216 lines
5.7 KiB
Markdown
216 lines
5.7 KiB
Markdown
\page ExampleDnaphysics Example dnaphysics
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\author S. Incerti (a, *), , H. Tran (a, *), V. Ivantchenko (b), M. Karamitros\n
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a. LP2i, IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France \n
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b. G4AI Ltd., UK
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* e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr \n
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## 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: \n
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Med. Phys. 51 (2024) 5873–5889 \n
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Med. Phys. 45 (2018) e722-e739 \n
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Phys. Med. 31 (2015) 861-874 \n
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Med. Phys. 37 (2010) 4692-4708 \n
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Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
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## 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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## SET-UP
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Make sure $G4LEDATA points to the low energy electromagnetic data files.
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## HOW TO RUN THE EXAMPLE
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In interactive mode, run:
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```
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./dnaphysics
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```
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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 be used to simulate the energy spectrum of
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deexcitation products.
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The radioactive.in macro can be used to simulate some radioactive nuclei.
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## 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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```
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/dna/test/addPhysics DNA_OptX
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```
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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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```
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/dna/test/addPhysics raddecay
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```
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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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```
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/dna/test/addIonsTrackingCut false
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```
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## 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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The plotDeexcitation.C ROOT macro file can be used to plot results of
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deexcitation.in.
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The plotRadioactive.C ROOT macro file can be used to plot results of
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radioactive.in.
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The plotElastic.C ROOT macro file can be used to show distribution of elastic
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scattering angles of the elastic process obtained with elastic.in. This macro also
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illustrates the usage of a dedicated UI command :
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```
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/step/recordOnlyFirstStep value
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```
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where value is 0 or 1. Setting value to 1 only records the first step and then kills
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the track and its secondaries.
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The naming scheme for particles and processes on the displayed ROOT plots
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adopts a local numbering, as follows (see SteppingAction.cc):
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- particles: \n
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gamma: 0 \n
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e-: 1 \n
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proton: 2 \n
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hydrogen: 3 \n
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alpha: 4 \n
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alpha+: 5 \n
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helium: 6 \n
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GenericIon (above helium): 7\n
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\n
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- processes: \n
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Capture: 1
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RadioactiveDecay: 2
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e-_G4DNAElectronSolvation: 10 \n
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e-_G4DNAElastic: 11 \n
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e-_G4DNAExcitation: 12 \n
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e-_G4DNAIonisation: 13 \n
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e-_G4DNAAttachment: 14 \n
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e-_G4DNAVibExcitation: 15 \n
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msc: 110 \n
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CoulombScat: 120 \n
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eIoni: 130 \n \n
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proton_G4DNAElastic: 21 \n
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proton_G4DNAExcitation: 22 \n
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proton_G4DNAIonisation: 23 \n
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proton_G4DNAChargeDecrease: 24 \n
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msc: 210 \n
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CoulombScat: 220 \n
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hIoni: 230 \n
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nuclearStopping: 240 \n \n
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hydrogen_G4DNAElastic: 31 \n
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hydrogen_G4DNAExcitation: 32 \n
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hydrogen_G4DNAIonisation: 33 \n
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hydrogen_G4DNAChargeIncrease: 35 \n \n
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alpha_G4DNAElastic: 41 \n
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alpha_G4DNAExcitation: 42 \n
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alpha_G4DNAIonisation: 43 \n
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alpha_G4DNAChargeDecrease: 44 \n
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msc: 410 \n
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CoulombScat: 420 \n
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ionIoni: 430 \n
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nuclearStopping: 440 \n \n
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alpha+_G4DNAElastic: 51 \n
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alpha+_G4DNAExcitation: 52 \n
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alpha+_G4DNAIonisation: 53 \n
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alpha+_G4DNAChargeDecrease: 54 \n
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alpha+_G4DNAChargeIncrease: 55 \n
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msc: 510 \n
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CoulombScat: 520 \n
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hIoni: 530 \n
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nuclearStopping: 540 \n
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helium_G4DNAElastic: 61 \n
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helium_G4DNAExcitation: 62 \n
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helium_G4DNAIonisation: 63 \n
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helium_G4DNAChargeIncrease: 65 \n \n
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GenericIon_G4DNAIonisation: 73 \n
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msc: 710 \n
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CoulombScat: 720 \n
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ionIoni: 730 \n
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nuclearStopping: 740 \n \n
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phot: 81 \n
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compt: 82 \n
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conv: 83 \n
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Rayl: 84 \n
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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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