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 \page ExampleChem5 Example chem5
 
 \author Ramos-Mendez (a) based on initial implementation of chem5 from \n
 P. Piersimoni (b), M. Karamitros (c)       \n
 (a) joserm84 _ gmail _ com \n
 
 This example is provided by the Geant4-DNA collaboration.
 (http://geant4-dna.org)
 
 Any report or published results obtained using the Geant4-DNA software shall 
 cite the following Geant4-DNA collaboration publications: \n
 Phys. Med. 31 (2015) 861-874    \n
 Med. Phys. 37 (2010) 4692-4708  \n
 Phys. Med. Biol. 63(10) (2018) 105014-12pp\n
 
 The example is a variation of the chem4 example, it shows how to activate 
 the chemistry code and score the radiochemical yield G using the constructors
 G4EmDNAPhysics_option8 and G4EmDNAChemistry_option1\n
 
 ## GEOMETRY DEFINITION
 The world volume is a simple box which represents a 'pseudo infinite'
 homogeneous medium.
 
 Two parameters define the geometry :
 - the material of the box -- for Geant4-DNA it has to be water.
 - the full size of the box.
 
 The default geometry is constructed in DetectorConstruction class.
 
 ## PHYSICS LIST
 
   PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option8 &
   G4EmDNAChemistry_option1 constructors.
 
 ## ACTION INITALIZATION
 
   The class ActionInitialization instantiates and registers
   to Geant4 kernel all user action classes.
 
   While in sequential mode the action classes are instantiated just once,
   via invoking the method
     ActionInitialization::Build()
   in multi-threading mode the same method is invoked for each thread worker
   and so all user action classes are defined thread-local.
 
   A run action class is instantiated both thread-local
   and global that's why its instance is created also in the method
     ActionInitialization::BuildForMaster()
   which is invoked only in multi-threading mode.
 
 ## AN EVENT: PRIMARY GENERATOR
 
   The primary kinematic consists of a single particle starting at the center
    of the box. The type of the particle and its energy are set in the
   PrimaryGeneratorAction class, and can be changed via the G4 build-in
   commands of G4ParticleGun class.
   The chemistry module is triggered in the StackingAction class when all
   physical tracks have been processed.
 
 ## DETECTOR RESPONSE : Scorers
 
 ### Species scorer
 
   Scorers are defined in DetectorConstruction::ConstructSDandField(). There is
   one G4MultiFunctionalDetector object which computes the energy deposition and
   the number of species along time in order to extract
   the radiochemical yields:
 ```
 (Number of species X) / (100 eV of deposited energy).
 ```
 
   Run::RecordEvent(), called at end of event, collects informations
   event per event from the hits collections, and accumulates statistic for
   RunAction::EndOfRunAction().
 
   In multi-threading mode the statistics accumulated per workers is merged
   to the master in Run::Merge().
 
   The information about G-value as a function of the time for each
   molecular specie is scored in ASCII format.
   
 ### Primary Killer
   The G-values are computing for a range of deposited energy. 
   An infinite volume is assumed as the geometrical scenario. Therefore the energy lost by the 
   primary particle equals the deposited energy from all secondary particles.
 
   The primary is killed once it has deposited more energy than a 
   minimum threshold. 
   IMPORTANT: However, when the primary particle looses more energy in 
   few interaction steps than the maximum allowed thresold, the event is 
   disregarded (=aborted). \n
   
   These two macro commands can be used to control the energy loss by the primary:
   
 ```
 /primaryKiller/eLossMin 10 keV 
 # after 10 keV of energy loss by the primary particle, the primary is killed
 
 /primaryKiller/eLossMax 10.1 keV 
 # if the primary particle losses more than 10.1 keV, the event is aborted
 ```
 
   The G-values are then computed for a deposited energy in the range [10 keV;10.1 keV].
 
   Note that if the upper boundary of the energy lost by the primary is not set, the chemistry may 
   take a lot of time to compute as the number of secondaries may be huge.
   This set of macros is embedded in the PrimaryKiller class.
   The species scorer must check whether the event was aborted before taking it or not into
   account for the computation of the results. 
 
 ## STACKING ACTION
 
   StackingAction::NewStage is called when a stack of tracks has been processed
   (for more details, look at the Geant4 documentation).
   A verification on whether physical tracks remain to be processed is done.
   If no tracks remain to be processed, the chemical module is then triggered.
 
 ## VISUALISATION
 
   The visualization manager is set via the G4VisExecutive class
   in the main() function in chem5.cc.
   The initialisation of the drawing is done via a set of /vis/ commands
   in the macro vis.mac. To activate the visualization mode run:
 ```
 ./chem5 -vis
 ```
 
 ## OUTPUT
 
   Physics initialization and the defined reaction table are printed.
   G4Scheduler processes the chemical stage time step after time step.
   Chemical reactions are printed.
     The molecular reaction as a function of the elapsed time can be displayed
    setting the macro command /scheduler/verbose 1
    
 ## RELEVANT MACRO COMMANDS
 ```
 /primaryKiller/eLossMax 10 keV   # after 10 keV of energy loss by the primary particle, the primary is killed
 /scheduler/verbose 1             # set the verbose level of the G4Scheduler class (time steps, reactions ...)
 /scheduler/endTime 1 microsecond # set the time at which the simulation stops
 /scheduler/whyDoYouStop          # for advanced users: print information at the end of the chemical stage 
                                  # to know why the simulation has stopped
 ```
 
 ## PLOT
  The information about all the molecular species is scored in a ASCII 
  tuple, each value corresponding to the G-value per time. This format is friendly
  with a wide variety of plotting software. 
  Experimental data of G-values for solvated electron and hydroxil radical (as a function of the time) 
  from the literature is available in data subdirectory, the references are provided
  in the header of each file. Further information is available in Phys. Med. Biol. 63(10) (2018) 105014-12pp.
 
 
   A gnuplot script (plot.gp) or python script (plot.py) files are provided to display the output data with the experimental data
 
 ## HOW TO START
 
  To run the example in batch mode
 
       ./chem5 -mac beam.in
 
   or
 
       ./chem5
 
   then the macro beam.in is processed by default
 
   In interactive mode, run:
 
       ./chem5 -gui
 
   or
 
       ./chem5 -gui gui.mac

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