geant4

\author Y. Perrot, H. Payno \n (a) ysperrot@gmail.com \n (b) henri.payno@gmail.com \n Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France

This example is provided by the Geant4-DNA collaboration.

These processes and models are further described at: http://geant4-dna.org

Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publications: \n Phys. Med. 31 (2015) 861-874 \n Med. Phys. 37 (2010) 4692-4708

Introduction

The clustering example simulates protons tracks in liquid water using Geant4-DNA processes and models. Energy deposit are clustered with a dedicated clustering algorithm to assess strand breaks. The default parameters of the clustering algorithm have been tuned to reproduce data published by Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3)

Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publication: Med. Phys. 37 (2010) 4692-4708

Set-up

It is similar to the geometry set-up proposed in Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3). It consists in a World volume containing a Target box made of liquid water of 1µm x 1µm x 0.5 µm. Energy deposits in the Target are registered (see SteppingAction) and the clustering algorithm is run at the end of each event (see EventAction)

How to run the example

To get help, run:

> ./clustering -h

In interactive mode, run:

> ./clustering -gui

In batch mode , run:

> ./clustering [-mac run.in] [-mt numberofThreads]

Two macros are available:

run.in: shoots 1000 protons of 500 keV
runOneEvent.in: shoots one proton of 500 keV

All UI clustering commands in these macros are described below in section 'More information'.

Simulation output

The output results consists in a clusters_output.root file, containing for each event:

the number of single strand break
the number of complex single strand break
the number of double strand break
the cluster size distribution
the absorbed dose in the Target

More information

Specific classes are available in this example:

ClusteringAlgo: contains the core clustering algorithm
ClusteringAlgoMessenger: defines all UI commands to tune the clustering algorithm

/clustering/algo/setMinPts

Minimal number of points to create a cluster

/clustering/algo/setSelectionProb

Probability to select potential damage according to the geometry

/clustering/algo/setEps

Maximal distance between points to create a cluster

/clustering/algo/setEmin

Energy to have a probability to create a strand break = 0

/clustering/algo/setEmax

Energy to have a probability to create a strand break = 1 allow

ClusterSBPoints: defines a cluster of strand break points
CommandLineParser: defines a parser for command line control as in other Geant4-DNA examples
RunInitObserver: allows initializations at new run (as in pdb4dna and microdosimetry)
SBPoint: defines a class for point of energy deposition

Acknowledgments

Ziad Francis for discussion about clustering algorithm.