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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:
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
This example shows how to activate the scavenging process in chemistry using the deterministic treatment of the IRT model (see chem6 example). It allows to define chemical reactions and the concentration of scavengers by means of a user text file (see section 10). The concentration of scavengers is assumed to be constant over time.
To run the example:
mkdir scavenger-build cd scavenger-build cmake ../pathToExamples/scavenger make
In interactive mode, run:
./scavenger
(Note: the interactive mode only allows the visualisation of the physical stage and does not work for the chemical stage)
In batch mode, the macro beam.in can be used as follows:
./scavenger beam.in
or
./scavenger beam.in 123
123 is the user's seed number
The world volume is a simple water 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_option2 and EmDNAChemistry constructors (the chemistry constructor uses the independent reaction time method).
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.
To not register a molecule, add this command: G4MoleculeCounter::Instance()->DontRegister(G4O2::Definition());
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 G4GeneralParticleSource 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 information event per event from the hits collections, and accumulates statistic for RunAction::EndOfRunAction().
In multi-threading mode the accumulated statistics per workers 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, the name of which can be given by the user through the macro command: /scoreSpecies/setRootFileName scorer.root. The ROOT program plotG.C can be used to plot the G values vs time for each species.
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 10 keV
# after 10 keV of energy loss by the primary particle, the primary is killed
/primaryKiller/eLossMax 10.1 keV
# if the primary particle loses more than 10.1 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. 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
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 scavenger.cc. The initialization of the drawing is done via a set of /vis/ commands in the macro vis.mac. To activate the visualization mode, run:
./scavenger
Physics initialization and the defined reaction table are printed. G4Scheduler processes the chemical stage after the physical stage has been completed.
/primaryKiller/eLossMin 10 keV
# after 10 keV of energy loss by the primary particle, the primary is killed
/primaryKiller/eLossMax 10.1 keV
# if the primary particle loses more than 10.1 keV, the event is aborted
/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 user macro file is beam.in (electron simulations with primary killer method).
This file is used to define chemical reactions and the concentration of scavengers for the EmDNAChemistry constructor.
Definition of scavengers:
scavenger: NAME CONCENTRATION # concentration in [mole/l]
Definition of chemical reactions:
REACTANTS -> PRODUCTS , RATE TYPE # reaction rate in [1/s/(mole/l)], for first order reaction in [1/s] # reaction type based on Frongillo et al., Rad. Phys. Chem., 1998
In any reaction, the molecules surrounded by square brackets [] are scavengers. In the products of a reaction, the user can also use [] to prevent a molecule from being produced.
In this example, we provide 2 reaction tables for 2 different scavengers: one with O2 and another with NO2-/NO3-. We encourage the user to add chemical reactions and/or scavengers. However, the parser does not allow the addition of molecules not defined in the model. This aspect will be improved in future releases. In the meantime, please refer to the NO2- or NO3- ions defined in EmDNAChemistry::ConstructMolecule() to add new molecules.
The information about all the molecular species is scored in a ROOT (https://root.cern) ntuple file scorer.root. The ROOT program plotG can be used to plot the G values vs time for each species.
Execute plotG as:
root plotG.C
or print G values to scorer.txt
root plotG.C > scorer.txt
The results show the molecular species (G values) as a function of time (ns). Please ignore the O_2^0 molecule. The function (plotG()) should have the same name as the file without file extension (plotG).
In physics: How can I display the tracking information?
/tracking/verbose 1
In chemistry: How can I display the reaction information?
/scheduler/verbose 1
How can I display the step by step information?
/scheduler/verbose 3
1.9.8