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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
The example shows how to activate the chemistry code and score the radiochemical yield G defined as
(Number of species X) / (100 eV of deposited energy).
in a range of deposited energy [X;Y] chosen by the user.
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 & G4EmDNAChemistry constructors. It will later be updated to use the G4EmDNAModelActivator constructor
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.
(parameters can be found in Prog. Nucl. Sci. Tec. 2 (2011))
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 all the molecular species is scored in a ROOT ntuple file Species.root. The root macro program PlotNtuple.C can be used to plot the G values vs time, for each species.
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).
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.
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 chem4.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:
./chem4 -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 1 keV # after 1 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 ROOT ntuple file Species.root during the run of chem4. The ROOT program plotG can be used to plot the G values vs time, for each species. It must be launched after chem4 has run. When "plotG" is executed, select the root file output by the chem4 application. You can also execute plotG as:
./plot/plotG Species.root
where Species.root is the file output by the chem4 application.
I have access to a track. How do I access to its molecular information?
#include "G4Molecule.hh" G4Track* thisIsMytrack = ... G4Molecule* thisIsMyMolecule = GetMolecule(thisIsMyTrack);
If the pointer thisIsMyMolecule is null, then this is NOT a chemical species
How do I get the molecule's name?
G4Molecule* thisIsMyMolecule = ... const G4String& moleculeName = thisIsMyMolecule->GetName();
How can I display the reaction information?
/scheduler/verbose 1
How can I display the step by step information?
/chem/tracking/verbose 1
1.9.8