Gabriele Cosmo
199 lines
5.3 KiB
Plaintext
199 lines
5.3 KiB
Plaintext
=========================================================
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Geant4 - dnaphysics example
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=========================================================
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README file
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----------------------
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CORRESPONDING AUTHOR
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S. Incerti (a, *), H. Tran (a, *), V. Ivantchenko (b), M. Karamitros
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a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
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b. G4AI Ltd., UK
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* e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr
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---->0. INTRODUCTION
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The dnaphysics example shows how to simulate track structures in liquid water
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using the Geant4-DNA physics processes and models.
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The Geant4-DNA processes and models are further described at:
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http://geant4-dna.org
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Any report or published results obtained using the Geant4-DNA software shall
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cite the following Geant4-DNA collaboration publications:
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Med. Phys. 51 (2024) 5873–5889
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Med. Phys. 45 (2018) e722-e739
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Phys. Med. 31 (2015) 861-874
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Med. Phys. 37 (2010) 4692-4708
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Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
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---->1. GEOMETRY SET-UP
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The geometry is a 100-micron side cube (World) made of liquid water (G4_WATER
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material). Particles are shot from the center of the volume. The World size
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can be changed directly in the dnaphysics.in macro file.
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The variable density feature of materials is illustrated in DetectorConstruction.
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The material density can be changed directly in the dnaphysics.in macro file.
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---->2. SET-UP
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Make sure $G4LEDATA points to the low energy electromagnetic data files.
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---->3. HOW TO RUN THE EXAMPLE
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In interactive mode, run:
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./dnaphysics
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In batch, the macro dnaphysics.in can be used. It shows how to shoot different
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particle types and how to use Geant4-DNA Physics constructors.
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The deexcitation.in macro can also be used to simulate the energy spectrum of deexcitation products.
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---->4. PHYSICS
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The PhysicsList uses Geant4-DNA Physics constructors and other
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electromagnetic physics constructors.
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Geant4-DNA Physics constructors can be selected using the command:
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/dna/test/addPhysics DNA_OptX
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where X is 0 to 8 (2, 4 or 6 are recommended).
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In addition, to also enable radioactive decay, one can use:
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/dna/test/addPhysics raddecay
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Warning regarding ions: when the incident particle type is ion
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(/gun/particle ion), specified with Z and A numbers (/gun/ion A Z),
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the Rudd ionisation extended model is used. The particles are tracked
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by default down to 0.5 MeV/u and undergo below a capture process.
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This tracking cut can be bypassed using:
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/dna/test/addIonsTrackingCut false
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---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
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The output results consists in a dna.root file, containing two ntuples, named
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"step" and "track", respectively:
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1) for each simulation step:
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- the type of particle for the current step
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- the type of process for the current step
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- the step PostStepPoint coordinates (in nm)
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- the energy deposit along the current step (in eV)
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- the step length (in nm)
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- the total energy loss along the current step (in eV)
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- the kinetic energy at PreStepPoint (in eV)
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- the cos of the scattering angle
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- the event ID
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- the track ID
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- the parent track ID
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- the step number
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This information is extracted from the SteppingAction class.
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The ROOT file can be easily analyzed using for example the provided ROOT macro
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file plot.C; to do so :
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* be sure to have ROOT installed on your machine
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* be sure to be in the directory containing the ROOT files created by dnaphysics
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* copy plot.C into this directory
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* from there, launch ROOT by typing root
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* under your ROOT session, type in : .X plot.C to execute the macro file
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* alternatively you can type directly under your session : root plot.C
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Also, the plotDeexcitation.C ROOT macro file can be used to plot results of deexcitation.in.
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The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
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-particles
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gamma: 0
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e-: 1
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proton: 2
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hydrogen: 3
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alpha: 4
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alpha+: 5
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helium: 6
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-processes
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Capture: 1
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e-_G4DNAElectronSolvation: 10
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e-_G4DNAElastic: 11
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e-_G4DNAExcitation: 12
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e-_G4DNAIonisation: 13
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e-_G4DNAAttachment: 14
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e-_G4DNAVibExcitation: 15
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msc: 110
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CoulombScat: 120
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eIoni: 130
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proton_G4DNAElastic: 21
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proton_G4DNAExcitation: 22
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proton_G4DNAIonisation: 23
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proton_G4DNAChargeDecrease: 24
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msc: 210
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CoulombScat: 220
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hIoni: 230
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nuclearStopping: 240
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hydrogen_G4DNAElastic: 31
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hydrogen_G4DNAExcitation: 32
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hydrogen_G4DNAIonisation: 33
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hydrogen_G4DNAChargeIncrease: 35
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alpha_G4DNAElastic: 41
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alpha_G4DNAExcitation: 42
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alpha_G4DNAIonisation: 43
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alpha_G4DNAChargeDecrease: 44
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msc: 410
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CoulombScat: 420
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ionIoni: 430
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nuclearStopping: 440
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alpha+_G4DNAElastic: 51
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alpha+_G4DNAExcitation: 52
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alpha+_G4DNAIonisation: 53
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alpha+_G4DNAChargeDecrease: 54
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alpha+_G4DNAChargeIncrease: 55
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msc: 510
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CoulombScat: 520
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hIoni: 530
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nuclearStopping: 540
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helium_G4DNAElastic: 61
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helium_G4DNAExcitation: 62
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helium_G4DNAIonisation: 63
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helium_G4DNAChargeIncrease: 65
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GenericIon_G4DNAIonisation: 73
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msc: 710
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CoulombSca: 720
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ionIoni: 730
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nuclearStopping: 740
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phot: 81
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compt: 82
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conv: 83
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Rayl: 84
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2) for each simulation track:
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- the type of particle for the current track (see 1))
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- the track position (in nm)
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- the track momentum direction
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- the track kinetic energy (in eV)
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- the track ID
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- the parent track ID
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---------------------------------------------------------------------------
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Should you have any enquiry, please do not hesitate to contact:
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incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr
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