| Geant4 Cross Reference |
>> 1 -------------------------------------------------------------------
>> 2 -------------------------------------------------------------------
>> 3
1 ========================================= 4 =========================================================
2 Geant4 - microdosimetry example << 5 Geant4 - Microdosimetry example
3 ========================================= 6 =========================================================
4 7
5 README file 8 README file
6 -------------------- 9 ----------------------
7 10
8 CORRESPONDING AUTHO << 11 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 12
15 ---->0. INTRODUCTION << 13 S. Incerti (a, *), V. Ivantchenko (b), M. Karamitros (a)
>> 14 a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
>> 15 (CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
>> 16 b. G4AI Ltd, UK
>> 17 * e-mail:incerti@cenbg.in2p3.fr
>> 18
>> 19 ---->0. INTRODUCTION.
>> 20
>> 21 The microdosimetry example simulates the track of two 5 MeV protons in liquid water.
>> 22 Geant4 standard EM models are used in the World volume while Geant4-DNA models
>> 23 are used in a Target volume, declared as a Region.
16 24
17 The microdosimetry example shows how to use Ge << 25 This example is provided by the Geant4-DNA collaboration.
18 in different regions of the geometry. <<
19 26
20 The Geant4-DNA processes and models are furthe << 27 These processes and models are further described at:
21 http://geant4-dna.org 28 http://geant4-dna.org
22 29
23 Any report or published results obtained using << 30 Any report or published results obtained using the Geant4-DNA software shall
24 cite the following Geant4-DNA collaboration pu 31 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 32 Phys. Med. 31 (2015) 861-874
28 Med. Phys. 37 (2010) 4692-4708 33 Med. Phys. 37 (2010) 4692-4708
29 Int. J. Model. Simul. Sci. Comput. 1 (2010) 15 <<
30 <<
31 ---->1. GEOMETRY SET-UP <<
32 34
33 The geometry is a 10-micron side cube (World) << 35 We also suggest these other references related to this example:
34 material) containing a 2 micron-thick slice (a << 36 Nucl. Instrum. and Meth. B 273 (2012) 95-97
>> 37 Prog. Nucl. Sci. Tec. 2 (2011) 898-903
35 38
36 Particles are shot from the World volume. << 39 ---->1. GEOMETRY SET-UP.
>> 40
>> 41 The geometry is a 1 mm side cube (World) made of liquid water containing a smaller cubic Target volume of liquid
>> 42 water, which dimensions are twenty times smaller than the dimensions of the World volume.
37 43
38 The variable density feature of materials is i << 44 --->2. SET-UP
39 The material can be changed directly in microd << 45
>> 46 Make sure G4LEDATA points to the low energy electromagnetic libraries.
40 47
41 ---->2. SET-UP << 48 The code can be compiled with cmake.
42 49
43 Make sure $G4LEDATA points to the low energy e << 50 It works in MT mode.
44 51
45 ---->3. HOW TO RUN THE EXAMPLE << 52 ---->3. HOW TO RUN THE EXAMPLE
46 53
47 In interactive mode, run: << 54 Normal mode, run:
48 55
49 ./microdosimetry << 56 ./microdosimetry -mt 2 -out microdosimetry
50 <<
51 In batch, the macro microdosimetry.in can be u <<
52 particle types. <<
53 <<
54 ---->4. PHYSICS <<
55 57
56 The PhysicsList uses Geant4 Physics in the Wor << 58 (or more generally
57 in the Target region. << 59 ./microdosimetry -mt 2 -out myRootFile
>> 60 )
58 61
59 1) Geant4 Physics in the World is selected via << 62 The macro microdosimetry.in is executed by default; to select another one:
60 63
61 /dna/test/addPhysics X << 64 ./microdosimetry -mac myMacro.mac
62 65
63 where X is any EM physics list, such as emstan << 66 To get visualization and interactivity:
64 67
65 2) Geant4-DNA activator is used in the regionT << 68 ./microdosimetry -gui
>> 69 ( OGL used by default)
66 70
67 /process/em/AddDNARegion regionTarget DNA_OptY << 71 or you may use your own visualization driver, for instance:
>> 72 ./microdosimetry -vis "DAWNFILE"
68 73
69 where Y = 0, 2, 4, or 6. << 74 ---->4. PHYSICS
70 <<
71 3) In addition to 1) or 2), to enable radioact <<
72 <<
73 /dna/test/addPhysics raddecay <<
74 75
75 4) Warning regarding ions: when the incident p << 76 This example shows:
76 (/gun/particle ion), specified with Z and A nu << 77 - how to use the Geant4-DNA processes,
77 the Rudd ionisation extended model is used. Th << 78 - how to count and save occurrences of processes
78 by default down to 0.5 MeV/u. This tracking cu << 79 - how to combine them with Standard EM Physics.
79 80
80 /dna/test/addIonsTrackingCut false << 81 A simple electron capture process is also provided in order to kill electrons
>> 82 below a chosen energy threshold, set in the Physics list.
81 83
>> 84 Look at the PhyscisList.cc file.
82 85
83 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS << 86 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
84 87
85 The output results consists in a dna.root file 88 The output results consists in a dna.root file, containing for each simulation step:
86 - the type of particle for the current step 89 - the type of particle for the current step
87 - the type of process for the current step 90 - the type of process for the current step
88 - the step PostStepPoint coordinates (in nm) << 91 - the track position of the current step (in nanometers)
89 - the energy deposit along the current step (i 92 - the energy deposit along the current step (in eV)
90 - the step length (in nm) 93 - the step length (in nm)
91 - the total energy loss along the current step 94 - the total energy loss along the current step (in eV)
92 - the kinetic energy at PreStepPoint (in eV) << 95 - the kinetic energy at PreStepPoint
93 - the cos of the scattering angle 96 - the cos of the scattering angle
94 - the event ID 97 - the event ID
95 - the track ID 98 - the track ID
96 - the parent track ID 99 - the parent track ID
97 - the step number 100 - the step number
98 101
99 This information is extracted from the Steppin << 102 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 : 103 file plot.C; to do so :
103 * be sure to have ROOT installed on your machi 104 * be sure to have ROOT installed on your machine
104 * be sure to be in the directory containing th << 105 * be sure to be in the microdosimetry directory
105 * copy plot.C into this directory << 106 * launch ROOT by typing root
106 * from there, launch ROOT by typing root <<
107 * under your ROOT session, type in : .X plot.C 107 * under your ROOT session, type in : .X plot.C to execute the macro file
108 * alternatively you can type directly under yo 108 * alternatively you can type directly under your session : root plot.C
109 109
110 The naming scheme on the displayed ROOT plots << 110 The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc),
111 << 111 as in the 'dnaphysics' example:
112 -particles <<
113 112
114 gamma: 0 << 113 -particles:
115 e-: 1 << 114 gamma : 0
116 proton: 2 << 115 e- : 1
117 hydrogen: 3 << 116 proton : 2
118 alpha: 4 << 117 hydrogen : 3
119 alpha+: 5 << 118 alpha : 4
120 helium: 6 << 119 alpha+ : 5
121 << 120 helium : 6
122 -processes << 121
123 << 122 -processes:
124 Capture: 1 << 123
125 (only if one uses G4EmmicrodosimetryActivator << 124 eCapture 1
126 << 125 (only if one uses G4EmDNAPhysicsActivator in PhysicsList)
127 e-_G4DNAElectronSolvation: 10 << 126
128 e-_G4DNAElastic: 11 << 127 e-_G4DNAElectronSolvation 10
129 e-_G4DNAExcitation: 12 << 128 e-_G4DNAElastic 11
130 e-_G4DNAIonisation: 13 << 129 e-_G4DNAExcitation 12
131 e-_G4DNAAttachment: 14 << 130 e-_G4DNAIonisation 13
132 e-_G4DNAVibExcitation: 15 << 131 e-_G4DNAAttachment 14
133 msc: 110 << 132 e-_G4DNAVibExcitation 15
134 CoulombScat: 120 << 133 msc 110
135 eIoni: 130 << 134 CoulombScat 120
136 << 135 eIoni 130
137 proton_G4DNAElastic: 21 << 136
138 proton_G4DNAExcitation: 22 << 137 proton_G4DNAElastic 21
139 proton_G4DNAIonisation: 23 << 138 proton_G4DNAExcitation 22
140 proton_G4DNAChargeDecrease: 24 << 139 proton_G4DNAIonisation 23
141 msc: 210 << 140 proton_G4DNAChargeDecrease 24
142 CoulombScat: 220 << 141 msc 210
143 hIoni: 230 << 142 CoulombScat 220
144 nuclearStopping: 240 << 143 hIoni 230
145 << 144 nuclearStopping 240
146 hydrogen_G4DNAElastic: 31 << 145
147 hydrogen_G4DNAExcitation: 32 << 146 hydrogen_G4DNAElastic 31
148 hydrogen_G4DNAIonisation: 33 << 147 hydrogen_G4DNAExcitation 32
149 hydrogen_G4DNAChargeIncrease: 35 << 148 hydrogen_G4DNAIonisation 33
150 << 149 hydrogen_G4DNAChargeIncrease 35
151 alpha_G4DNAElastic: 41 << 150
152 alpha_G4DNAExcitation: 42 << 151 alpha_G4DNAElastic 41
153 alpha_G4DNAIonisation: 43 << 152 alpha_G4DNAExcitation 42
154 alpha_G4DNAChargeDecrease: 44 << 153 alpha_G4DNAIonisation 43
155 msc: 410 << 154 alpha_G4DNAChargeDecrease 44
156 CoulombScat: 420 << 155 msc 410
157 ionIoni: 430 << 156 CoulombScat 420
158 nuclearStopping: 440 << 157 ionIoni 430
159 << 158 nuclearStopping 440
160 alpha+_G4DNAElastic: 51 << 159
161 alpha+_G4DNAExcitation: 52 << 160 alpha+_G4DNAElastic 51
162 alpha+_G4DNAIonisation: 53 << 161 alpha+_G4DNAExcitation 52
163 alpha+_G4DNAChargeDecrease: 54 << 162 alpha+_G4DNAIonisation 53
164 alpha+_G4DNAChargeIncrease: 55 << 163 alpha+_G4DNAChargeDecrease 54
165 msc: 510 << 164 alpha+_G4DNAChargeIncrease 55
166 CoulombScat: 520 << 165 msc 510
167 hIoni: 530 << 166 CoulombScat 520
168 nuclearStopping: 540 << 167 hIoni 530
169 << 168 nuclearStopping 540
170 helium_G4DNAElastic: 61 << 169
171 helium_G4DNAExcitation: 62 << 170 helium_G4DNAElastic 61
172 helium_G4DNAIonisation: 63 << 171 helium_G4DNAExcitation 62
173 helium_G4DNAChargeIncrease: 65 << 172 helium_G4DNAIonisation 63
174 << 173 helium_G4DNAChargeIncrease 65
175 GenericIon_G4DNAIonisation: 73 << 174
176 msc: 710 << 175 GenericIon_G4DNAIonisation 73
177 CoulombSca: 720 << 176 msc 710
178 ionIoni: 730 << 177 CoulombScat 720
179 nuclearStopping: 740 << 178 ionIoni 730
180 << 179 nuclearStopping 740
181 phot: 81 <<
182 compt: 82 <<
183 conv: 83 <<
184 Rayl: 84 <<
185 180
186 ---------------------------------------------- 181 ---------------------------------------------------------------------------
187 182
188 Should you have any enquiry, please do not hes << 183 Should you have any enquiry, please do not hesitate to contact:
189 incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr << 184 incerti@cenbg.in2p3.fr