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1 =================================================================
2 Geant4 - clustering
3 =================================================================
4
5
6 Authors: Y. Perrot (a), H. Payno (b)
7
8 (a) ysperrot@gmail.com
9 (b) henri.payno@gmail.com
10
11 Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
12
13 This example is provided by the Geant4-DNA collaboration.
14
15 These processes and models are further described at:
16 http://geant4-dna.org
17
18 Any report or published results obtained using the Geant4-DNA software shall
19 cite the following Geant4-DNA collaboration publications:
20 Phys. Med. 31 (2015) 861-874
21 Med. Phys. 37 (2010) 4692-4708
22
23 ---> 1. Introduction
24
25 The clustering example simulates protons tracks in liquid water using Geant4-DNA processes and models.
26 Energy deposit are clustered with a dedicated clustering algorithm to assess strand breaks.
27 The default parameters of the clustering algorithm have been tuned to reproduce data published by
28 Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3)
29
30 Any report or published results obtained using the Geant4-DNA software shall
31 cite the following Geant4-DNA collaboration publication:
32 Med. Phys. 37 (2010) 4692-4708
33
34 ----> 2. Set-up
35
36 It is similar to the geometry set-up proposed in Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3).
37 It consists in a World volume containing a Target box made of liquid water of 1µm x 1µm x 0.5 µm.
38 Energy deposits in the Target are registered (see SteppingAction.cc) and the clustering algorithm is run at the end of each event
39 (see EventAction.cc)
40
41 ----> 3. How to run the example
42
43 To get help, run:
44
45 > ./clustering -h
46
47 In interactive mode, run:
48
49 > ./clustering -gui
50
51 In batch mode , run:
52
53 > ./clustering [-mac run.in] [-mt numberofThreads]
54
55 Two macros are available:
56
57 run.in: shoots 1000 protons of 500 keV
58
59 runOneEvent.in: shoots one proton of 500 keV
60
61 All UI clustering commands in these macros are described below in section 5.
62
63 ----> 4. Simulation output
64
65 The output results consists in a clusters_output.root file, containing for each event:
66 - the number of single strand break
67 - the number of complex single strand break
68 - the number of double strand break
69 - the cluster size distribution
70 - the absorbed dose in the Target
71
72 ----> 5. More information
73
74 Specific classes are available in this example:
75
76 * ClusteringAlgo: contains the core clustering algorithm
77
78 * ClusteringAlgoMessenger: defines all UI commands to tune
79 the clustering algorithm
80
81 /clustering/algo/setMinPts:
82 Minimal number of points to create a cluster
83
84 /clustering/algo/setSelectionProb:
85 Probability to select potential damage according to the geometry
86
87 /clustering/algo/setEps:
88 Maximal distance between points to create a cluster
89
90 /clustering/algo/setEmin:
91 Energy to have a probability to create a strand break = 0
92
93 /clustering/algo/setEmax:
94 Energy to have a probability to create a strand break = 1
95 allow
96 * ClusterSBPoints: defines a cluster of strand break points
97
98 * CommandLineParser: defines a parser for command line control
99 as in other Geant4-DNA examples
100
101 * RunInitObserver: allows initializations at new run
102 (as in pdb4dna and microdosimetry)
103
104 * SBPoint: defines a class for point of energy deposition
105
106 ----> Acknowledgments :
107
108 Ziad Francis for discussion about clustering algorithm.
109
