dna/svalue/README.md

0001 \page Examplesvalue Example svalue
0002
0003 \author S. Incerti et al. (a, *) \n
0004 a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
0005 * e-mail: incerti@lp2ib.in2p3.fr
0006
0007 ## INTRODUCTION.
0008
0009 The svalue example shows how to calculate monoenergetic S values in liquid water
0010 using the Geant4-DNA physics processes and models.
0011
0012 It is adapted from TestEm12.
0013
0014 This example is provided by the Geant4-DNA collaboration.
0015
0016 These processes and models are further described at:
0017 http://geant4-dna.org
0018
0019 Any report or published results obtained using the Geant4-DNA software shall
0020 cite the following Geant4-DNA collaboration publications: \n
0021 Med. Phys. 51 (2024) 5873–5889 \n
0022 Med. Phys. 45 (2018) e722-e739 \n
0023 Phys. Med. 31 (2015) 861-874   \n
0024 Med. Phys. 37 (2010) 4692-4708 \n
0025 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
0026
0027 ## GEOMETRY SET-UP
0028
0029 The geometry is a spherical nucleus surrounded by a spherical shell
0030 representing the cytoplasm. Nucleus radius and shell thickness can be selected
0031 from the provided macro file svalue.in, as well as materials
0032 (G4_WATER or G4_Galactic). The world is a sphere with radius 1e3 larger than
0033 the radius of the nucleus
0034
0035 Particles are shot randomly inside the cytoplasm.
0036
0037 Particle type and energy can be controlled by the
0038 svalue.in macro file.
0039
0040 The PrimaryGeneratorAction class is adapted (G4 state dependent)
0041 in order to enable generic physics list usage
0042 (empty modular physics list).
0043
0044 An alternative MyPrimaryGeneratorActionFromFile class is provided as an example
0045 for reading input data from a file in MT mode for the generation of primaries.
0046 The MyFileReader class is provided as well. They are documented in:
0047 https://twiki.cern.ch/twiki/bin/view/Geant4/QuickMigrationGuideForGeant4V10
0048
0049 ## SET-UP
0050
0051 Make sure G4LEDATA points to the low energy electromagnetic data files.
0052
0053 Set the variable MYFILE as 1 in MyFile.hh if you wish to use a spectrum file
0054 of incident energies. By default, this variable is not defined. The file name and
0055 number of lines to read can be specified in MyFile.cc. A spectrum.txt file is provided
0056 as example.
0057
0058 The code can be compiled with cmake.
0059
0060 It works in MT mode.
0061
0062 ## HOW TO RUN THE EXAMPLE
0063
0064 In interactive mode, run:
0065
0066 ```
0067 ./svalue svalue.in
0068 ```
0069
0070 The svalue.in macro allows a full control of the simulation.
0071
0072 Two alternative macros, svalue-iodine125.in and svalue-iodine131.in
0073 are provided for the simulation of radioactive sources.
0074
0075 The svalue-spectrum.in macro shows how to shoot particles
0076 from the spectrum.txt file of energies (unit: eV), which has been created
0077 using the spectrum.C sample ROOT macro.
0078
0079 ## PHYSICS
0080
0081 You can select Geant4-DNA physics constructor in svalue.in.
0082
0083 A tracking cut can be applied if requested.
0084
0085 ## SIMULATION OUTPUT AND RESULT ANALYSIS
0086
0087 The output results consist in a text file (s.txt), containing :
0088 - the radius of the nucleus (in nm)
0089 - the thickness of the cytoplasm (in nm)
0090 - the energy of incident particles (in eV)
0091 - the S value for the cytoplasm (in Gy/Bq.s)
0092 - the rms on S value for the cytoplasm (in Gy/Bq.s)
0093 - the S value for the nucleus (in Gy/Bq.s)
0094 - the rms on S value for the nucleus (in Gy/Bq.s)
0095
0096 One can use the plot.C ROOT macro file to display results.
0097
0098 Note: rms values correspond to standard deviation.