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1 -------------------------------------------------------------------
2
3 =========================================================
4 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
5 =========================================================
6
7 Chem4
8 -------
9
10 CORRESPONDING AUTHORS
11 P. Piersimoni (a), M. Karamitros (b)
12 (a) pierluigi.piersimoni _ gmail _ com
13 (b) matkara _ gmail _ com
14
15 This example is provided by the Geant4-DNA collaboration.
16 (http://geant4-dna.org)
17
18 Any report or published results obtained using the Geant4-DNA software shall
19 cite the following Geant4-DNA collaboration publications:
20 Phys. Med. 31 (2015) 861-874
21 Med. Phys. 37 (2010) 4692-4708
22
23 The example shows how to activate chemistry code and score the radiochemical yield G
24 defined as
25 (Number of species X) / (100 eV of deposited energy).
26 in a range of deposited energy [X;Y] chosen by the user.
27
28 1 - GEOMETRY DEFINITION
29
30 The world volume is a simple box which represents a 'pseudo infinite'
31 homogeneous medium.
32
33 Two parameters define the geometry :
34 - the material of the box -- for Geant4-DNA it has to be water.
35 - the full size of the box.
36
37 The default geometry is constructed in DetectorConstruction class.
38
39 2 - PHYSICS LIST
40
41 PhysicsList is Geant4 modular physics list using G4EmDNAPhysics &
42 G4EmDNAChemistry constructors.
43 It will later be updated to use the G4EmDNAModelActivator constructor
44
45 3 - CHEMISTRY MODEL AND CHEMICAL REACTION LIST
46
47 ## UI species are defined by format :
48 username [ molecule | charge | D(m2/s) | Radius(nm) ]
49 where : *username* is decided by users, *molecule* is used by Geant4,
50 *D* is diffusion constant, *Radius* is reaction radius.
51 Spaces between characters are needed.
52
53 ## UI reactions are defined by format :
54 /chem/reaction/add H + H -> H2 | Fix | 1.2e10 | 0
55 where : *H* is username, *1.2e10* is reaction rate, *0* is reaction type.
56 Spaces between characters are needed.
57
58 (parameters can be found in Prog. Nucl. Sci. Tec. 2 (2011))
59
60 4 - ACTION INITALIZATION
61
62 The class ActionInitialization instantiates and registers
63 to Geant4 kernel all user action classes.
64
65 While in sequential mode the action classes are instantiated just once,
66 via invoking the method:
67 ActionInitialization::Build()
68 in multi-threading mode the same method is invoked for each thread worker
69 and so all user action classes are defined thread-local.
70
71 A run action class is instantiated both thread-local
72 and global that's why its instance is created also in the method:
73 ActionInitialization::BuildForMaster()
74 which is invoked only in multi-threading mode.
75
76 5 - AN EVENT: THE PRIMARY GENERATOR
77
78 The primary kinematic consists of a single particle starting at the center
79 of the box. The type of the particle and its energy are set in the
80 PrimaryGeneratorAction class, and can be changed via the G4 build-in
81 commands of G4ParticleGun class.
82 The chemistry module is triggered in the StackingAction class when all
83 physical tracks have been processed.
84
85 6 - DETECTOR RESPONSE: Scorers
86
87 6.1 - Species scorer
88
89 Scorers are defined in DetectorConstruction::ConstructSDandField(). There is
90 one G4MultiFunctionalDetector object which computes the energy deposition and
91 the number of species along time in order to extract
92 the radiochemical yields:
93 (Number of species X) / (100 eV of deposited energy).
94
95 Run::RecordEvent(), called at end of event, collects informations
96 event per event from the hits collections, and accumulates statistic for
97 RunAction::EndOfRunAction().
98
99 In multi-threading mode the statistics accumulated per workers is merged
100 to the master in Run::Merge().
101 The information about all the molecular species is scored in a ROOT
102 ntuple file Species.root. The root macro program PlotNtuple.C can be used to
103 plot the G values vs time, for each species.
104
105 6.2 - Primary killer
106
107 The G-values are computing for a range of deposited energy.
108 We are in an infinite volume. Therefore the energy lost by the
109 primary equals the deposited energy since all secondary particles
110 will finally slow down to the thermal energy.
111 The primary is killed once it has deposited more energy than a
112 minimum threshold.
113
114 **IMPORTANT**: However, when the primary particle looses more energy
115 in few interaction steps than the maximum allowed thresold,
116 the event is disregarded (=aborted).
117
118 These two macro commands can be used to control the energy loss by
119 the primary:
120
121 /primaryKiller/eLossMin 1 keV
122 # after 1 keV of energy loss by the primary particle, the primary is killed
123
124 /primaryKiller/eLossMax 2 keV
125 # if the primary particle losses more than 2 keV, the event is aborted
126
127 The G-values are then computed for a deposited energy in the range [1 keV;2 keV].
128
129 Note that if the upper boundary of the energy lost by the primary is
130 not set, the chemistry may take a lot of time to compute.
131 This set of macros is embedded in the PrimaryKiller class.
132 The species scorer must check whether the event was aborted before taking it or not into
133 account for the computation of the results.
134
135 7 - STACKING ACTION
136
137 StackingAction::NewStage is called when a stack of tracks has been processed
138 (for more details, look at the Geant4 documentation).
139 A verification on whether physical tracks remain to be processed is done.
140 If no tracks remain to be processed, the chemical module is then triggered.
141
142 8 - VISUALISATION
143
144 The visualization manager is set via the G4VisExecutive class
145 in the main() function in chem4.cc.
146 The initialisation of the drawing is done via a set of /vis/ commands
147 in the macro vis.mac. To activate the visualization mode run:
148 ./chem4 -vis
149
150 9 - OUTPUT
151
152 Physics initialization and the defined reaction table are printed.
153 G4Scheduler processes the chemical stage time step after time step.
154 Chemical reactions are printed.
155 The molecular reaction as a function of the elapsed time can be displayed
156 setting the macro command /scheduler/verbose 1
157
158 10 - RELEVANT MACRO COMMANDS
159 /primaryKiller/eLossMin 1 keV # after 1 keV of energy loss by the primary particle, the primary is killed
160 /primaryKiller/eLossMax 2 keV # if the primary particle losses more than 2 keV, the event is aborted
161 /scheduler/verbose 1 # set the verbose level of the G4Scheduler class (time steps, reactions ...)
162 /scheduler/endTime 1 microsecond # set the time at which the simulation stops
163 /scheduler/whyDoYouStop # for advanced users: print information at the end of the chemical stage to know why the simulation has stopped
164
165 11 - PLOT
166 The information about all the molecular species is scored in a ROOT
167 ntuple file Species.root during the run of chem4.
168 The ROOT program plotG can be used to plot the G values vs time,
169 for each species. It must be launched after
170 chem4 has run. When "plotG" is executed, select the root file output by the
171 chem4 application.
172 You can also execute plotG as:
173 .plot/plotG Species.root
174 where Species.root is the file output by the chem4 application.
175
176 12 - OTHER INFORMATION
177 I have access to a track. How do I access to its molecular information?
178 #include "G4Molecule.hh"
179 G4Track* thisIsMytrack = ...
180 G4Molecule* thisIsMyMolecule = GetMolecule(thisIsMyTrack);
181 If the pointer thisIsMyMolecule is null, then this is NOT a chemical species
182
183 How do I get the molecule's name?
184 G4Molecule* thisIsMyMolecule = ...
185 const G4String& moleculeName = thisIsMyMolecule->GetName();
186
187 How can I display the reaction information?
188 - Use this macro command: /scheduler/verbose 1
189
190 How can I display the step by step information?
191 1. Add ITTrackingInteraction to the G4Scheduler singleton (cf. chem3)
192 2. Use /chem/tracking/verbose 1
193
194 13 - HOW TO START ?
195
196 To run the example in batch mode:
197 ./chem4 -mac beam.in
198 or
199 ./chem4
200 then the macro beam.in is processed by default
201
202 In interactive mode, run:
203 ./chem4 -gui
204 or
205 ./chem4 -gui gui.mac
