| Geant4 Cross Reference |
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4 Geant4 - an Object-Oriented Toolkit for S
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6
7 Chem5
8 -------
9
10 Jose Ramos-Mendez(a) and Bruce Faddegon
11 Department of Radiation Oncology,
12 University of California San Francisco.
13
14 (a) CORRESPONDING AUTHOR
15 joserm84 _ gmail _ com
16
17 This example is provided by the Geant4-DNA col
18 (http://geant4-dna.org)
19
20 Any report or published results obtained using
21 cite the following Geant4-DNA collaboration pu
22 Phys. Med. 31 (2015) 861-874
23 Med. Phys. 37 (2010) 4692-4708
24
25 Any report or published results obtained using
26 cite the following publication:
27 Phys. Med. Biol. 63(10) (2018) 105014-12pp
28
29 The example is a variation of chem4, it shows
30 chemistry code and score the radiochemical yie
31 G4EmDNAPhysics_option8 and G4EmDNAChemistry_op
32
33 1 - GEOMETRY DEFINITION
34
35 The world volume is a simple box which rep
36 homogeneous medium.
37
38 Two parameters define the geometry :
39 - the material of the box -- for Geant4-DN
40 - the full size of the box.
41
42 The default geometry is constructed in Det
43
44 2 - PHYSICS LIST
45
46 PhysicsList is Geant4 modular physics list
47 G4EmDNAChemistry_option1 constructors.
48
49 3 - ACTION INITALIZATION
50
51 The class ActionInitialization instantiate
52 to Geant4 kernel all user action classes.
53
54 While in sequential mode the action classe
55 via invoking the method:
56 ActionInitialization::Build()
57 in multi-threading mode the same method is
58 and so all user action classes are defined
59
60 A run action class is instantiated both th
61 and global that's why its instance is crea
62 ActionInitialization::BuildForMaster()
63 which is invoked only in multi-threading m
64
65 4 - AN EVENT: THE PRIMARY GENERATOR
66
67 The primary kinematic consists of a single
68 of the box. The type of the particle and i
69 PrimaryGeneratorAction class, and can be c
70 commands of G4ParticleGun class.
71 The chemistry module is triggered in the S
72 physical tracks have been processed.
73
74 5 - DETECTOR RESPONSE: Scorers
75
76 5.1 - Species scorer
77
78 Scorers are defined in DetectorConstructio
79 one G4MultiFunctionalDetector object which
80 the number of species along time in order
81 the radiochemical yields:
82 (Number of species X) / (100 eV of deposit
83
84 Run::RecordEvent(), called at end of event
85 event per event from the hits collections,
86 RunAction::EndOfRunAction().
87
88 In multi-threading mode the statistics acc
89 to the master in Run::Merge().
90
91 The information about G-value as a functio
92 molecular specie is scored in a ASCII form
93
94
95 5.2 - Primary killer
96
97 The G-values are computing for a range of
98 An infinite volume is assumed as geometric
99 primary particle equals the deposited ener
100
101 The primary is killed once it has deposite
102 minimum threshold.
103
104 **IMPORTANT**: However, when the primary p
105 in few interaction steps than the maximum
106 the event is disregarded (=aborted).
107
108 These two macro commands can be used to co
109 the primary:
110
111 /primaryKiller/eLossMin 10 keV
112 # after 10 keV of energy loss by the prima
113
114 /primaryKiller/eLossMax 10.1 keV
115 # if the primary particle losses more than
116
117 The G-values are then computed for a depos
118
119 Note that if the upper boundary of the ene
120 not set, the chemistry may take a lot of t
121 This set of macros is embedded in the Prim
122 The species scorer must check whether the
123 account for the computation of the results
124
125 6 - STACKING ACTION
126
127 StackingAction::NewStage is called when a
128 (for more details, look at the Geant4 doc
129 A verification on whether physical tracks
130 If no tracks remain to be processed, the
131
132 7 - VISUALISATION
133
134 The visualization manager is set via the G
135 in the main() function in chem5.cc.
136 The initialisation of the drawing is done
137 in the macro vis.mac. To activate the visu
138 ./chem5 -vis
139
140 8 - OUTPUT
141
142 Physics initialization and the defined rea
143 G4Scheduler processes the chemical stage t
144 Chemical reactions are printed.
145 The molecular reaction as a function of th
146 setting the macro command /scheduler/verbo
147
148 9 - RELEVANT MACRO COMMANDS
149 /primaryKiller/eLossMin 10 keV # after 10
150 /primaryKiller/eLossMax 10.1 keV # if the
151 /scheduler/verbose 1 # set the verbose lev
152 /scheduler/endTime 1 microsecond # set the
153 /scheduler/whyDoYouStop # for advanced use
154 #the chemical stag
155
156 10 - PLOT
157 The information about all the molecular sp
158 tuple, each value corresponding to the G-v
159 with a wide variety of plotting software.
160 Experimental data of G-values for solvated
161 from the literature is available in data s
162 in the header of each file. Further inform
163
164 A gnuplot script (plot.gp) file is provide
165
166 11 - HOW TO START ?
167
168 To run the example in batch mode:
169 ./chem5 -mac beam.in
170 or
171 ./chem5
172 then the macro beam.in is processed by def
173
174 In interactive mode, run:
175 ./chem5 -gui
176 or
177 ./chem5 -gui gui.mac