EIC code displayed by LXR master/​geant4/​examples/​extended/​medical/​dna/​chem6/​README	Source navigation Diff markup Identifier search General search
	Version: master test Revert   Change

Warning, /geant4/examples/extended/medical/dna/chem6/README is written in an unsupported language. File is not indexed.

 $Id: $
 -------------------------------------------------------------------
 
      =========================================================
      Geant4 - an Object-Oriented Toolkit for Simulation in HEP
      =========================================================
 
                             Chem6
                             -------
 
 CORRESPONDING AUTHORS
 W. G. Shin (a), S. Incerti (b)
 (a) ukguen _ gmail _ com
 (b) incerti _ cenbg _ in2p3 _ fr
 
 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:
 
 
 J. Appl. Phys. 125 (2019) 104301
 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
     Based on chem4 and chem5 examples, this example provides scoring of the 
     radiochemical yield G defined as
         (Number of species X) / (100 eV of deposited energy).
     as a function of time and LET.
     The example uses the IRT approach by default.
 
     The details are described in the following paper:
     J. Appl. Phys. 125 (2019) 104301
 
  1 - GEOMETRY DEFINITION
 
     The world volume is a simple water box which represents a 'pseudo infinite'
     homogeneous medium.
 
     The default geometry is constructed in DetectorConstruction class.
 
     The size of detector can be controlled by PrimaryKiller class (see section 5.2).
 
  2 - PHYSICS LIST
 
     PhysicsList is Geant4 modular physics list using:
 
     G4EmDNAPhysics_option2 constructor
     - the accelerated physics constructor based on G4EmDNAPhysics constructor.
 
     G4EmDNAChemistry_option3 constructor.
     - the chemistry constructor is based on the pre-chemical stage of PARTRAC
     and chemical parameters of RITRACKS.
     - this chemistry constructor uses independent reaction time method as a
     default.
 
  3 - 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.
 
     ## UI time step model is defined only for: Step-by-Step (SBS),
     independent reaction time (IRT) or synchronized IRT (IRT_syn).
     *Note* : SBS is supposed for totally diffusion-controlled (TDC) reaction
     only then please set reaction type 0 if use this model.
     Only G4EmDNAChemistry_option3 can change time step model
 
     (parameters can be found in Med. Phys. 48 (2021) 890-901
     and Med. Phys. 47 (2020) 5919-5930)
 
  4 - 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.
 
  5 - 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.
 
  6 - DETECTOR RESPONSE: Scorers
 
         6.1 - Species scorer
 
     This scorer computes the energy deposition and the number of species along
     time in order to extract the radiochemical yields as in chem4 example.
 
     Run::RecordEvent(), called at end of event, collects informations
     event per event from the hits collections, and accumulates statistics for
     RunAction::EndOfRunAction().
 
     In multi-threading mode the statistics accumulated per worker 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 Species(runID).root.
     e.g.) Species0.root Species1.root ...
 
     G values at the last time bin are scored in a text file Species.txt in order to
     obtain G versus LET results.
     The G versus LET results are accumulated all along, thus, user should remove Species.txt
     file directly in order to initialize the results.
 
         6.2 - 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 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. 
     This set of commands 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
     # kills the particles (primary and secondary) outside of the virtual volume
 
         6.3. - LET scorer
 
     In order to obtain G versus LET results, LET values are simultaneously calculated 
     during the simulation in ScorerLET class.
 
     A macro command can be used to control the LET scorer:
 
     /scorer/LET/cutoff
     # selects cut-off energy for restricted LET.
 
  7 - TIMESTEP ACTION
 
     The user defined time steps can be given by G4UserTimeStepAction::AddTimeStep() method.
     This method is not recommended for IRT method.
 
     These two method are called before and after every time steps:
 
     TimeStepAction::UserPreTimeStepAction()
     TimeStepAction::UserPostTimeStepAction()
 
     This method is called when a chemical reaction is occurred:
 
     TimeStepAction::UserReactionAction(const G4Track&, const G4Track&, const std::vector<G4Track*>*)
      In order to access to molecular information,
      #include "G4Molecule.hh"
      G4Molecule* thisIsMyMolecule = GetMolecule(thisIsMyTrack);
      const G4String& moleculeName = thisIsMyMolecule->GetName();
 
  8 - 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.
 
  9 - 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
 
  10 - RELEVANT MACRO FILES
 
     Two user macro files can be used:
 
     ./chem6 beam.in
     # electron simulations w primary killer method.
 
     ./chem6 beam_HCP.in
     # protons and alphas are generated at the edge of a 5x5x5 um3 water phantom.
 
 11 - PLOT
 
     Two root macros can be used:
 
     root plotG_time.C
     # plot G values as a function of time according to the molecular species by importing Species0.root.
     # The function (plotG_time()) should have the same name as the file without file extension (plotG_time).
 
     root plotG_LET.C
     # plot G values as a function of LET according to the molecular species by importing Species.txt.

This page was automatically generated by the 2.3.7 LXR engine. The LXR team