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Geant4 - dnaphysics example
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README file
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CORRESPONDING AUTHOR
S. Incerti (a,*), V. Ivantchenko (b), M. Karamitros (a)
a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan
(CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
* e-mail:incerti@cenbg.in2p3.fr
---->0. INTRODUCTION.
The dnaphysics example shows how to simulate track structures in liquid water
using the Geant4-DNA physics processes and models.
Below 1 MeV, Geant4-DNA models are used while, above this energy,
G4EmStandardPhysics_option4 models are used.
Geant4-DNA models for electrons are based on a combination of default models with option4 models.
The Geant4-DNA processes and models are further described at:
http://geant4-dna.org
Any report or published results obtained using the Geant4-DNA software shall
cite the following Geant4-DNA collaboration publications:
Med. Phys. 45, e722-e739 (2018)
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708
Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
---->1. GEOMETRY SET-UP.
The geometry is a 100-micron side cube (World) made of liquid water (G4_WATER
material). Particles are shot from the center of the volume.
The variable density feature of materials is illustrated.
Material can be changed directly in dna.mac macro file.
---->2. SET-UP
Make sure $G4LEDATA points to the low energy electromagnetic data files.
The code can be compiled with cmake.
It works in MT mode.
---->3. HOW TO RUN THE EXAMPLE
In interactive mode, run:
./dnaphysics
In batch, the macro dnaphysics.in can be used. It shows how to shoot different
particle types.
The combination of G4EmStandardPhysics_option4 and Geant4-DNA models in the World
is activated thanks to the following UI command in dnaphysics.in:
/process/em/AddDNARegion World DNA_Opt0
For now, only the "DNA_Opt0" configuration is allowed.
---->4. PHYSICS
This example shows:
- how to use the Geant4-DNA models, which are activated automatically at low energy,
below 1 MeV, and G4EmStandardPhysics_option4 models above
(look at the PhysicsList.cc file)
- how to count and save occurrences of processes
(look at the SteppingAction.cc file)
Alternatively, the direct usage of Geant4-DNA physics constructors is also shown
in comment in the PhysicsList.cc file.
---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
The output results consists in a dna.root file, containing for each simulation step:
- the type of particle for the current step
- the type of process for the current step
- the track position of the current step (in nanometers)
- the energy deposit along the current step (in eV)
- the step length (in nm)
- the total energy loss along the current step (in eV)
- the kinetic energy at PreStepPoint
- the cos of the scattering angle
- the event ID
- the track ID
- the parent track ID
- the step number
This file can be easily analyzed using for example the provided ROOT macro
file plot.C; to do so :
* be sure to have ROOT installed on your machine
* be sure to be in the directory containing the ROOT files created by dnaphysics
* copy plot.C into this directory
* from there, launch ROOT by typing root
* under your ROOT session, type in : .X plot.C to execute the macro file
* alternatively you can type directly under your session : root plot.C
The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc):
This is the same naming scheme as in the "microdosimetry" advanced example.
-particles:
gamma : 0
e- : 1
proton : 2
hydrogen : 3
alpha : 4
alpha+ : 5
helium : 6
-processes:
Capture 1
(only if one uses G4EmDNAPhysicsActivator in PhysicsList)
e-_G4DNAElectronSolvation 10
e-_G4DNAElastic 11
e-_G4DNAExcitation 12
e-_G4DNAIonisation 13
e-_G4DNAAttachment 14
e-_G4DNAVibExcitation 15
msc 110
CoulombScat 120
eIoni 130
proton_G4DNAElastic 21
proton_G4DNAExcitation 22
proton_G4DNAIonisation 23
proton_G4DNAChargeDecrease 24
msc 210
CoulombScat 220
hIoni 230
nuclearStopping 240
hydrogen_G4DNAElastic 31
hydrogen_G4DNAExcitation 32
hydrogen_G4DNAIonisation 33
hydrogen_G4DNAChargeIncrease 35
alpha_G4DNAElastic 41
alpha_G4DNAExcitation 42
alpha_G4DNAIonisation 43
alpha_G4DNAChargeDecrease 44
msc 410
CoulombScat 420
ionIoni 430
nuclearStopping 440
alpha+_G4DNAElastic 51
alpha+_G4DNAExcitation 52
alpha+_G4DNAIonisation 53
alpha+_G4DNAChargeDecrease 54
alpha+_G4DNAChargeIncrease 55
msc 510
CoulombScat 520
hIoni 530
nuclearStopping 540
helium_G4DNAElastic 61
helium_G4DNAExcitation 62
helium_G4DNAIonisation 63
helium_G4DNAChargeIncrease 65
GenericIon_G4DNAIonisation 73
msc 710
CoulombScat 720
ionIoni 730
nuclearStopping 740
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Should you have any enquiry, please do not hesitate to contact:
incerti@cenbg.in2p3.fr
Gabriele Cosmo