110 lines
3.4 KiB
Plaintext
110 lines
3.4 KiB
Plaintext
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Geant4 - clustering
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Authors: Y. Perrot (a), H. Payno (b)
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(a) ysperrot@gmail.com
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(b) henri.payno@gmail.com
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Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
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This example is provided by the Geant4-DNA collaboration.
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These processes and models are further described at:
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http://geant4-dna.org
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Any report or published results obtained using the Geant4-DNA software shall
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cite the following Geant4-DNA collaboration publications:
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Phys. Med. 31 (2015) 861-874
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Med. Phys. 37 (2010) 4692-4708
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---> 1. Introduction
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The clustering example simulates protons tracks in liquid water using Geant4-DNA processes and models.
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Energy deposit are clustered with a dedicated clustering algorithm to assess strand breaks.
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The default parameters of the clustering algorithm have been tuned to reproduce data published by
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Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3)
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Any report or published results obtained using the Geant4-DNA software shall
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cite the following Geant4-DNA collaboration publication:
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Med. Phys. 37 (2010) 4692-4708
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----> 2. Set-up
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It is similar to the geometry set-up proposed in Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3).
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It consists in a World volume containing a Target box made of liquid water of 1µm x 1µm x 0.5 µm.
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Energy deposits in the Target are registered (see SteppingAction.cc) and the clustering algorithm is run at the end of each event
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(see EventAction.cc)
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----> 3. How to run the example
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To get help, run:
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> ./clustering -h
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In interactive mode, run:
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> ./clustering -gui
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In batch mode , run:
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> ./clustering [-mac run.in] [-mt numberofThreads]
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Two macros are available:
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run.in: shoots 1000 protons of 500 keV
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runOneEvent.in: shoots one proton of 500 keV
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All UI clustering commands in these macros are described below in section 5.
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----> 4. Simulation output
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The output results consists in a clusters_output.root file, containing for each event:
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- the number of single strand break
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- the number of complex single strand break
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- the number of double strand break
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- the cluster size distribution
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- the absorbed dose in the Target
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----> 5. More information
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Specific classes are available in this example:
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* ClusteringAlgo: contains the core clustering algorithm
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* ClusteringAlgoMessenger: defines all UI commands to tune
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the clustering algorithm
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/clustering/algo/setMinPts:
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Minimal number of points to create a cluster
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/clustering/algo/setSelectionProb:
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Probability to select potential damage according to the geometry
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/clustering/algo/setEps:
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Maximal distance between points to create a cluster
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/clustering/algo/setEmin:
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Energy to have a probability to create a strand break = 0
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/clustering/algo/setEmax:
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Energy to have a probability to create a strand break = 1
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allow
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* ClusterSBPoints: defines a cluster of strand break points
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* CommandLineParser: defines a parser for command line control
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as in other Geant4-DNA examples
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* RunInitObserver: allows initializations at new run
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(as in pdb4dna and microdosimetry)
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* SBPoint: defines a class for point of energy deposition
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----> Acknowledgments :
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Ziad Francis for discussion about clustering algorithm.
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