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0001 =========================================================
0002 Geant4 - dnaphysics example
0003 =========================================================
0004
0005 README file
0006 ----------------------
0007
0008 CORRESPONDING AUTHOR
0009
0010 S. Incerti (a, *), H. Tran (a, *), V. Ivantchenko (b), M. Karamitros
0011 a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
0012 b. G4AI Ltd., UK
0013 * e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr
0014
0015 ---->0. INTRODUCTION
0016
0017 The dnaphysics example shows how to simulate track structures in liquid water
0018 using the Geant4-DNA physics processes and models.
0019
0020 The Geant4-DNA processes and models are further described at:
0021 http://geant4-dna.org
0022
0023 Any report or published results obtained using the Geant4-DNA software shall
0024 cite the following Geant4-DNA collaboration publications:
0025 Med. Phys. 51 (2024) 5873–5889
0026 Med. Phys. 45 (2018) e722-e739
0027 Phys. Med. 31 (2015) 861-874
0028 Med. Phys. 37 (2010) 4692-4708
0029 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
0030
0031 ---->1. GEOMETRY SET-UP
0032
0033 The geometry is a 100-micron side cube (World) made of liquid water (G4_WATER
0034 material). Particles are shot from the center of the volume. The World size
0035 can be changed directly in the dnaphysics.in macro file.
0036
0037 The variable density feature of materials is illustrated in
0038 DetectorConstruction. The material density can be changed directly in the
0039 dnaphysics.in macro file.
0040
0041 ---->2. SET-UP
0042
0043 Make sure $G4LEDATA points to the low energy electromagnetic data files.
0044
0045 ---->3. HOW TO RUN THE EXAMPLE
0046
0047 In interactive mode, run:
0048
0049 ./dnaphysics
0050
0051 In batch, the macro dnaphysics.in can be used. It shows how to shoot different
0052 particle types and how to use Geant4-DNA Physics constructors.
0053
0054 The deexcitation.in macro can be used to simulate the energy spectrum of
0055 deexcitation products.
0056
0057 The radioactive.in macro can be used to simulate some radioactive nuclei.
0058
0059 ---->4. PHYSICS
0060
0061 The PhysicsList uses Geant4-DNA Physics constructors and other
0062 electromagnetic physics constructors.
0063
0064 Geant4-DNA Physics constructors can be selected using the command:
0065
0066 /dna/test/addPhysics DNA_OptX
0067
0068 where X is 0 to 8 (2, 4 or 6 are recommended).
0069
0070 In addition, to also enable radioactive decay, one can use:
0071
0072 /dna/test/addPhysics raddecay
0073
0074 Warning regarding ions: when the incident particle type is ion
0075 (/gun/particle ion), specified with Z and A numbers (/gun/ion A Z),
0076 the Rudd ionisation extended model is used. The particles are tracked
0077 by default down to 0.5 MeV/u and undergo below a capture process.
0078 This tracking cut can be bypassed using:
0079
0080 /dna/test/addIonsTrackingCut false
0081
0082 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
0083
0084 The output results consists in a dna.root file, containing two ntuples, named
0085 "step" and "track", respectively:
0086
0087 1) for each simulation step:
0088
0089 - the type of particle for the current step
0090 - the type of process for the current step
0091 - the step PostStepPoint coordinates (in nm)
0092 - the energy deposit along the current step (in eV)
0093 - the step length (in nm)
0094 - the total energy loss along the current step (in eV)
0095 - the kinetic energy at PreStepPoint (in eV)
0096 - the cos of the scattering angle
0097 - the event ID
0098 - the track ID
0099 - the parent track ID
0100 - the step number
0101
0102 This information is extracted from the SteppingAction class.
0103
0104 The ROOT file can be easily analyzed using for example the provided ROOT macro
0105 file plot.C; to do so :
0106 * be sure to have ROOT installed on your machine
0107 * be sure to be in the directory containing the ROOT files created by dnaphysics
0108 * copy plot.C into this directory
0109 * from there, launch ROOT by typing root
0110 * under your ROOT session, type in : .X plot.C to execute the macro file
0111 * alternatively you can type directly under your session : root plot.C
0112
0113 The plotDeexcitation.C ROOT macro file can be used to plot results of
0114 deexcitation.in.
0115
0116 The plotRadioactive.C ROOT macro file can be used to plot results of
0117 radioactive.in.
0118
0119 The plotElastic.C ROOT macro file can be used to show distribution of elastic
0120 scattering angles of the elastic process obtained with elastic.in. This macro also
0121 illustrates the usage of a dedicated UI command :
0122 /step/recordOnlyFirstStep value
0123 where value is 0 or 1.
0124 Setting value to 1 only records the first step and then kills the track and its
0125 secondaries.
0126
0127 The naming scheme for particles and processes on the displayed ROOT plots adopts
0128 a local numbering, as follows (see SteppingAction.cc):
0129
0130 -particles
0131
0132 gamma: 0
0133 e-: 1
0134 proton: 2
0135 hydrogen: 3
0136 alpha: 4
0137 alpha+: 5
0138 helium: 6
0139 GenericIon (above helium): 7
0140
0141 -processes
0142
0143 Capture: 1
0144
0145 RadioactiveDecay: 2
0146
0147 e-_G4DNAElectronSolvation: 10
0148 e-_G4DNAElastic: 11
0149 e-_G4DNAExcitation: 12
0150 e-_G4DNAIonisation: 13
0151 e-_G4DNAAttachment: 14
0152 e-_G4DNAVibExcitation: 15
0153 msc: 110
0154 CoulombScat: 120
0155 eIoni: 130
0156
0157 proton_G4DNAElastic: 21
0158 proton_G4DNAExcitation: 22
0159 proton_G4DNAIonisation: 23
0160 proton_G4DNAChargeDecrease: 24
0161 msc: 210
0162 CoulombScat: 220
0163 hIoni: 230
0164 nuclearStopping: 240
0165
0166 hydrogen_G4DNAElastic: 31
0167 hydrogen_G4DNAExcitation: 32
0168 hydrogen_G4DNAIonisation: 33
0169 hydrogen_G4DNAChargeIncrease: 35
0170
0171 alpha_G4DNAElastic: 41
0172 alpha_G4DNAExcitation: 42
0173 alpha_G4DNAIonisation: 43
0174 alpha_G4DNAChargeDecrease: 44
0175 msc: 410
0176 CoulombScat: 420
0177 ionIoni: 430
0178 nuclearStopping: 440
0179
0180 alpha+_G4DNAElastic: 51
0181 alpha+_G4DNAExcitation: 52
0182 alpha+_G4DNAIonisation: 53
0183 alpha+_G4DNAChargeDecrease: 54
0184 alpha+_G4DNAChargeIncrease: 55
0185 msc: 510
0186 CoulombScat: 520
0187 hIoni: 530
0188 nuclearStopping: 540
0189
0190 helium_G4DNAElastic: 61
0191 helium_G4DNAExcitation: 62
0192 helium_G4DNAIonisation: 63
0193 helium_G4DNAChargeIncrease: 65
0194
0195 GenericIon_G4DNAIonisation: 73
0196 msc: 710
0197 CoulombSca: 720
0198 ionIoni: 730
0199 nuclearStopping: 740
0200
0201 phot: 81
0202 compt: 82
0203 conv: 83
0204 Rayl: 84
0205
0206 2) for each simulation track:
0207
0208 - the type of particle for the current track (see 1))
0209 - the track position (in nm)
0210 - the track momentum direction
0211 - the track kinetic energy (in eV)
0212 - the track ID
0213 - the parent track ID
