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0001 \page Exampleclustering Example clustering
0002
0003 \author Y. Perrot, H. Payno \n
0004 (a) ysperrot@gmail.com \n
0005 (b) henri.payno@gmail.com \n
0006 Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
0007
0008 This example is provided by the Geant4-DNA collaboration.
0009
0010 These processes and models are further described at:
0011 http://geant4-dna.org
0012
0013 Any report or published results obtained using the Geant4-DNA software shall
0014 cite the following Geant4-DNA collaboration publications: \n
0015 Phys. Med. 31 (2015) 861-874 \n
0016 Med. Phys. 37 (2010) 4692-4708
0017
0018 ## Introduction
0019
0020 The clustering example simulates protons tracks in liquid water using Geant4-DNA processes and models.
0021 Energy deposit are clustered with a dedicated clustering algorithm to assess strand breaks.
0022 The default parameters of the clustering algorithm have been tuned to reproduce data published by
0023 Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3)
0024
0025 Any report or published results obtained using the Geant4-DNA software shall
0026 cite the following Geant4-DNA collaboration publication:
0027 Med. Phys. 37 (2010) 4692-4708
0028
0029 ## Set-up
0030
0031 It is similar to the geometry set-up proposed in Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3).
0032 It consists in a World volume containing a Target box made of liquid water of 1µm x 1µm x 0.5 µm.
0033 Energy deposits in the Target are registered (see SteppingAction) and the clustering algorithm is run at the end of each event
0034 (see EventAction)
0035
0036 ## How to run the example
0037
0038 To get help, run:
0039
0040 ```
0041 > ./clustering -h
0042 ```
0043
0044 In interactive mode, run:
0045
0046 ```
0047 > ./clustering -gui
0048 ```
0049
0050 In batch mode , run:
0051
0052 ```
0053 > ./clustering [-mac run.in] [-mt numberofThreads]
0054 ```
0055
0056 Two macros are available:
0057
0058 - run.in: shoots 1000 protons of 500 keV
0059
0060 - runOneEvent.in: shoots one proton of 500 keV
0061
0062 All UI clustering commands in these macros are described below in section 'More information'.
0063
0064 ## Simulation output
0065
0066 The output results consists in a clusters_output.root file, containing for each event:
0067 - the number of single strand break
0068 - the number of complex single strand break
0069 - the number of double strand break
0070 - the cluster size distribution
0071 - the absorbed dose in the Target
0072
0073 ## More information
0074
0075 Specific classes are available in this example:
0076
0077 - ClusteringAlgo: contains the core clustering algorithm
0078
0079 - ClusteringAlgoMessenger: defines all UI commands to tune
0080 the clustering algorithm
0081
0082 ```
0083 /clustering/algo/setMinPts
0084 ```
0085 Minimal number of points to create a cluster
0086
0087 ```
0088 /clustering/algo/setSelectionProb
0089 ```
0090 Probability to select potential damage according to the geometry
0091
0092 ```
0093 /clustering/algo/setEps
0094 ```
0095 Maximal distance between points to create a cluster
0096
0097 ```
0098 /clustering/algo/setEmin
0099 ```
0100 Energy to have a probability to create a strand break = 0
0101
0102 ```
0103 /clustering/algo/setEmax
0104 ```
0105 Energy to have a probability to create a strand break = 1
0106 allow
0107
0108 - ClusterSBPoints: defines a cluster of strand break points
0109
0110 - CommandLineParser: defines a parser for command line control
0111 as in other Geant4-DNA examples
0112
0113 - RunInitObserver: allows initializations at new run
0114 (as in pdb4dna and microdosimetry)
0115
0116 - SBPoint: defines a class for point of energy deposition
0117
0118 ## Acknowledgments
0119
0120 Ziad Francis for discussion about clustering algorithm.
0121
