    Chapter 3.3: Note On Geant4 Datasets:           48    Chapter 3.3: Note On Geant4 Datasets:
 50    http://geant4.web.cern.ch/geant4/UserDocume     49    http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides
 51                                           /Ins     50                                           /InstallationGuide/html/ch03s03.html
 52  3- ACTION INITALIZATION                           51  3- ACTION INITALIZATION
 53                                                    52 
 54    B3[a,b]::ActionInitialization class instant <<  53    B3[a,b]ActionInitialization class instantiates and registers to Geant4 kernel 
 55    all user action classes.                        54    all user action classes.
 56                                                    55 
 57    While in sequential mode the action classes     56    While in sequential mode the action classes are instatiated just once,
 58    via invoking the method:                        57    via invoking the method:
 59       B3[a,b]::ActionInitialization::Build()   <<  58       B3[a,b]ActionInitialization::Build() 
 60    in multi-threading mode the same method is      59    in multi-threading mode the same method is invoked for each thread worker
 61    and so all user action classes are defined      60    and so all user action classes are defined thread-local.
 62                                                    61 
 63    A run action class is instantiated both thr <<  62    A run action class is instantiated both thread-local 
 64    and global that's why its instance is creat     63    and global that's why its instance is created also in the method
 65       B3[a,b]::ActionInitialization::BuildForM <<  64       B3[a,b]ActionInitialization::BuildForMaster() 
 66    which is invoked only in multi-threading mo     65    which is invoked only in multi-threading mode.
 67                                                <<  66        
 68  4- PRIMARY GENERATOR                              67  4- PRIMARY GENERATOR
 69                                                <<  68   
 70    The default particle beam is an ion (F18),  <<  69    The default particle beam is an ion (F18), at rest, randomly distributed 
 71    within a zone inside a patient and is defin <<  70    within a zone inside a patient and is defined in 
 72    B3::PrimaryGeneratorAction::GeneratePrimari <<  71    B3PrimaryGeneratorAction::GeneratePrimaries().
 73    The type of a primary particle can be chang <<  72    The type of a primary particle can be changed with G4ParticleGun commands 
 74    (see run2.mac).                                 73    (see run2.mac).
 75                                                <<  74    
 76  5- DETECTOR RESPONSE:  scorers                    75  5- DETECTOR RESPONSE:  scorers
 77                                                    76 
 78    A 'good' event is an event in which an iden <<  77    A 'good' event is an event in which an identical energy of 511 keV is 
 79    deposited in two separate Crystals. A count <<  78    deposited in two separate Crystals. A count of the number of such events 
 80    corresponds to a measure of the efficiency  <<  79    corresponds to a measure of the efficiency of the PET system. 
 81    The total dose deposited in a patient durin <<  80    The total dose deposited in a patient during a run is also computed. 
 82                                                <<  81    
 83    Scorers are defined in B3::DetectorConstruc <<  82    Scorers are defined in B3DetectorConstruction::ConstructSDandField(). There are
 84    two G4MultiFunctionalDetector objects: one  <<  83    two G4MultiFunctionalDetector objects: one for the Crystal (EnergyDeposit), 
 85    and one for the Patient (DoseDeposit)           84    and one for the Patient (DoseDeposit)
 86                                                    85 
 87    The scorers hits are saved in form of ntupl <<  86    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:                                87    in this example:
 93                                                    88 
 94    B3a:                                            89    B3a:
 95                                                <<  90    
 96    At the end of event, the values acummulated <<  91    At the end of event, the values acummulated in B3aEventAction are passed 
 97    in B3a::RunAction and summed over the whole <<  92    in B3aRunAction and summed over the whole run (see B3aEventAction::EndOfevent()). 
 98    In multi-threading mode the data accumulate <<  93    In multi-threading mode the data accumulated in G4Parameter objects per
 99    workers is merged to the master in B3a::Run <<  94    workers is merged to the master in B3aRunAction::EndOfRunAction() and the final
100    result is printed on the screen.                95    result is printed on the screen.
101                                                <<  96    
102    G4Accumulable<> type instead of G4double an <<  97    G4Parameter<> type instead of G4double and G4int types is used for the B3aRunAction
103    data members in order to facilitate merging <<  98    data members in order to facilitate merging of the values accumulated on workers 
104    to the master.  Currently the accumulables  <<  99    to the master.  Currently the parameters have to be registered to G4ParametersManager
105    and G4AccumulablesManager::Merge() has to b << 100    and G4ParametersManager::Merge() has to be called from the users code. This is planned
106    to be further simplified with a closer inte << 101    to be further simplified with a closer integration of G4Parameter classes in
107    the Geant4 kernel next year.                   102    the Geant4 kernel next year.
108                                                   103 
109    B3b:                                           104    B3b:
110                                                   105 
111    B3b::Run::RecordEvent(), called at end of e << 106    B3bRun::RecordEvent(), called at end of event, collects informations 
112    event per event from the hits collections,  << 107    event per event from the hits collections, and accumulates statistic for 
113    B3b::RunAction::EndOfRunAction().           << 108    B3bRunAction::EndOfRunAction().  
114    In addition, results for dose are accumulat << 109    
115    standard floating-point summation and using << 110    In multi-threading mode the statistics accumulated per workers is merged 
116    class called G4StatAnalysis. The G4StatAnal << 111    to the master in B3bRun::Merge().
117    (1) the sum, (2) sum^2, (3) number of entri << 112       
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                               113  6- STACKING ACTION
128                                                << 114  
129    Beta decay of Fluor generates a neutrino. O    115    Beta decay of Fluor generates a neutrino. One wishes not to track this
130    neutrino; therefore one kills it immediatel    116    neutrino; therefore one kills it immediately, before created particles
131    are put in a stack.                            117    are put in a stack.
132    The function B3::StackingAction::ClassifyNe << 118    The function B3StackingAction::ClassifyNewTrack() is invoked by G4 kernel
133    each time a new particle is created.        << 119    each time a new particle is created.       
134                                                   120 
135  The following paragraphs are common to all ba    121  The following paragraphs are common to all basic examples
136                                                   122 
137  A- VISUALISATION                                 123  A- VISUALISATION
138                                                   124 
139    The visualization manager is set via the G4    125    The visualization manager is set via the G4VisExecutive class
140    in the main() function in exampleB3.cc.     << 126    in the main() function in exampleB3.cc.    
141    The initialisation of the drawing is done v    127    The initialisation of the drawing is done via a set of /vis/ commands
142    in the macro vis.mac. This macro is automat    128    in the macro vis.mac. This macro is automatically read from
143    the main function when the example is used     129    the main function when the example is used in interactive running mode.
144                                                   130 
145    By default, vis.mac opens an OpenGL viewer     131    By default, vis.mac opens an OpenGL viewer (/vis/open OGL).
146    The user can change the initial viewer by c    132    The user can change the initial viewer by commenting out this line
147    and instead uncommenting one of the other /    133    and instead uncommenting one of the other /vis/open statements, such as
148    HepRepFile or DAWNFILE (which produce files    134    HepRepFile or DAWNFILE (which produce files that can be viewed with the
149    HepRApp and DAWN viewers, respectively).  N    135    HepRApp and DAWN viewers, respectively).  Note that one can always
150    open new viewers at any time from the comma    136    open new viewers at any time from the command line.  For example, if
151    you already have a view in, say, an OpenGL     137    you already have a view in, say, an OpenGL window with a name
152    "viewer-0", then                               138    "viewer-0", then
153       /vis/open DAWNFILE                          139       /vis/open DAWNFILE
154    then to get the same view                      140    then to get the same view
155       /vis/viewer/copyView viewer-0               141       /vis/viewer/copyView viewer-0
156    or to get the same view *plus* scene-modifi    142    or to get the same view *plus* scene-modifications
157       /vis/viewer/set/all viewer-0                143       /vis/viewer/set/all viewer-0
158    then to see the result                         144    then to see the result
159       /vis/viewer/flush                           145       /vis/viewer/flush
160                                                   146 
161    The DAWNFILE, HepRepFile drivers are always    147    The DAWNFILE, HepRepFile drivers are always available
162    (since they require no external libraries),    148    (since they require no external libraries), but the OGL driver requires
163    that the Geant4 libraries have been built w    149    that the Geant4 libraries have been built with the OpenGL option.
164                                                   150 
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    151    For more information on visualization, including information on how to
171    install and run DAWN, OpenGL and HepRApp, s    152    install and run DAWN, OpenGL and HepRApp, see the visualization tutorials,
172    for example,                                   153    for example,
173    http://geant4.slac.stanford.edu/Presentatio    154    http://geant4.slac.stanford.edu/Presentations/vis/G4[VIS]Tutorial/G4[VIS]Tutorial.html
174    (where [VIS] can be replaced by DAWN, OpenG    155    (where [VIS] can be replaced by DAWN, OpenGL and HepRApp)
175                                                   156 
176    The tracks are automatically drawn at the e    157    The tracks are automatically drawn at the end of each event, accumulated
177    for all events and erased at the beginning     158    for all events and erased at the beginning of the next run.
178                                                   159 
179  B- USER INTERFACES                               160  B- USER INTERFACES
180                                                << 161  
181    The user command interface is set via the G    162    The user command interface is set via the G4UIExecutive class
182    in the main() function in exampleB3.cc      << 163    in the main() function in exampleB3.cc 
183                                                << 164    The selection of the user command interface is then done automatically 
184    The selection of the user command interface << 165    according to the Geant4 configuration or it can be done explicitly via 
185    according to the Geant4 configuration or it << 166    the third argument of the G4UIExecutive constructor (see exampleB4a.cc). 
186    the third argument of the G4UIExecutive con << 167  
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                                     168 C- HOW TO RUN
194                                                   169 
195     - Execute exampleB3a in the 'interactive m    170     - Execute exampleB3a in the 'interactive mode' with visualization
196         % ./exampleB3a                         << 171         % exampleB3a
197       and type in the commands from run1.mac l << 172       and type in the commands from run1.mac line by line:  
198         Idle> /control/verbose 2                  173         Idle> /control/verbose 2
199         Idle> /tracking/verbose 2                 174         Idle> /tracking/verbose 2
200         Idle> /run/beamOn 1                    << 175         Idle> /run/beamOn 1 
201         Idle> ...                                 176         Idle> ...
202         Idle> exit                                177         Idle> exit
203       or                                          178       or
204         Idle> /control/execute run1.mac           179         Idle> /control/execute run1.mac
205         ....                                      180         ....
206         Idle> exit                                181         Idle> exit
207                                                   182 
208     - Execute exampleB3a in the 'batch' mode f << 183     - Execute exampleB3a in the 'batch' mode from macro files 
209      (without visualization)                      184      (without visualization)
210         % ./exampleB3a run2.mac                << 185         % exampleB3a run2.mac
211         % ./exampleB3a exampleB3.in > exampleB << 186         % exampleB3a exampleB3.in > exampleB3.out
212                                                << 
213                                                   187 
                                                   >> 188