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0002
0003 =========================================================
0004 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
0005 =========================================================
0006
0007 UHDR (Ultra High Dose Rate)
0008 --------------------------
0009 This example is provided by the Geant4-DNA collaboration
0010 (http://geant4-dna.org).
0011
0012 Any report or published results obtained using the Geant4-DNA software
0013 shall cite the following Geant4-DNA collaboration publications:
0014 Med. Phys. 45 (2018) e722-e739
0015 Phys. Med. 31 (2015) 861-874
0016 Med. Phys. 37 (2010) 4692-4708
0017 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
0018
0019 0 - INTRODUCTION
0020
0021 This example shows how to activate the mesoscopic model in chemistry and
0022 combine with SBS model (Tran et al.,Int. J. Mol. Sci. 22 (2021) 6023).
0023 It allows to simulate chemical reactions longtime (beyond 1 us) of post-irradiation.
0024
0025 To run the example:
0026 mkdir UHRD-build
0027 cd UHRD-build
0028 cmake ../pathToExamples/UHRD
0029 make
0030
0031 In batch mode, the macro beam.in can be used as follows:
0032 ./UHRD beam.in
0033 or
0034 ./UHRD beam.in 123
0035 # 123 is the user's seed number
0036
0037 1 - GEOMETRY DEFINITION
0038
0039 The world volume is a simple water box 3.2 x 3.2 x 3.2 um3 for 0.01 Gy of cut-off
0040 absorbed dose and 1.6 x 1.6 x 1.6 um3 for 1 Gy. This example is limited to these geometries.
0041 The choice of simulation volume is a compromise between a sufficient number of chemical species a
0042 nd an achievable computation time.
0043
0044 Two parameters define the geometry :
0045 - the material of the box for the physical stage is water.
0046 - for the chemistry stage, the concentration of scavengers in [mole/l]
0047 is added. This concentration is supposed to have no effect on the
0048 physical stage. pH is defined as scavengers of H3O^1, OH^-1.
0049 In this example, we consider that chemical molecules diffuse and react in a
0050 bounded volume (that is, limited by geometrical boundaries) which is also
0051 the irradiated water box volume of the physical stage.
0052 The bouncing of chemical molecules on the volume border is applied
0053 for both SBS and mesoscopic models.
0054 The bouncing is not applied for physical stage.
0055
0056 2 - PHYSICS LIST
0057
0058 PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option2
0059 and EmDNAChemistry constructors (the chemistry constructor uses the
0060 Step-by-step method).
0061
0062 3 - CHEMISTRY WORLD
0063
0064 This object is controlled by DetectorContruction. It defines the chemistry volume,
0065 scavengers and pH of water.
0066
0067 4 - AN EVENT: THE PRIMARY GENERATOR
0068
0069 This example utilizes the G4SingleParticleSource.
0070 Each event consists of multiple incident particles.
0071 A large number has been chosen to ensure that the stack remains non-empty until the desired
0072 energy deposition is achieved (which is then converted to a cutoff dose).
0073 With each /run/beamOn command, a group of particles is emitted. The cutoff dose
0074 (dose threshold) determined by users.
0075 The actual dose is calculated based on the real energy deposited in the volume.
0076
0077 5 - DETECTOR RESPONSE: Scorer
0078
0079 There is one G4MultiFunctionalDetector object which computes the
0080 energy deposition and the number of species along time in order to
0081 extract the G-value:
0082 (Number of species X) / (100 eV of deposited energy).
0083
0084 These two macro commands can be used to control the scoring time:
0085 /scorer/species/addTimeToRecord 1 ps
0086 # user can select time bin to score G values.
0087 /scorer/species/nOfTimeBins
0088 # or user can automatically select time bin logarithmically.
0089
0090
0091 6 - PULSE ACTION
0092
0093 This functionality is not available for this version.
0094
0095 7 - OUTPUT
0096
0097 G-value
0098
0099 8 - RELEVANT MACRO COMMANDS AND MACRO FILE
0100
0101 The user macro files are: beam.in (conventional), UHDR.in (Ultra High Dose Rate)
0102
0103 9 - REACTION BUILDER
0104
0105 Reaction lists are collected by builders for specific applications.
0106 ChemNO2_NO3ScavengerBuilder is to build the reaction list with NO2-/NO3-.
0107 ChemPureWaterBuilder is to build the reaction list with pH.
0108 ChemOxygenWaterBuilder is to build the reaction list with ROS.
0109 ChemFrickeReactionBuilder is to build the reaction list of Fricke Dosimeter.
0110
0111 10 - PLOT
0112
0113 The information about all the molecular species is scored in a ROOT
0114 (https://root.cern) ntuple file Dose_xxx.root (xxx is seed number).
0115 The ROOT program plot_time
0116 can be used to plot the G values vs time for each species.
0117
0118 Execute plot_time as:
0119 \verbatim
0120 root plot_time.C
0121 \endverbatim
0122
0123 or print G values to scorer.txt
0124 \verbatim
0125 root plot_time.C > scorer.txt
0126 \endverbatim
0127
0128 The results show the molecular species (G values) as a function of
0129 time (ns). Please correct the dose in the TTree *tree = (TTree *) dir->Get("0.010000");
0130
0131 11 - Periodic Boundary Condition (PBC)
0132
0133 The Periodic Boundary Condition is implemented based on https://github.com/amentumspace/g4pbc
0134 to calculate microdosimetry.
0135 This requires a maximum dose (xxx) to abort the event. This to avoid the high energy of
0136 secondary electrons deposit a large energy inside the micro volume.
0137
0138 /scorer/Dose/abortedDose xxx Gy
0139
0140 Use the following command to activate or deactivate PBC.
0141
0142 /UHDR/Detector/PBC true
0143
0144 Funding: FNS Synergia grant MAGIC-FNS CRSII5_186369.
0145 Contact: H. Tran (tran@lp2ib.in2p3.fr)
0146 CNRS, lp2i, UMR 5797, Université de Bordeaux, F-33170 Gradignan, France
