dna/jetcounter/README.md

0001 \page Examplejetcounter Example jetcounter
0002
0003 \author M. Pietrzak (*), M. Mietelska, A. Bancer, A. Rucinski and B. Brzozowska \n
0004 * e-mail:marcin.pietrzak@fuw.edu.pl  or marcin.pietrzak@ncbj.gov.pl \n
0005
0006 This example is provided by the Geant4-DNA collaboration \n
0007 Any report or published results obtained using the Geant4-DNA software \n
0008 shall cite the following Geant4-DNA collaboration publications: \n
0009 [1] Med. Phys. 37 (2010) 4692-4708 \n
0010 [2] Phys. Med. 31 (2015) 861-874 \n
0011 In addition, for this example, please cite: \n
0012 [3] M. Pietrzak et al 2021 Phys. Med. Biol. 66 225008 (doi: 10.1088/1361-6560/ac33eb). \n
0013
0014 ## INTRODUCTION
0015
0016 The jetcounter example provides a setup for simulation of a typical experiment with the Jet Counter nanodosemeter.
0017
0018 This example allows the calculation of the ionisation cluster size distribution (ICSD) (the number of ionisations per projectile)
0019 in a real sized cylindrical interaction volume (IV) of the Jet Counter device.
0020
0021 The results of each of the simulation are provided in the plain text format.
0022 Each thread produces its own output file.
0023
0024 Each row in the output file consist information from a single event, where single primary particle (projectile) was generated.
0025 Each row contains 4 numbers (columns):
0026     -# Ionisation cluster size.
0027     -# Initial energy of the projectile.
0028     -# Interaction energy of the projectile.
0029     -# Final energy of the projectile.
0030
0031 Geometry visualization is available through vis.mac file.
0032
0033 Script written in Python is provided for visualization of the results.
0034
0035
0036 ## GEOMETRY SET-UP
0037
0038 - The height of the interaction volume (IV) is equal to 20 mm and its diameter is equal to 10 mm.
0039 - The beam axis enters the IV perpendicularly to its axis of rotation, 5 mm from the top.
0040 - The IV is filled with liquid water material (G4_WATER), but its density is set to 0.45 µg/cm³,
0041 which corresponds to the nitrogen gas density in real experimental conditions. For details see [3].
0042 - The beam divergence is restricted by a cylindrical collimator (3 mm in diameter, 23 mm in length) adjacent to the source.
0043 - There is a wall around the IV in the form of a cylinder opened on both ends. The wall thickness is 0.98 mg/cm² (7 µm).
0044 - The wall is composed of two layers:
0045     * outer layer is made of Mylar, 0.96 mg/cm² in thickness;
0046     * inner layer is made of liquid water (G4_WATER), 0.02 mg/cm² in thickness.
0047 - There is a silicon (trigger) detector in the form of a thin disk placed behind the IV.
0048
0049
0050 ## PRIMARY PARTICLES
0051
0052 If the beam energy is set to any positive value, the beam is mono-energetic with the given energy.
0053 If the beam energy is set to -1 (default value), the energy spectrum file is used.
0054 The energy spectrum of the beam is based on experimental data. Its mean energy is 4.6 MeV,
0055 which is the energy of alpha particles from gold-plated americium (241-Am) source.
0056 This source is chosen in the primaries.in macro file.
0057
0058
0059 ## PHYSICS LIST
0060
0061 The PhysicsList used in this example show how to combine Geant4-DNA physics and standard physics in different regions
0062 using the G4EmDNAPhysicsActivator.
0063 -# G4EmDNAPhysics is active in the IV and inner layer of the wall (both made of G4_WATER).
0064 -# G4EmLivermorePhysics is active in other parts of the setup.
0065
0066 The G4DNAPhysics_option is chosen in the init_phys.in macro file. Hence, it can be changed without the need of recompilation.
0067
0068
0069 ## SET UP
0070
0071 Make sure G4LEDATA points to the low energy electromagnetic data files.
0072
0073 ## HOW TO RUN THE EXAMPLE
0074
0075 For the visualization:
0076
0077 ```
0078 ./jetcounter vis
0079 ```
0080
0081 For the complete simulation:
0082
0083 ```
0084 ./jetcounter run
0085 ```
0086
0087 In run.mac macro file will read init_phys.in and primaries.in.
0088
0089 However, it is recommended to first increase the number of simulated events in the run.mac file to at least 4000.
0090
0091 To produce figures from simulation results
0092  (requires numpy and matplotlib Python libraries):
0093
0094 ```
0095  python3 plot.py
0096 ```