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1 $Id: $
2 -------------------------------------------------------------------
3
4 =========================================================
5 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
6 =========================================================
7
8 Chem6
9 -------
10
11 CORRESPONDING AUTHORS
12 W. G. Shin (a), S. Incerti (b)
13 (a) ukguen _ gmail _ com
14 (b) incerti _ cenbg _ in2p3 _ fr
15
16 This example is provided by the Geant4-DNA collaboration.
17 (http://geant4-dna.org)
18
19 Any report or published results obtained using the Geant4-DNA software shall
20 cite the following Geant4-DNA collaboration publications:
21
22
23 J. Appl. Phys. 125 (2019) 104301
24 Med. Phys. 45 (2018) e722-e739
25 Phys. Med. 31 (2015) 861-874
26 Med. Phys. 37 (2010) 4692-4708
27 Int. J. Model. Simul. Sci . Comput. 1 (2010) 157-178
28
29 0 - INTRODUCTION
30 Based on chem4 and chem5 examples, this example provides scoring of the
31 radiochemical yield G defined as
32 (Number of species X) / (100 eV of deposited energy).
33 as a function of time and LET.
34 The example uses the IRT approach by default.
35
36 The details are described in the following paper:
37 J. Appl. Phys. 125 (2019) 104301
38
39 1 - GEOMETRY DEFINITION
40
41 The world volume is a simple water box which represents a 'pseudo infinite'
42 homogeneous medium.
43
44 The default geometry is constructed in DetectorConstruction class.
45
46 The size of detector can be controlled by PrimaryKiller class (see section 5.2).
47
48 2 - PHYSICS LIST
49
50 PhysicsList is Geant4 modular physics list using:
51
52 G4EmDNAPhysics_option2 constructor
53 - the accelerated physics constructor based on G4EmDNAPhysics constructor.
54
55 G4EmDNAChemistry_option3 constructor.
56 - the chemistry constructor is based on the pre-chemical stage of PARTRAC
57 and chemical parameters of RITRACKS.
58 - this chemistry constructor uses independent reaction time method as a
59 default.
60
61 3 - CHEMISTRY MODEL AND CHEMICAL REACTION LIST
62
63 ## UI species are defined by format :
64 username [ molecule | charge | D(m2/s) | Radius(nm) ]
65 where : *username* is decided by users, *molecule* is used by Geant4,
66 *D* is diffusion constant, *Radius* is reaction radius.
67 Spaces between characters are needed.
68
69 ## UI reactions are defined by format :
70 /chem/reaction/add H + H -> H2 | Fix | 1.2e10 | 0
71 where : *H* is username, *1.2e10* is reaction rate, *0* is reaction type.
72 Spaces between characters are needed.
73
74 ## UI time step model is defined only for: Step-by-Step (SBS),
75 independent reaction time (IRT) or synchronized IRT (IRT_syn).
76 *Note* : SBS is supposed for totally diffusion-controlled (TDC) reaction
77 only then please set reaction type 0 if use this model.
78 Only G4EmDNAChemistry_option3 can change time step model
79
80 (parameters can be found in Med. Phys. 48 (2021) 890-901
81 and Med. Phys. 47 (2020) 5919-5930)
82
83 4 - ACTION INITALIZATION
84
85 The class ActionInitialization instantiates and registers
86 to Geant4 kernel all user action classes.
87
88 While in sequential mode the action classes are instantiated just once,
89 via invoking the method:
90 ActionInitialization::Build()
91 In multi-threading mode the same method is invoked for each thread worker
92 and so all user action classes are defined thread-local.
93
94 A run action class is instantiated both thread-local
95 and global that's why its instance is created also in the method:
96 ActionInitialization::BuildForMaster()
97 which is invoked only in multi-threading mode.
98
99 5 - AN EVENT: THE PRIMARY GENERATOR
100
101 The primary kinematic consists of a single particle starting at the center
102 of the box. The type of the particle and its energy are set in the
103 PrimaryGeneratorAction class, and can be changed via the G4 build-in
104 commands of G4ParticleGun class.
105 The chemistry module is triggered in the StackingAction class when all
106 physical tracks have been processed.
107
108 6 - DETECTOR RESPONSE: Scorers
109
110 6.1 - Species scorer
111
112 This scorer computes the energy deposition and the number of species along
113 time in order to extract the radiochemical yields as in chem4 example.
114
115 Run::RecordEvent(), called at end of event, collects informations
116 event per event from the hits collections, and accumulates statistics for
117 RunAction::EndOfRunAction().
118
119 In multi-threading mode the statistics accumulated per worker is merged
120 to the master in Run::Merge().
121
122 These two macro commands can be used to control the scoring time:
123
124 /scorer/species/addTimeToRecord 1 ps
125 # user can select time bin to score G values.
126
127 /scorer/species/nOfTimeBins
128 # or user can automatically select time bin logarithmically.
129
130 The information about all the molecular species is scored in a ROOT
131 ntuple file Species(runID).root.
132 e.g.) Species0.root Species1.root ...
133
134 G values at the last time bin are scored in a text file Species.txt in order to
135 obtain G versus LET results.
136 The G versus LET results are accumulated all along, thus, user should remove Species.txt
137 file directly in order to initialize the results.
138
139 6.2 - Primary killer
140
141 The G-values are computed for a range of deposited energy.
142 We are in an infinite volume. Therefore the energy lost by the
143 primary equals the deposited energy since all secondary particles
144 will finally slow down to the thermal energy.
145 The primary is killed once it has deposited more energy than a
146 minimum threshold.
147
148 **IMPORTANT**: However, when the primary particle loses more energy
149 in few interaction steps than the maximum allowed threshold,
150 the event is disregarded (=aborted).
151
152 These two macro commands can be used to control the energy loss by
153 the primary:
154
155 /primaryKiller/eLossMin 1 keV
156 # after 1 keV of energy loss by the primary particle, the primary is killed
157
158 /primaryKiller/eLossMax 2 keV
159 # if the primary particle losses more than 2 keV, the event is aborted
160
161 The G-values are then computed for a deposited energy in the range [1 keV;2 keV].
162
163 Note that if the upper boundary of the energy lost by the primary is
164 not set, the chemistry may take a lot of time to compute.
165 This set of commands is embedded in the PrimaryKiller class.
166 The species scorer must check whether the event was aborted before taking
167 it or not into account for the computation of the results.
168
169 The size of detector can be controlled by this class using user macro command:
170
171 /primaryKiller/setSize 5 5 5 um
172 # kills the particles (primary and secondary) outside of the virtual volume
173
174 6.3. - LET scorer
175
176 In order to obtain G versus LET results, LET values are simultaneously calculated
177 during the simulation in ScorerLET class.
178
179 A macro command can be used to control the LET scorer:
180
181 /scorer/LET/cutoff
182 # selects cut-off energy for restricted LET.
183
184 7 - TIMESTEP ACTION
185
186 The user defined time steps can be given by G4UserTimeStepAction::AddTimeStep() method.
187 This method is not recommended for IRT method.
188
189 These two method are called before and after every time steps:
190
191 TimeStepAction::UserPreTimeStepAction()
192 TimeStepAction::UserPostTimeStepAction()
193
194 This method is called when a chemical reaction is occurred:
195
196 TimeStepAction::UserReactionAction(const G4Track&, const G4Track&, const std::vector<G4Track*>*)
197 In order to access to molecular information,
198 #include "G4Molecule.hh"
199 G4Molecule* thisIsMyMolecule = GetMolecule(thisIsMyTrack);
200 const G4String& moleculeName = thisIsMyMolecule->GetName();
201
202 8 - STACKING ACTION
203
204 StackingAction::NewStage is called when a stack of tracks has been processed
205 (for more details, look at the Geant4 documentation).
206 A verification on whether physical tracks remain to be processed is done.
207 If no tracks remain to be processed, the chemical module is then triggered.
208
209 9 - OUTPUT
210
211 Physics initialization and the defined reaction table are printed.
212 G4Scheduler processes the chemical stage time step after time step.
213 Chemical reactions are printed.
214 The molecular reaction as a function of the elapsed time can be displayed
215 setting the macro command /scheduler/verbose 1
216
217 10 - RELEVANT MACRO FILES
218
219 Two user macro files can be used:
220
221 ./chem6 beam.in
222 # electron simulations w primary killer method.
223
224 ./chem6 beam_HCP.in
225 # protons and alphas are generated at the edge of a 5x5x5 um3 water phantom.
226
227 11 - PLOT
228
229 Two root macros can be used:
230
231 root plotG_time.C
232 # plot G values as a function of time according to the molecular species by importing Species0.root.
233 # The function (plotG_time()) should have the same name as the file without file extension (plotG_time).
234
235 root plotG_LET.C
236 # plot G values as a function of LET according to the molecular species by importing Species.txt.
