Gabriele Cosmo
180 lines
5.2 KiB
Plaintext
180 lines
5.2 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,*), V. Ivantchenko (b), M. Karamitros (a)
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a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
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(CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
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* e-mail:incerti@cenbg.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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Below 1 MeV, Geant4-DNA models are used while, above this energy,
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G4EmStandardPhysics_option4 models are used.
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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. 45, e722-e739 (2018)
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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.
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The variable density feature of materials is illustrated.
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Material can be changed directly in dna.mac 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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The code can be compiled with cmake.
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It works in MT mode.
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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.
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The combination of G4EmStandardPhysics_option4 and Geant4-DNA models in the World
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is activated thanks to the following UI command in dnaphysics.in:
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/process/em/AddDNARegion World DNA_Opt0
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For now, only the "DNA_Opt0" configuration is allowed.
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---->4. PHYSICS
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This example shows:
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- how to use the Geant4-DNA models, which are activated automatically at low energy,
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below 1 MeV, and G4EmStandardPhysics_option4 models above
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(look at the PhysicsList.cc file)
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- how to count and save occurrences of processes
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(look at the SteppingAction.cc file)
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Alternatively, the direct usage of Geant4-DNA physics constructors is also shown
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in comment in the PhysicsList.cc file.
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---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
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The output results consists in a dna.root file, containing 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 track position of the current step (in nanometers)
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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
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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 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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The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
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This is the same naming scheme as in the "microdosimetry" advanced example.
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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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(only if one uses G4EmDNAPhysicsActivator in PhysicsList)
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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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CoulombScat 720
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ionIoni 730
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nuclearStopping 740
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---------------------------------------------------------------------------
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Should you have any enquiry, please do not hesitate to contact:
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incerti@cenbg.in2p3.fr
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