| Geant4 Cross Reference |
1
2 ==========================================
3 Geant4 - an Object-Oriented Toolkit for Si
4 ==========================================
5
6 Extended Example saxs
7 --------------------
8
9 The example saxs implements the typical setu
10 Scattering (SAXS) experiment. It is meant to
11 usage of molecular interference (MI) of Rayl
12 of photons inside the matter, which is imple
13 G4PenelopeRayleighModelMI model.
14
15 1- GEOMETRY
16
17 The setup consists of a phantom/sample unde
18 to collimate the photon beam and a shielded
19 the photons scattered by the phantom (see S
20
21 The geometry is scalable through the intera
22 in the SAXSDetectorConstructionMessenger cl
23 quantities, such as the setup (scattering)
24 and size of all the volumes, as well as the
25 set via macro commands.
26
27 Two macro files come with this example: sax
28
29 In the saxs.in macro, the phantom is a cyli
30 a height of 10 mm made of a mixture of 80%
31 In general, if the argument of /det/setPhan
32 as in this case, the material is a biologic
33 defined as a mixture of fat, water, collage
34 The weight fraction of the mixture componen
35 /det/setComp0, /det/setComp1, /det/setComp2
36 The tissue form factor (including MI) is au
37 weighed sum of the form factors of the basi
38 In this case, no slits are foreseen and the
39 positioned 400 mm downstream of the phantom
40 transmitted and scattered by the phantom, w
41 by a pencil beam with an energy of 20 keV.
42
43 In the saxs_slits.in macro, the phantom is
44 diameter and a height of 10 mm. The phantom
45 material ("CustomMat") whose density and co
46 /det/setCustomMatDensity and /det/setCustom
47 /det/setCustomMatNmassfract, /det/setCustom
48 respectively. In general, a custom material
49 specifying the mass fraction of H, C, N, O,
50 commands analogous to those mentioned above
51 composition corresponds to that of ammonium
52 For a custom material, the user can provide
53 the material form factor (with MI) through
54 command. As an example, the file myFF.dat c
55 NH4NO3 measured by Harding in 1999.
56 In this case the slits upstream and downstr
57 are present. This setup is suitable for bot
58 polychromatic beams. To speed-up the simula
59 photon beam was chosen, but a polychromatic
60
61 2- PHYSICS
62
63 In this example, only electromagnetic proce
64 They are defined in a custom physics list t
65 choose among various EM PhysicsList constru
66 by choosing G4EmPenelopePhysicsMI and setti
67 it is possible to enable the molecular inte
68 is the default configuration.
69
70 3- ACTION INITALIZATION
71
72 SAXSActionInitialization class instantiates
73 Geant4 kernel all user action classes. Whil
74 the action classes are instatiated just onc
75 method: SAXSActionInitialization::Build(),
76 in multi-threading mode the same method is
77 worker and so all user action classes are d
78
79 A run action class is instantiated both thr
80 That's why its instance is created also in
81 SAXSActionInitialization::BuildForMaster(),
82 invoked only in multi-threading mode.
83
84 4- PRIMARY GENERATOR
85
86 The primary generator action class employs
87 generator. The primary beam has to be defin
88 commands of the G4GeneralParticleSource in
89 In particular, a photon beam directed towar
90 to test the MI effects. The X-ray beam can
91 polychromatic, parallel or divergent.
92
93 5- EVENT AND DETECTOR RESPONSE
94
95 An event consists of the generation of a si
96 transported through the phantom and then to
97
98 The interactions of the photons inside the
99 the scattering events, are scored in a dedi
100 SAXSSteppingAction class.
101
102 The hits of the particles on the sensitive
103 downstream of the phantom (SAXSSensitiveDet
104 in a dedicated ntuple through the SAXSSensi
105
106 6- ANALYSIS:
107
108 The analysis tools are used to accumulate s
109 ntuple are created in SAXSRunAction::SAXSRu
110 constructor for the following quantities:
111
112 Ntuple1 (part) - Particles impinging on the
113 - energy of the particles
114 - position of the hits
115 - momentum of the particles
116 - time of the hits
117 - type of impinging particles
118 - ID number of the impinging particles
119 - number of scattering events a primary had
120 - event number of the hits
121
122 Ntuple2 (scatt) - Interactions of photons in
123 - ID of the process occurred
124 (0-> transportation, 1->Rayleigh, 2->Com
125 - initial energy of the particles
126 - scattering angle
127
128 The ntuples are saved in the output file in
129
130 When running in multi-threading mode, the n
131 on threads are automatically merged in a si
132
133 The default output format is root. Two root
134 this example to analyze the output file: sc
135 ADXRD.C. The first can be used to analyze t
136 the second can be used for part ntuple.
137
138 7- HOW TO RUN
139
140 - Execute saxs in the 'interactive mode' w
141 % ./saxs
142 and type in the commands line by line:
143 Idle> /control/verbose 2
144 Idle> /tracking/verbose 1
145 Idle> ...
146 Idle> /run/beamOn 10
147 Idle> ...
148 Idle> exit
149 or it is possible to run a macro file (t
150 primary beam is defined through the usua
151 Idle> /control/execute test.in
152 Idle> /run/beamOn 10
153 ....
154 Idle> exit
155
156 - Execute saxs in the 'batch' mode from ma
157 (without visualization)
158 % ./saxs saxs.in [Ncores]
159 % ./saxs saxs_slits.in [Ncores]
160 Ncores (optional argument) is the number
161 MT mode.
162
163
164 The following paragraphs are common to all ba
165
166 A- VISUALISATION
167
168 The visualization manager is set via the G4
169 in the main() function in saxs.cc.
170 The initialisation of the drawing is done v
171 in the macro vis.mac. This macro is automat
172 the main function when the example is used
173
174 By default, vis.mac opens an OpenGL viewer
175 The user can change the initial viewer by c
176 and instead uncommenting one of the other /
177 HepRepFile or DAWNFILE (which produce files
178 HepRApp and DAWN viewers, respectively). N
179 open new viewers at any time from the comma
180 you already have a view in, say, an OpenGL
181 "viewer-0", then
182 /vis/open DAWNFILE
183 then to get the same view
184 /vis/viewer/copyView viewer-0
185 or to get the same view *plus* scene-modifi
186 /vis/viewer/set/all viewer-0
187 then to see the result
188 /vis/viewer/flush
189
190 The DAWNFILE, HepRepFile drivers are always
191 (since they require no external libraries),
192 that the Geant4 libraries have been built w
193
194 vis.mac has additional commands that demons
195 of the vis system, such as displaying text,
196 shows how to change viewpoint and style.
197 To see even more commands use help or ls or
198 in the Application Developers Guide.
199
200 For more information on visualization, incl
201 install and run DAWN, OpenGL and HepRApp, s
202 for example,
203 http://geant4.slac.stanford.edu/Presentatio
204 (where [VIS] can be replaced by DAWN, OpenG
205
206 The tracks are automatically drawn at the e
207 for all events and erased at the beginning
208
209 B- USER INTERFACES
210
211 The user command interface is set via the G
212 in the main() function in saxs.cc
213 The selection of the user command interface
214 according to the Geant4 configuration or it
215 the third argument of the G4UIExecutive con
216
217