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Geant4/examples/extended/medical/dna/microdosimetry/README

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  1      =========================================================
  2       Geant4 - microdosimetry 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 microdosimetry example shows how to use Geant4 and Geant4-DNA physics models
 18 in different regions of the geometry.
 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 10-micron side cube (World) made of liquid water (G4_WATER
 34 material) containing a 2 micron-thick slice (along X) of water (Target).
 35 
 36 Particles are shot from the World volume.
 37 
 38 The variable density feature of materials is illustrated in DetectorConstruction.
 39 The material can be changed directly in microdosimetry.in macro file.
 40 
 41 ---->2. SET-UP
 42 
 43 Make sure $G4LEDATA points to the low energy electromagnetic data files.
 44 
 45 ---->3. HOW TO RUN THE EXAMPLE
 46 
 47 In interactive mode, run:
 48 
 49 ./microdosimetry
 50 
 51 In batch, the macro microdosimetry.in can be used. It shows how to shoot different
 52 particle types.
 53 
 54 ---->4. PHYSICS
 55 
 56 The PhysicsList uses Geant4 Physics in the World region and Geant4-DNA Physics
 57 in the Target region.
 58 
 59 1) Geant4 Physics in the World is selected via the command:
 60 
 61 /dna/test/addPhysics X
 62 
 63 where X is any EM physics list, such as emstandard_opt4 (see PhysicsList.cc).
 64 
 65 2) Geant4-DNA activator is used in the regionTarget region using:
 66 
 67 /process/em/AddDNARegion regionTarget DNA_OptY
 68 
 69 where Y = 0, 2, 4, or 6.
 70 
 71 3) In addition to 1) or 2), to enable radioactive decay, one can use:
 72 
 73 /dna/test/addPhysics raddecay
 74 
 75 4) Warning regarding ions: when the incident particle type is ion
 76 (/gun/particle ion), specified with Z and A numbers (/gun/ion A Z),
 77 the Rudd ionisation extended model is used. The particles are tracked
 78 by default down to 0.5 MeV/u. This tracking cut can be bypassed using :
 79 
 80 /dna/test/addIonsTrackingCut false
 81 
 82 
 83 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
 84 
 85 The output results consists in a dna.root file, containing for each simulation step:
 86 - the type of particle for the current step
 87 - the type of process for the current step
 88 - the step PostStepPoint coordinates (in nm)
 89 - the energy deposit along the current step (in eV)
 90 - the step length (in nm)
 91 - the total energy 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 
 99 This information is extracted from the SteppingAction class.
100 
101 The ROOT file can be easily analyzed using for example the provided ROOT macro
102 file plot.C; to do so :
103 * be sure to have ROOT installed on your machine
104 * be sure to be in the directory containing the ROOT files created by microdosimetry
105 * copy plot.C into this directory
106 * from there, launch ROOT by typing root
107 * under your ROOT session, type in : .X plot.C to execute the macro file
108 * alternatively you can type directly under your session : root plot.C
109 
110 The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
111 
112 -particles
113 
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 in PhysicsList)
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 ---------------------------------------------------------------------------
187 
188 Should you have any enquiry, please do not hesitate to contact:
189 incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr