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Geant4/examples/extended/medical/dna/chem3/README

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  1 -------------------------------------------------------------------
  2 
  3      =========================================================
  4      Geant4 - an Object-Oriented Toolkit for Simulation in HEP
  5      =========================================================
  6 
  7                              Chem3
  8                             -------
  9 
 10 This example is provided by the Geant4-DNA collaboration.
 11 
 12 These processes and models are further described at:
 13 http://geant4-dna.org
 14 
 15 Any report or published results obtained using the Geant4-DNA software shall 
 16 cite the following Geant4-DNA collaboration publications:
 17 Phys. Med. 31 (2015) 861-874
 18 Med. Phys. 37 (2010) 4692-4708
 19 
 20 How to implement user actions in the chemistry module.
 21 
 22  1 - GEOMETRY DEFINITION
 23 
 24   It is a simple box which represents a 'semi infinite' homogeneous medium.
 25 
 26   Two parameters define the geometry :
 27    - the material of the box -- for Geant4-DNA it has to be water.
 28    - the full size of the box.
 29 
 30   The default geometry is constructed in DetectorConstruction class, but all of 
 31   the above parameters can be changed interactively via the commands defined in 
 32   the DetectorMessenger class.
 33   
 34  2 - PHYSICS LIST
 35   
 36   The physics list is initialized in G4EmDNAChemistry, together with chemical
 37   stage models configuration.
 38    
 39  3 - AN EVENT: THE PRIMARY GENERATOR
 40  
 41   The primary kinematic consists of a single particle starting at the center of 
 42   the sphere. The type of the particle and its energy are set in the 
 43   PrimaryGeneratorAction class, and can be changed via the G4 build-in commands 
 44   of G4ParticleGun class.
 45   The chemistry module is triggered in the StackingAction class when all 
 46   physical tracks have been processed.
 47 
 48  4 - HOW TO START ?
 49 
 50   Run the example from build directory.
 51 
 52   To run the example in batch mode:
 53     ./chem3 -mac beam.in
 54   or
 55     ./chem3
 56   then the macro beam.in is processed by default
 57 
 58   In interactive mode, run:
 59     ./chem3 -gui
 60   or
 61     ./chem3 -gui gui.mac
 62 
 63   The user interface will be launched. Continue using /run/beamOn 1 command.
 64   By default, the vis.mac visualization macro is called.
 65   The vis_vm,.mac macro is used only in the context of the G4DNA tutorial
 66   hands-ons.
 67 
 68  5 - OUTPUT
 69 
 70   Physics initialization and the defined reaction table are printed.
 71   G4ITStepManager processes the chemical stage time step after time step.
 72   Chemical reactions are printed.
 73   In the GUI window a cummulative trajectory of the chemical species is drawn.
 74 
 75   The functions in TimeStepAction show how to get species
 76   ID, positions at each time step or in a chemical reaction
 77 
 78  6 - TIME EVOLUTION VISUALIZATION
 79 
 80   User can start a visualization of the chemical track evolution in time and space
 81   using /control/execute movie.mac. (The movie.mac macro then executes
 82   the movie_prep.mac, movie_chemistry.mac and movie_physics.mac macros.)
 83   Note, that in default setup the simulation requires machine with 6 GB of RAM.
 84   To lower memory requirements, either decrease energy of the incident electron
 85   in prep.mac or/and shorten the simulation using SetEndTime setting in 
 86   src/ActionInitialization.cc.