| Geant4 Cross Reference |
1 =========================================
2 Geant4 - dnadamage1 example
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4
5 README file
6 --------------------
7
8
9 This is a new example and it may contain bugs.
10 It was developed by Hoang Tran.
11 Damage analysis was developed by Le Tuan Anh.
12 If you find a bug, please contact IRSN:
13 yann.perrot@irsn.fr or carmen.villagrasa@irsn
14
15 ---->0. INTRODUCTION.
16
17 The dnadamage1 example shows a simple way to s
18 using the Geant4-DNA physics and chemical proc
19 Moreover, a clustering algorithm is introduced
20
21 This example is based on the work described in
22 and is provided by the Geant4-DNA collaboratio
23
24 Any report or published results obtained using
25 cite the following Geant4-DNA collaboration pu
26 Phys. Med. 31 (2015) 861-874
27 Med. Phys. 37 (2010) 4692-4708
28
29 ---->1. GEOMETRY SET-UP.
30
31 The geometry is chromatical fiber in a 40-nm s
32 material). Particles are randomly shot in a ci
33
34 The DNA chromatical fiber geometry is generate
35 For detail, please see: Sc. Rep. 7 (2017) 1192
36
37 ---->2. SET-UP
38
39 The code can be compiled with cmake.
40 It works in MT mode.
41 Chemistry stage is automatically activated.
42
43 ---->3. HOW TO RUN THE EXAMPLE
44
45 In interactive mode, run:
46
47 ./dnadamage1
48 (Note: interactive mode needs at least 6Go of
49
50 In batch, the macro dnadamage1.in can be used
51 particle types and energies.
52
53 ./dnadamage1 dnadamage1.in
54
55 ---->4. PHYSICS
56
57 This example shows:
58 - how to use the Geant4-DNA processes (physics
59 (look at the PhysicsList.cc file)
60 - how to count and save energy depositions giv
61 of 17.5 eV in teh nucleotide backbone region.
62 (look at the SteppingAction.cc file)
63 -how to forbid water radicals to be created at
64 )
65
66 ---->5. CHEMISTRY
67
68 This example shows:
69 - how to add a parallel world for chemistry
70 - how to add a new reaction of free radicals w
71 (look at the G4EmDNAChemistry_option2)
72 - how to count and save occurrences of chemica
73 (look at to TimeStepAction.cc file)
74
75
76 ---->6. SIMULATION OUTPUT AND RESULT ANALYSIS
77
78 This file can be easily analyzed using the pro
79 file analysis.C (and scandamges.C, molecule.C)
80 "A new standard DNA damage (SDD) data format"
81 to do so :
82 * be sure to have ROOT installed on your machi
83 * be sure to be in the directory containing th
84 * copy analysis.C (and scandamges.C, molecule.
85 * from there, launch ROOT by typing root
86 * under your ROOT session, type in : .X analys
87 * alternatively you can type directly under yo
88
89
90 Results will be obtained:
91 * Count numbers of direct and indirect SB (str
92 * Count numbers of SSB, DSB (simple, complex)
93 * In function scandamges(), users change:
94 * Break-energy to select direct damages
95 * probability to select indirect damages
96 * minium distance between two clusters (
97 to see how they affect direct/indirect SB, SSB
98 * Damages in SDD format
99 ----------------------------------------------
100
101 Contact: ngoc-hoang.tran@irsn.fr, carmen.villa
102