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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
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Chem5
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Jose Ramos-Mendez(a) and Bruce Faddegon
Department of Radiation Oncology,
University of California San Francisco.
(a) CORRESPONDING AUTHOR
joserm84 _ gmail _ com
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:
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708
Any report or published results obtained using this example shall
cite the following publication:
Phys. Med. Biol. 63(10) (2018) 105014-12pp
The example is a variation of chem4, it shows how to activate
chemistry code and score the radiochemical yield G using the contructors
G4EmDNAPhysics_option8 and G4EmDNAChemistry_option1
1 - GEOMETRY DEFINITION
The world volume is a simple box which represents a 'pseudo infinite'
homogeneous medium.
Two parameters define the geometry :
- the material of the box -- for Geant4-DNA it has to be water.
- the full size of the box.
The default geometry is constructed in DetectorConstruction class.
2 - PHYSICS LIST
PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option8 &
G4EmDNAChemistry_option1 constructors.
3 - 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.
4 - 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.
5 - DETECTOR RESPONSE: Scorers
5.1 - Species scorer
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 a ASCII format
5.2 - Primary killer
The G-values are computing for a range of deposited energy.
An infinite volume is assumed as geometric 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 10 keV of energy loss by the primary particle, the primary is killed
/primaryKiller/eLossMax 10.1 keV
# if the primary particle losses more than 10.1 keV, the event is aborted
The G-values are then computed for a deposited energy in the range [10.0 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.
6 - 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.
7 - VISUALISATION
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
8 - 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
9 - RELEVANT MACRO COMMANDS
/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 losses 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
10 - PLOT
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
