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0001 =================================================================
0002 Geant4 - clustering
0003 =================================================================
0004
0005
0006 Authors: Y. Perrot (a), H. Payno (b)
0007
0008 (a) ysperrot@gmail.com
0009 (b) henri.payno@gmail.com
0010
0011 Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
0012
0013 This example is provided by the Geant4-DNA collaboration.
0014
0015 These processes and models are further described at:
0016 http://geant4-dna.org
0017
0018 Any report or published results obtained using the Geant4-DNA software shall
0019 cite the following Geant4-DNA collaboration publications:
0020 Phys. Med. 31 (2015) 861-874
0021 Med. Phys. 37 (2010) 4692-4708
0022
0023 ---> 1. Introduction
0024
0025 The clustering example simulates protons tracks in liquid water using Geant4-DNA processes and models.
0026 Energy deposit are clustered with a dedicated clustering algorithm to assess strand breaks.
0027 The default parameters of the clustering algorithm have been tuned to reproduce data published by
0028 Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3)
0029
0030 Any report or published results obtained using the Geant4-DNA software shall
0031 cite the following Geant4-DNA collaboration publication:
0032 Med. Phys. 37 (2010) 4692-4708
0033
0034 ----> 2. Set-up
0035
0036 It is similar to the geometry set-up proposed in Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3).
0037 It consists in a World volume containing a Target box made of liquid water of 1µm x 1µm x 0.5 µm.
0038 Energy deposits in the Target are registered (see SteppingAction.cc) and the clustering algorithm is run at the end of each event
0039 (see EventAction.cc)
0040
0041 ----> 3. How to run the example
0042
0043 To get help, run:
0044
0045 > ./clustering -h
0046
0047 In interactive mode, run:
0048
0049 > ./clustering -gui
0050
0051 In batch mode , run:
0052
0053 > ./clustering [-mac run.in] [-mt numberofThreads]
0054
0055 Two macros are available:
0056
0057 run.in: shoots 1000 protons of 500 keV
0058
0059 runOneEvent.in: shoots one proton of 500 keV
0060
0061 All UI clustering commands in these macros are described below in section 5.
0062
0063 ----> 4. Simulation output
0064
0065 The output results consists in a clusters_output.root file, containing for each event:
0066 - the number of single strand break
0067 - the number of complex single strand break
0068 - the number of double strand break
0069 - the cluster size distribution
0070 - the absorbed dose in the Target
0071
0072 ----> 5. More information
0073
0074 Specific classes are available in this example:
0075
0076 * ClusteringAlgo: contains the core clustering algorithm
0077
0078 * ClusteringAlgoMessenger: defines all UI commands to tune
0079 the clustering algorithm
0080
0081 /clustering/algo/setMinPts:
0082 Minimal number of points to create a cluster
0083
0084 /clustering/algo/setSelectionProb:
0085 Probability to select potential damage according to the geometry
0086
0087 /clustering/algo/setEps:
0088 Maximal distance between points to create a cluster
0089
0090 /clustering/algo/setEmin:
0091 Energy to have a probability to create a strand break = 0
0092
0093 /clustering/algo/setEmax:
0094 Energy to have a probability to create a strand break = 1
0095 allow
0096 * ClusterSBPoints: defines a cluster of strand break points
0097
0098 * CommandLineParser: defines a parser for command line control
0099 as in other Geant4-DNA examples
0100
0101 * RunInitObserver: allows initializations at new run
0102 (as in pdb4dna and microdosimetry)
0103
0104 * SBPoint: defines a class for point of energy deposition
0105
0106 ----> Acknowledgments :
0107
0108 Ziad Francis for discussion about clustering algorithm.
0109
