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1 =========================================================
2 Geant4 - dnaphysics example
3 =========================================================
4
5 README file
6 ----------------------
7
8 CORRESPONDING AUTHOR
9
10 S. Incerti (a, *), H. Tran (a, *), V. Ivantchenko (b), M. Karamitros
11 a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
12 b. G4AI Ltd., UK
13 * e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr
14
15 ---->0. INTRODUCTION
16
17 The dnaphysics example shows how to simulate track structures in liquid water
18 using the Geant4-DNA physics processes and models.
19
20 The Geant4-DNA processes and models are further described at:
21 http://geant4-dna.org
22
23 Any report or published results obtained using the Geant4-DNA software shall
24 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
28 Med. Phys. 37 (2010) 4692-4708
29 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
30
31 ---->1. GEOMETRY SET-UP
32
33 The geometry is a 100-micron side cube (World) made of liquid water (G4_WATER
34 material). Particles are shot from the center of the volume. The World size
35 can be changed directly in the dnaphysics.in macro file.
36
37 The variable density feature of materials is illustrated in DetectorConstruction.
38 The material density can be changed directly in the dnaphysics.in macro file.
39
40 ---->2. SET-UP
41
42 Make sure $G4LEDATA points to the low energy electromagnetic data files.
43
44 ---->3. HOW TO RUN THE EXAMPLE
45
46 In interactive mode, run:
47
48 ./dnaphysics
49
50 In batch, the macro dnaphysics.in can be used. It shows how to shoot different
51 particle types and how to use Geant4-DNA Physics constructors.
52
53 The deexcitation.in macro can also be used to simulate the energy spectrum of deexcitation products.
54
55 ---->4. PHYSICS
56
57 The PhysicsList uses Geant4-DNA Physics constructors and other
58 electromagnetic physics constructors.
59
60 Geant4-DNA Physics constructors can be selected using the command:
61
62 /dna/test/addPhysics DNA_OptX
63
64 where X is 0 to 8 (2, 4 or 6 are recommended).
65
66 In addition, to also enable radioactive decay, one can use:
67
68 /dna/test/addPhysics raddecay
69
70 Warning regarding ions: when the incident particle type is ion
71 (/gun/particle ion), specified with Z and A numbers (/gun/ion A Z),
72 the Rudd ionisation extended model is used. The particles are tracked
73 by default down to 0.5 MeV/u and undergo below a capture process.
74 This tracking cut can be bypassed using:
75
76 /dna/test/addIonsTrackingCut false
77
78 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
79
80 The output results consists in a dna.root file, containing two ntuples, named
81 "step" and "track", respectively:
82
83 1) for each simulation step:
84
85 - the type of particle for the current step
86 - the type of process for the current step
87 - the step PostStepPoint coordinates (in nm)
88 - the energy deposit along the current step (in eV)
89 - the step length (in nm)
90 - the total energy loss along the current step (in eV)
91 - the kinetic energy at PreStepPoint (in eV)
92 - the cos of the scattering angle
93 - the event ID
94 - the track ID
95 - the parent track ID
96 - the step number
97
98 This information is extracted from the SteppingAction class.
99
100 The ROOT file can be easily analyzed using for example the provided ROOT macro
101 file plot.C; to do so :
102 * be sure to have ROOT installed on your machine
103 * be sure to be in the directory containing the ROOT files created by dnaphysics
104 * copy plot.C into this directory
105 * from there, launch ROOT by typing root
106 * under your ROOT session, type in : .X plot.C to execute the macro file
107 * alternatively you can type directly under your session : root plot.C
108
109 Also, the plotDeexcitation.C ROOT macro file can be used to plot results of deexcitation.in.
110
111 The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
112
113 -particles
114
115 gamma: 0
116 e-: 1
117 proton: 2
118 hydrogen: 3
119 alpha: 4
120 alpha+: 5
121 helium: 6
122
123 -processes
124
125 Capture: 1
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
186 2) for each simulation track:
187
188 - the type of particle for the current track (see 1))
189 - the track position (in nm)
190 - the track momentum direction
191 - the track kinetic energy (in eV)
192 - the track ID
193 - the parent track ID
194
195 ---------------------------------------------------------------------------
196
197 Should you have any enquiry, please do not hesitate to contact:
198 incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr
