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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
Phys. Med. Biol. 63(10) (2018) 105014-12pp
The example is a variation of the chem4 example, it shows how to activate the chemistry code and score the radiochemical yield G using the constructors G4EmDNAPhysics_option8 and G4EmDNAChemistry_option1
The world volume is a simple box which represents a 'pseudo infinite' homogeneous medium.
Two parameters define the geometry :
The default geometry is constructed in DetectorConstruction class.
PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option8 & G4EmDNAChemistry_option1 constructors.
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.
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.
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 ASCII format.
The G-values are computing for a range of deposited energy. An infinite volume is assumed as the geometrical 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 1 keV of energy loss by the primary particle, the primary is killed /primaryKiller/eLossMax 10.1 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 [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 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.
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.
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
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
/primaryKiller/eLoss 10 keV # after 10 keV of energy loss by the primary particle, the primary is killed
/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 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
1.9.8