Author: W. G. Shin (a), S. Incerti (b)
(a) ukguen _ gmail _ com
(b) incerti _ cenbg _ in2p3 _ fr
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

INTRODUCTION

Based on chem4 example, this example provides to score the radiochemical yield G defined as

(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 detector can be controlled by PrimaryKiller class (see section ACTION INITALIZATION) in order to prevent crash.

PHYSICS LIST

PhysicsList is Geant4 modular physics list using:

G4EmDNAPhysics_option2 constructor:

the accelerated physics constructor based on G4EmDNAPhysics constructor.

G4EmDNAChemistry_option3 constructor:

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 this model. Only G4EmDNAChemistry_option3 can change 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 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 Species(runID).root. e.g.) Species0.root Species1.root ...

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).
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 is occurred:

TimeStepAction::UserReactionAction(const G4Track&, const G4Track&, const std::vector<G4Track*>*)

In order to access to molecular information:

#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 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 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.