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      =========================================================
      Geant4 - an Object-Oriented Toolkit for Simulation in HEP
      =========================================================
 
                             scavenger
                             ---------
 
 CORRESPONDING AUTHORS
 F. Chappuis (a), L. Desorgher (b), H. Tran (c)
 (a) flore.chappuis@chuv.ch
 (b) laurent.desorgher@chuv.ch
 (c) tran@cenbg.in2p3.fr
 
 (a,b) Institute of Radiation Physics (IRA), Lausanne University Hospital 
       and University of Lausanne, CH-1007 Lausanne, Switzerland
 (c) CNRS, CENBG, UMR 5797, Université de Bordeaux, F-33170 Gradignan, France
 
 Funding: FNS Synergia grant MAGIC-FNS CRSII5_186369.
 
 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:
 Med. Phys. 45 (2018) e722-e739
 Phys. Med. 31 (2015) 861-874
 Med. Phys. 37 (2010) 4692-4708
 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
 
  0 - INTRODUCTION
  
     This example shows how to activate the scavenging process in chemistry
     using the deterministic treatment of the IRT model (see chem6 example).
     It allows to define chemical reactions and the concentration of
     scavengers by means of a user text file (see section 10). The
     concentration of scavengers is assumed to be constant over time.
     
     To run the example:
       mkdir scavenger-build
       cd scavenger-build
       cmake ../pathToExamples/scavenger
       make
 
       In interactive mode, run:
         ./scavenger
         (Note: the interactive mode only allows the visualisation of the
         physical stage and does not work for the chemical stage)
       
       In batch mode, the macro beam.in can be used as follows:
         ./scavenger beam.in
         or
         ./scavenger beam.in 123
         # 123 is the user's seed number
 
  1 - GEOMETRY DEFINITION
 
     The world volume is a simple water box which represents a 'pseudo infinite'
     homogeneous medium.
 
     Two parameters define the geometry :
     - the material of the box for the physical stage is water.
     - for the chemistry stage, the concentration of scavengers in [mole/l]
       is added. This concentration is supposed to have no effect on the 
       physical stage.
 
     The default geometry is constructed in DetectorConstruction class.
 
  2 - PHYSICS LIST
 
     PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option2
     and EmDNAChemistry constructors (the chemistry constructor uses the
     independent reaction time method).
 
  3 - ACTION INITIALIZATION
 
     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.
 
     To not register a molecule, add this command:
     G4MoleculeCounter::Instance()->DontRegister(G4O2::Definition());
 
  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 G4GeneralParticleSource 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 information
     event per event from the hits collections, and accumulates statistic
     for RunAction::EndOfRunAction().
 
     In multi-threading mode the accumulated statistics per workers is 
     merged to the master in Run::Merge().
     
     These two macro commands can be used to control the scoring time:
       /scorer/species/addTimeToRecord 1 ps
       # user can select time bin to score G values.
       /scorer/species/nOfTimeBins
       # or user can automatically select time bin logarithmically.
     
     The information about all the molecular species is scored in a ROOT
     ntuple file, the name of which can be given by the user through the
     macro command: /scoreSpecies/setRootFileName scorer.root.
     The ROOT program plotG.C can be used to plot the G values vs time
     for each species.
     
         5.2 - Primary killer
 
     The G values are computed 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 loses more energy 
     in few interaction steps than the maximum allowed threshold, 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 loses 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. 
     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.
 
     The size of detector can be controlled by this class using user
     macro command:
       /primaryKiller/setSize 5 5 5 um
       # kill the particles (primary and secondary) outside of the virtual volume
 
  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 - VISUALIZATION
 
     The visualization manager is set via the G4VisExecutive class in the
     main() function in scavenger.cc.
     The initialization of the drawing is done via a set of /vis/ commands
     in the macro vis.mac. To activate the visualization mode, run: 
     ./scavenger
 
  8 - OUTPUT
 
     Physics initialization and the defined reaction table are printed.
     G4Scheduler processes the chemical stage after the physical stage
     has been completed
 
  9 - RELEVANT MACRO COMMANDS AND MACRO FILE
     
     /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 loses 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
 
     The user macro file is: beam.in
     (electron simulations with primary killer method)
     
  10 - REACTION PARSER FILE
  
     This file is used to define chemical reactions and the concentration 
     of scavengers for the EmDNAChemistry constructor. 
     
     Definition of scavengers:
       scavenger: NAME  CONCENTRATION
       # concentration in [mole/l]
       
     Definition of chemical reactions:
       REACTANTS -> PRODUCTS , RATE   TYPE
       # reaction rate in [1/s/(mole/l)], for first order reaction in [1/s]
       # reaction type based on Frongillo et al., Rad. Phys. Chem., 1998
       
     In any reaction, the molecules surrounded by square brackets [] are
     scavengers. In the products of a reaction, the user can also use [] 
     to prevent a molecule from being produced.
     
     In this example, we provide 2 reaction tables for 2 different scavengers:
     one with O2 and another with NO2-/NO3-. We encourage the user to add 
     chemical reactions and/or scavengers. However, the parser does not allow
     the addition of molecules not defined in the model. This aspect will be
     improved in future releases. In the meantime, please refer to the NO2- 
     or NO3- ions defined in EmDNAChemistry::ConstructMolecule() to add new
     molecules.
     
  11 - PLOT
 
     The information about all the molecular species is scored in a ROOT
     (https://root.cern) ntuple file scorer.root. The ROOT program plotG
     can be used to plot the G values vs time for each species.
     Execute plotG as: 
       root plotG.C
     or print G values to scorer.txt
       root plotG.C > scorer.txt
 
 
     The results show the molecular species (G values) as a function of
     time (ns). Please ignore the O_2^0 molecule.
     The function (plotG()) should have the same name as the
     file without file extension (plotG).
     
  12 - OTHER
     
     In physics:
       How can I display the tracking information?
         /tracking/verbose 1
     
     In chemistry:
       How can I display the reaction information?
         /scheduler/verbose 1
       How can I display the step by step information?
         /scheduler/verbose 3

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