| Geant4 Cross Reference |
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>> 2 $Id: README 73136 2013-08-19 14:28:09Z sincerti $
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>> 4
1 ========================================= 5 =========================================================
2 Geant4 - microdosimetry example << 6 Geant4 - Microdosimetry example
3 ========================================= 7 =========================================================
4 8
5 README file 9 README file
6 -------------------- 10 ----------------------
7 11
8 CORRESPONDING AUTHO << 12 CORRESPONDING AUTHOR
9 <<
10 S. Incerti (a, *), H. Tran (a, *), V. Ivantche <<
11 a. LP2i, IN2P3 / CNRS / Bordeaux University, 3 <<
12 b. G4AI Ltd., UK <<
13 * e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib <<
14 13
15 ---->0. INTRODUCTION << 14 S. Incerti (a, *), V. Ivanchenko (b), M. Karamitros (a)
>> 15 a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
>> 16 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
>> 17 b. G4AI Ltd, UK
>> 18 * e-mail:incerti@cenbg.in2p3.fr
>> 19
>> 20 ---->0. INTRODUCTION.
>> 21
>> 22 The microdosimetry example simulates the track of two 5 MeV protons in liquid water.
>> 23 Geant4 standard EM models are used in the World volume while Geant4-DNA models
>> 24 are used in a Target volume, declared as a Region.
16 25
17 The microdosimetry example shows how to use Ge << 26 This example is provided by the Geant4-DNA collaboration.
18 in different regions of the geometry. <<
19 27
20 The Geant4-DNA processes and models are furthe << 28 These processes and models are further described at:
21 http://geant4-dna.org 29 http://geant4-dna.org
22 30
23 Any report or published results obtained using << 31 Any report or published results obtained using the Geant4-DNA software shall
24 cite the following Geant4-DNA collaboration pu 32 cite the following Geant4-DNA collaboration publications:
25 Med. Phys. 51 (2024) 5873–5889 <<
26 Med. Phys. 45 (2018) e722-e739 <<
27 Phys. Med. 31 (2015) 861-874 33 Phys. Med. 31 (2015) 861-874
28 Med. Phys. 37 (2010) 4692-4708 34 Med. Phys. 37 (2010) 4692-4708
29 Int. J. Model. Simul. Sci. Comput. 1 (2010) 15 <<
30 <<
31 ---->1. GEOMETRY SET-UP <<
32 35
33 The geometry is a 10-micron side cube (World) << 36 We also suggest these other references related to this example:
34 material) containing a 2 micron-thick slice (a << 37 Nucl. Instrum. and Meth. B 273 (2012) 95-97
>> 38 Prog. Nucl. Sci. Tec. 2 (2011) 898-903
35 39
36 Particles are shot from the World volume. << 40 ---->1. GEOMETRY SET-UP.
>> 41
>> 42 The geometry is a 1 mm side cube (World) made of liquid water containing a smaller cubic Target volume of liquid
>> 43 water, which dimensions are twenty times smaller than the dimensions of the World volume.
37 44
38 The variable density feature of materials is i << 45 --->2. SET-UP
39 The material can be changed directly in microd << 46
>> 47 Make sure G4LEDATA points to the low energy electromagnetic libraries.
40 48
41 ---->2. SET-UP << 49 The code can be compiled with cmake.
42 50
43 Make sure $G4LEDATA points to the low energy e << 51 It works in MT mode.
44 52
45 ---->3. HOW TO RUN THE EXAMPLE << 53 ---->3. HOW TO RUN THE EXAMPLE
46 54
47 In interactive mode, run: << 55 Normal mode, run:
48 56
49 ./microdosimetry << 57 ./microdosimetry -mt 2 -out microdosimetry
50 <<
51 In batch, the macro microdosimetry.in can be u <<
52 particle types. <<
53 <<
54 ---->4. PHYSICS <<
55 58
56 The PhysicsList uses Geant4 Physics in the Wor << 59 (or more generally
57 in the Target region. << 60 ./microdosimetry -mt 2 -out myRootFile
>> 61 )
58 62
59 1) Geant4 Physics in the World is selected via << 63 The macro microdosimetry.in is executed by default to select another one:
60 64
61 /dna/test/addPhysics X << 65 ./microdosimetry -mac myMacro.mac
62 66
63 where X is any EM physics list, such as emstan << 67 To get visualization and interactivity:
64 68
65 2) Geant4-DNA activator is used in the regionT << 69 ./microdosimetry -gui
>> 70 ( OGL used by default)
66 71
67 /process/em/AddDNARegion regionTarget DNA_OptY << 72 or you may use your own visualization driver, for instance:
>> 73 ./microdosimetry -vis "DAWNFILE"
68 74
69 where Y = 0, 2, 4, or 6. << 75 ---->4. PHYSICS
70 <<
71 3) In addition to 1) or 2), to enable radioact <<
72 <<
73 /dna/test/addPhysics raddecay <<
74 76
75 4) Warning regarding ions: when the incident p << 77 This example shows:
76 (/gun/particle ion), specified with Z and A nu << 78 - how to use the Geant4-DNA processes,
77 the Rudd ionisation extended model is used. Th << 79 - how to count and save occurrences of processes
78 by default down to 0.5 MeV/u. This tracking cu << 80 - how to combine them with Standard EM Physics.
79 81
80 /dna/test/addIonsTrackingCut false << 82 A simple electron capture process is also provided in order to kill electrons
>> 83 below a chosen energy threshold, set in the Physics list.
81 84
>> 85 Look at the PhyscisList.cc file.
82 86
83 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS << 87 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
84 88
85 The output results consists in a dna.root file << 89 The output results consists in a microdosimetry.root file, containing for each simulation step:
86 - the type of particle for the current step 90 - the type of particle for the current step
87 - the type of process for the current step 91 - the type of process for the current step
88 - the step PostStepPoint coordinates (in nm) << 92 - the track position of the current step (in nanometers)
89 - the energy deposit along the current step (i 93 - the energy deposit along the current step (in eV)
90 - the step length (in nm) 94 - the step length (in nm)
91 - the total energy loss along the current step << 95 - the total enery loss along the current step (in eV)
92 - the kinetic energy at PreStepPoint (in eV) <<
93 - the cos of the scattering angle <<
94 - the event ID <<
95 - the track ID <<
96 - the parent track ID <<
97 - the step number <<
98 96
99 This information is extracted from the Steppin << 97 This file can be easily analyzed using for example the provided ROOT macro
100 <<
101 The ROOT file can be easily analyzed using for <<
102 file plot.C; to do so : 98 file plot.C; to do so :
103 * be sure to have ROOT installed on your machi 99 * be sure to have ROOT installed on your machine
104 * be sure to be in the directory containing th << 100 * be sure to be in the microdosimetry directory
105 * copy plot.C into this directory << 101 * launch ROOT by typing root
106 * from there, launch ROOT by typing root <<
107 * under your ROOT session, type in : .X plot.C 102 * under your ROOT session, type in : .X plot.C to execute the macro file
108 * alternatively you can type directly under yo 103 * alternatively you can type directly under your session : root plot.C
109 104
110 The naming scheme on the displayed ROOT plots 105 The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
111 106
112 -particles << 107 -particles:
>> 108 e- : 1
>> 109 proton : 2
>> 110 hydrogen : 3
>> 111 alpha : 4
>> 112 alpha+ : 5
>> 113 helium : 6
>> 114
>> 115 -processes:
>> 116 msc 10
>> 117 e-_G4DNAElastic 11
>> 118 e-_G4DNAExcitation 12
>> 119 e-_G4DNAIonisation 13
>> 120 e-_G4DNAAttachment 14
>> 121 e-_G4DNAVibExcitation 15
>> 122 eCapture 16
>> 123
>> 124 proton_G4DNAExcitation 17
>> 125 proton_G4DNAIonisation 18
>> 126 proton_G4DNAChargeDecrease 19
>> 127
>> 128 hydrogen_G4DNAExcitation 20
>> 129 hydrogen_G4DNAIonisation 21
>> 130 hydrogen_G4DNAChargeIncrease 22
>> 131
>> 132 alpha_G4DNAExcitation 23
>> 133 alpha_G4DNAIonisation 24
>> 134 alpha_G4DNAChargeDecrease 25
>> 135
>> 136 alpha+_G4DNAExcitation 26
>> 137 alpha+_G4DNAIonisation 27
>> 138 alpha+_G4DNAChargeDecrease 28
>> 139 alpha+_G4DNAChargeIncrease 29
>> 140
>> 141 helium_G4DNAExcitation 30
>> 142 helium_G4DNAIonisation 31
>> 143 helium_G4DNAChargeIncrease 32
>> 144
>> 145 hIoni 33
>> 146 eIoni 34
113 147
114 gamma: 0 <<
115 e-: 1 <<
116 proton: 2 <<
117 hydrogen: 3 <<
118 alpha: 4 <<
119 alpha+: 5 <<
120 helium: 6 <<
121 <<
122 -processes <<
123 <<
124 Capture: 1 <<
125 (only if one uses G4EmmicrodosimetryActivator <<
126 <<
127 e-_G4DNAElectronSolvation: 10 <<
128 e-_G4DNAElastic: 11 <<
129 e-_G4DNAExcitation: 12 <<
130 e-_G4DNAIonisation: 13 <<
131 e-_G4DNAAttachment: 14 <<
132 e-_G4DNAVibExcitation: 15 <<
133 msc: 110 <<
134 CoulombScat: 120 <<
135 eIoni: 130 <<
136 <<
137 proton_G4DNAElastic: 21 <<
138 proton_G4DNAExcitation: 22 <<
139 proton_G4DNAIonisation: 23 <<
140 proton_G4DNAChargeDecrease: 24 <<
141 msc: 210 <<
142 CoulombScat: 220 <<
143 hIoni: 230 <<
144 nuclearStopping: 240 <<
145 <<
146 hydrogen_G4DNAElastic: 31 <<
147 hydrogen_G4DNAExcitation: 32 <<
148 hydrogen_G4DNAIonisation: 33 <<
149 hydrogen_G4DNAChargeIncrease: 35 <<
150 <<
151 alpha_G4DNAElastic: 41 <<
152 alpha_G4DNAExcitation: 42 <<
153 alpha_G4DNAIonisation: 43 <<
154 alpha_G4DNAChargeDecrease: 44 <<
155 msc: 410 <<
156 CoulombScat: 420 <<
157 ionIoni: 430 <<
158 nuclearStopping: 440 <<
159 <<
160 alpha+_G4DNAElastic: 51 <<
161 alpha+_G4DNAExcitation: 52 <<
162 alpha+_G4DNAIonisation: 53 <<
163 alpha+_G4DNAChargeDecrease: 54 <<
164 alpha+_G4DNAChargeIncrease: 55 <<
165 msc: 510 <<
166 CoulombScat: 520 <<
167 hIoni: 530 <<
168 nuclearStopping: 540 <<
169 <<
170 helium_G4DNAElastic: 61 <<
171 helium_G4DNAExcitation: 62 <<
172 helium_G4DNAIonisation: 63 <<
173 helium_G4DNAChargeIncrease: 65 <<
174 <<
175 GenericIon_G4DNAIonisation: 73 <<
176 msc: 710 <<
177 CoulombSca: 720 <<
178 ionIoni: 730 <<
179 nuclearStopping: 740 <<
180 <<
181 phot: 81 <<
182 compt: 82 <<
183 conv: 83 <<
184 Rayl: 84 <<
185 148
186 ---------------------------------------------- 149 ---------------------------------------------------------------------------
187 150
188 Should you have any enquiry, please do not hes << 151 Should you have any enquiry, please do not hesitate to contact:
189 incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr << 152 incerti@cenbg.in2p3.fr