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1 -------------------------------------------------------------------
2
3 =========================================================
4 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
5 =========================================================
6
7 UHDR (Ultra High Dose Rate)
8 --------------------------
9 This example is provided by the Geant4-DNA collaboration
10 (http://geant4-dna.org).
11
12 Any report or published results obtained using the Geant4-DNA software
13 shall cite the following Geant4-DNA collaboration publications:
14 Med. Phys. 45 (2018) e722-e739
15 Phys. Med. 31 (2015) 861-874
16 Med. Phys. 37 (2010) 4692-4708
17 Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
18
19 0 - INTRODUCTION
20
21 This example shows how to activate the mesoscopic model in chemistry and
22 combine with SBS model (Tran et al.,Int. J. Mol. Sci. 22 (2021) 6023).
23 It allows to simulate chemical reactions longtime (beyond 1 us) of post-irradiation.
24
25 To run the example:
26 mkdir UHDR-build
27 cd UHDR-build
28 cmake ../pathToExamples/UHDR
29 make
30
31 To visualize (only for physical stage)
32 ./UHDR
33
34 In batch mode, the macro beam.in can be used as follows:
35 ./UHDR beam.in
36 or
37 ./UHDR beam.in 123
38 # 123 is the user's seed number
39
40 1 - GEOMETRY DEFINITION
41
42 The world volume is a simple water box 3.2 x 3.2 x 3.2 um3 for 0.01 Gy of cut-off
43 absorbed dose and 1.6 x 1.6 x 1.6 um3 for 1 Gy. This example is limited to these geometries.
44 The choice of simulation volume is a compromise between a sufficient number of chemical species a
45 nd an achievable computation time.
46
47 Two parameters define the geometry :
48 - the material of the box for the physical stage is water.
49 - for the chemistry stage, the concentration of scavengers in [mole/l]
50 is added. This concentration is supposed to have no effect on the
51 physical stage. pH is defined as scavengers of H3O^1, OH^-1.
52 In this example, we consider that chemical molecules diffuse and react in a
53 bounded volume (that is, limited by geometrical boundaries) which is also
54 the irradiated water box volume of the physical stage.
55 The bouncing of chemical molecules on the volume border is applied
56 for both SBS and mesoscopic models.
57 The bouncing is not applied for physical stage.
58
59 2 - PHYSICS LIST
60
61 PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option2
62 and EmDNAChemistry constructors (the chemistry constructor uses the
63 Step-by-step method).
64
65 3 - CHEMISTRY WORLD
66
67 This object is controlled by DetectorContruction. It defines the chemistry volume,
68 scavengers and pH of water.
69
70 4 - AN EVENT: THE PRIMARY GENERATOR
71
72 This example utilizes the G4SingleParticleSource.
73 Each event consists of multiple incident particles.
74 A large number has been chosen to ensure that the stack remains non-empty until the desired
75 energy deposition is achieved (which is then converted to a cutoff dose).
76 With each /run/beamOn command, a group of particles is emitted. The cutoff dose
77 (dose threshold) determined by users.
78 The actual dose is calculated based on the real energy deposited in the volume.
79
80 5 - DETECTOR RESPONSE: Scorer
81
82 There is one G4MultiFunctionalDetector object which computes the
83 energy deposition and the number of species along time in order to
84 extract the G-value:
85 (Number of species X) / (100 eV of deposited energy).
86
87 These two macro commands can be used to control the scoring time:
88 /scorer/species/addTimeToRecord 1 ps
89 # user can select time bin to score G values.
90 /scorer/species/nOfTimeBins
91 # or user can automatically select time bin logarithmically.
92
93
94 6 - PULSE ACTION
95
96 This functionality is not available for this version.
97
98 7 - OUTPUT
99
100 G-value
101
102 8 - RELEVANT MACRO COMMANDS AND MACRO FILE
103
104 The user macro files are: beam.in (conventional), UHDR.in (Ultra High Dose Rate)
105
106 9 - REACTION BUILDER
107
108 Reaction lists are collected by builders for specific applications.
109 ChemNO2_NO3ScavengerBuilder is to build the reaction list with NO2-/NO3-.
110 ChemPureWaterBuilder is to build the reaction list with pH.
111 ChemOxygenWaterBuilder is to build the reaction list with ROS.
112 ChemFrickeReactionBuilder is to build the reaction list of Fricke Dosimeter.
113
114 10 - PLOT
115
116 The information about all the molecular species is scored in a ROOT
117 (https://root.cern) ntuple file Dose_xxx.root (xxx is seed number).
118 The ROOT program plot_time
119 can be used to plot the G values vs time for each species.
120
121 Execute plot_time as:
122
123 root plot_time.C
124
125
126 or print G values to scorer.txt
127
128 root plot_time.C > scorer.txt
129
130
131 The results show the molecular species (G values) as a function of
132 time (ns). Please correct the dose in the TTree *tree = (TTree *) dir->Get("0.010000");
133
134 11 - Periodic Boundary Condition (PBC)
135
136 The Periodic Boundary Condition is implemented based on https://github.com/amentumspace/g4pbc
137 to calculate microdosimetry. The periodic boundary condition (PBC) is used to simulate the
138 behavior of secondary electrons during the physical stage.
139 When an electron exits an edge of a cubic volume, it re-enters from the opposite edge.
140 The PBC helps reduce the edge effects in dose calculations for micrometer-sized volumes
141
142
143 The PBC requires a maximum dose (xxx) to abort the event. This to avoid the high energy of
144 secondary electrons deposit a large energy inside the micro volume.
145
146 /scorer/Dose/abortedDose xxx Gy
147
148 Use the following command to activate or deactivate PBC.
149
150 /UHDR/Detector/PBC true
151
152 Funding: FNS Synergia grant MAGIC-FNS CRSII5_186369.
153 Contact: H. Tran (tran@lp2ib.in2p3.fr)
154 CNRS, lp2i, UMR 5797, Université de Bordeaux, F-33170 Gradignan, France
