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      =========================================================
      Geant4 - an Object-Oriented Toolkit for Simulation in HEP
      =========================================================
 
                             Chem5
                             -------
 
 Jose Ramos-Mendez(a) and Bruce Faddegon
 Department of Radiation Oncology, 
 University of California San Francisco.
 
 (a) CORRESPONDING AUTHOR 
 joserm84 _ gmail _ com
 
 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:
 Phys. Med. 31 (2015) 861-874
 Med. Phys. 37 (2010) 4692-4708
 
 Any report or published results obtained using this example shall 
 cite the following publication:
 Phys. Med. Biol. 63(10) (2018) 105014-12pp
 
 The example is a variation of chem4, it shows how to activate 
 chemistry code and score the radiochemical yield G using the contructors
 G4EmDNAPhysics_option8 and G4EmDNAChemistry_option1
 
  1 - 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.
 
  2 - PHYSICS LIST
 
     PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option8 &
     G4EmDNAChemistry_option1 constructors.
 
  3 - 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.
 
  4 - AN EVENT: THE 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.
 
  5 - DETECTOR RESPONSE: Scorers
  
             5.1 - 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 a ASCII format
     
     
         5.2 - Primary killer
 
     The G-values are computing for a range of deposited energy. 
     An infinite volume is assumed as geometric 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). 
     
     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 [10.0 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. 
     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. 
 
  6 - 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.
 
  7 - 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
 
  8 - 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
 
 9 - RELEVANT MACRO COMMANDS
     /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
     /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
     
 10 - 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) file is provided to display the output data with the experimental data
     

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