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 \page ExampleChem6 Example chem6
 
 \author W. G. Shin (a), A. Paillet (b), S. Incerti (b)            \n
 (a) ukguen _ gmail _ com                                          \n
 (b) incerti _ lp2ib _ in2p3 _ fr                                  \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
 Med. Phys. 45 (2018) e722-e739                            \n
 Phys. Med. 31 (2015) 861-874                              \n
 Med. Phys. 37 (2010) 4692-4708                            \n
 Int. J. Model. Simul. Sci . Comput. 1 (2010) 157-178      \n
 
 ## INTRODUCTION
   Based on chem4 example, this example provides to score the radiochemical yield G
   defined as \n
 ```
 (Number of species X) / (100 eV of deposited energy).
 ```
   as a function of time and LET.
 
   The details are described in the following paper:
   J. Appl. Phys. 125 (2019) 104301
 
 ## 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 the detector can be controlled by PrimaryKiller class.
 
 ## PHYSICS LIST
 
   PhysicsList is Geant4 modular physics list using:
 
   G4EmDNAPhysics_option2 constructor by default:
   - the accelerated physics constructor based on G4EmDNAPhysics constructor.
 
   A UI command is available to change the Physics constructor, e.g.:
 
     /chem/phys/registerPhysics G4EmDNAPhysics_option4
 
   G4EmDNAChemistry_option3 constructor by default:
   - 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.
 
 
 ## 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 of this model. Only G4EmDNAChemistry_option3 can change the time step model
 
   (parameters can be found in Med. Phys. 48 (2021) 890-901
   and Med. Phys. 47 (2020) 5919-5930)
 
 ## 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
 
   This scorer computes the energy deposition and the number of species along
   time in order to extract the radiochemical yields as chem4 example.
 
   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 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 ...
 
   A UI command is available to change this file name, e.g. for newName:
 
     /chem/output/fileName newName
 
   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.
   
 ### 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. 
   
   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
 ```
 
 ### 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
 # select cut-off energy for restricted LET.
 ```
 
 ## 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 has occurred:
   - TimeStepAction::UserReactionAction(const G4Track&, const G4Track&, const std::vector<G4Track*>*)
 
 In order to access to molecular information:
 ```cpp
 #include "G4Molecule.hh"
 G4Molecule* thisIsMyMolecule = GetMolecule(thisIsMyTrack);
 const G4String& moleculeName = thisIsMyMolecule->GetName();
 ```
 
 ## 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.
 
 ## 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 FILES
 
   Two user macro files, beam.in and beam_HCP.in, 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.
 ```
 
 
 ## PLOT
 
   Two root macros, plotG_time.C and root plotG_LET.C, 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.
 ```

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