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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. 45, (2018) e722-e739
0026 Phys. Med. 31 (2015) 861-874
0027 Med. Phys. 37 (2010) 4692-4708
0028 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
0029
0030 ---->1. GEOMETRY SET-UP
0031
0032 The geometry is a 100-micron side cube (World) made of liquid water (G4_WATER
0033 material). Particles are shot from the center of the volume.
0034
0035 The variable density feature of materials is illustrated in DetectorConstruction.
0036 The material can be changed directly in the dnaphysics.in macro file.
0037
0038 ---->2. SET-UP
0039
0040 Make sure $G4LEDATA points to the low energy electromagnetic data files.
0041
0042 ---->3. HOW TO RUN THE EXAMPLE
0043
0044 In interactive mode, run:
0045
0046 ./dnaphysics
0047
0048 In batch, the macro dnaphysics.in can be used. It shows how to shoot different
0049 particle types and how to use Geant4-DNA Physics constructors.
0050
0051 The deexcitation.in macro can also be used to simulate the energy spectrum of deexcitation products.
0052
0053 ---->4. PHYSICS
0054
0055 The PhysicsList uses Geant4-DNA Physics constructors and other
0056 electromagnetic physics constructors.
0057
0058 Geant4-DNA Physics constructors can be selected using the command:
0059
0060 /dna/test/addPhysics DNA_OptX
0061
0062 where X is 0 to 8 (2, 4 or 6 are recommended).
0063
0064 In addition, to also enable radioactive decay, one can use:
0065
0066 /dna/test/addPhysics raddecay
0067
0068 Warning regarding ions: when the incident particle type is ion
0069 (/gun/particle ion), specified with Z and A numbers (/gun/ion A Z),
0070 the Rudd ionisation extended model is used. The particles are tracked
0071 by default down to 0.5 MeV/u and undergo below a capture process.
0072 This tracking cut can be bypassed using:
0073
0074 /dna/test/addIonsTrackingCut false
0075
0076 ---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
0077
0078 The output results consists in a dna.root file, containing two ntuples, named
0079 "step" and "track", respectively:
0080
0081 1) for each simulation step:
0082
0083 - the type of particle for the current step
0084 - the type of process for the current step
0085 - the step PostStepPoint coordinates (in nm)
0086 - the energy deposit along the current step (in eV)
0087 - the step length (in nm)
0088 - the total energy loss along the current step (in eV)
0089 - the kinetic energy at PreStepPoint (in eV)
0090 - the cos of the scattering angle
0091 - the event ID
0092 - the track ID
0093 - the parent track ID
0094 - the step number
0095
0096 This information is extracted from the SteppingAction class.
0097
0098 The ROOT file can be easily analyzed using for example the provided ROOT macro
0099 file plot.C; to do so :
0100 * be sure to have ROOT installed on your machine
0101 * be sure to be in the directory containing the ROOT files created by dnaphysics
0102 * copy plot.C into this directory
0103 * from there, launch ROOT by typing root
0104 * under your ROOT session, type in : .X plot.C to execute the macro file
0105 * alternatively you can type directly under your session : root plot.C
0106
0107 Also, the plotDeexcitation.C ROOT macro file can be used to plot results of deexcitation.in.
0108
0109 The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
0110
0111 -particles
0112
0113 gamma: 0
0114 e-: 1
0115 proton: 2
0116 hydrogen: 3
0117 alpha: 4
0118 alpha+: 5
0119 helium: 6
0120
0121 -processes
0122
0123 Capture: 1
0124
0125 e-_G4DNAElectronSolvation: 10
0126 e-_G4DNAElastic: 11
0127 e-_G4DNAExcitation: 12
0128 e-_G4DNAIonisation: 13
0129 e-_G4DNAAttachment: 14
0130 e-_G4DNAVibExcitation: 15
0131 msc: 110
0132 CoulombScat: 120
0133 eIoni: 130
0134
0135 proton_G4DNAElastic: 21
0136 proton_G4DNAExcitation: 22
0137 proton_G4DNAIonisation: 23
0138 proton_G4DNAChargeDecrease: 24
0139 msc: 210
0140 CoulombScat: 220
0141 hIoni: 230
0142 nuclearStopping: 240
0143
0144 hydrogen_G4DNAElastic: 31
0145 hydrogen_G4DNAExcitation: 32
0146 hydrogen_G4DNAIonisation: 33
0147 hydrogen_G4DNAChargeIncrease: 35
0148
0149 alpha_G4DNAElastic: 41
0150 alpha_G4DNAExcitation: 42
0151 alpha_G4DNAIonisation: 43
0152 alpha_G4DNAChargeDecrease: 44
0153 msc: 410
0154 CoulombScat: 420
0155 ionIoni: 430
0156 nuclearStopping: 440
0157
0158 alpha+_G4DNAElastic: 51
0159 alpha+_G4DNAExcitation: 52
0160 alpha+_G4DNAIonisation: 53
0161 alpha+_G4DNAChargeDecrease: 54
0162 alpha+_G4DNAChargeIncrease: 55
0163 msc: 510
0164 CoulombScat: 520
0165 hIoni: 530
0166 nuclearStopping: 540
0167
0168 helium_G4DNAElastic: 61
0169 helium_G4DNAExcitation: 62
0170 helium_G4DNAIonisation: 63
0171 helium_G4DNAChargeIncrease: 65
0172
0173 GenericIon_G4DNAIonisation: 73
0174 msc: 710
0175 CoulombSca: 720
0176 ionIoni: 730
0177 nuclearStopping: 740
0178
0179 phot: 81
0180 compt: 82
0181 conv: 83
0182 Rayl: 84
0183
0184 2) for each simulation track:
0185
0186 - the type of particle for the current track (see 1))
0187 - the track position (in nm)
0188 - the track momentum direction
0189 - the track kinetic energy (in eV)
0190 - the track ID
0191 - the parent track ID
0192
0193 ---------------------------------------------------------------------------
0194
0195 Should you have any enquiry, please do not hesitate to contact:
0196 incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr
