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 \page ExampleChem4 Example chem4
 
 \author P. Piersimoni (a), M. Karamitros (b)       \n
 (a) pierluigi.piersimoni _ gmail _ com             \n
 (b) matkara _ 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
 
 The example shows how to activate the chemistry code and score the radiochemical yield G
 defined as \n
 ```
 (Number of species X) / (100 eV of deposited energy).
 ```
 in a range of deposited energy [X;Y] chosen by the user.\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 &
   G4EmDNAChemistry constructors.
   It will later be updated to use the G4EmDNAModelActivator constructor
 
 ## CHEMISTRY MODEL AND CHEMICAL REACTION LIST
 
   UI species are defined by format :
   username [ molecule | charge | D(m2/s) | Radius(nm) ]
   where : *username* is decided by users, *molecule* is used by Geant4,
   *D* is diffusion constant, *Radius* is reaction radius.
   Spaces between characters are needed.
 
   UI reactions are defined by format :
   ```
   /chem/reaction/add H + H -> H2  | Fix |  1.2e10 | 0
     where : *H* is username, *1.2e10* is reaction rate, *0* is reaction type.
   ```  
   Spaces between characters are needed.
 
   (parameters can be found in Prog. Nucl. Sci. Tec. 2 (2011))
 
 ## 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 all the molecular species is scored in a ROOT
   ntuple file Species.root. The root macro program PlotNtuple.C can be used to
   plot the G values vs time, for each species.
   
 ### Primary Killer
   The G-values are computing for a range of deposited energy. 
   We are in an infinite volume. Therefore the energy lost by the 
   primary equals the deposited energy since all secondary particles 
   will finally slow down to the thermal energy. 
   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 1 keV 
 # after 1 keV of energy loss by the primary particle, the primary is killed
 
 /primaryKiller/eLossMax 2 keV 
 # if the primary particle losses more than 2 keV, the event is aborted
 ```
 
   The G-values are then computed for a deposited energy in the range [1 keV;2 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 chem4.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:
 ```
 ./chem4 -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 1 keV    # after 1 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 ROOT
   ntuple file Species.root during the run of chem4.
   The ROOT program plotG can be used to plot the G values vs time, 
   for each species. It must be launched after 
   chem4 has run. When "plotG" is executed, select the root file output by the 
   chem4 application.
   You can also execute plotG as: 
 ```
 ./plot/plotG Species.root 
 ```
   where Species.root is the file output by the chem4 application.
   
 ## OTHER INFORMATION
   I have access to a track. How do I access to its molecular information?
 ```cpp
 #include "G4Molecule.hh"
 G4Track* thisIsMytrack = ...
 G4Molecule* thisIsMyMolecule = GetMolecule(thisIsMyTrack);
 ```
  If the pointer thisIsMyMolecule is null, then this is NOT a chemical species 
 
   How do I get the molecule's name?
 ```cpp
 G4Molecule* thisIsMyMolecule = ...
 const G4String& moleculeName = thisIsMyMolecule->GetName();
 ```
 
 How can I display the reaction information?
  - Use this macro command: 
 ```
 /scheduler/verbose 1
 ```
 
 How can I display the step by step information?
  1. Add ITTrackingInteraction to the G4Scheduler singleton (cf. chem3)
  2. Use  
 ```
 /chem/tracking/verbose 1
 ```
 
 ## HOW TO START
 
  To run the example in batch mode
 
       ./chem4 -mac beam.in
 
   or
 
       ./chem4
 
   then the macro beam.in is processed by default
 
   In interactive mode, run:
 
       ./chem4 -gui
 
   or
 
       ./chem4 -gui gui.mac

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