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1
2 =========================================================
3 Geant4 - an Object-Oriented Toolkit for Simulation in HEP
4 =========================================================
5
6 Extended Example saxs
7 --------------------
8
9 The example saxs implements the typical setup of a Small Angle X-ray
10 Scattering (SAXS) experiment. It is meant to illustrate the
11 usage of molecular interference (MI) of Rayleigh (coherent) scattering
12 of photons inside the matter, which is implemented in the
13 G4PenelopeRayleighModelMI model.
14
15 1- GEOMETRY
16
17 The setup consists of a phantom/sample under investigation, slits
18 to collimate the photon beam and a shielded detector to collect
19 the photons scattered by the phantom (see SAXSDetectorConstruction).
20
21 The geometry is scalable through the interactive commands defined
22 in the SAXSDetectorConstructionMessenger class. All the significant
23 quantities, such as the setup (scattering) rotation angle, the position
24 and size of all the volumes, as well as the phantom material can be
25 set via macro commands.
26
27 Two macro files come with this example: saxs.in and saxs_slits.in.
28
29 In the saxs.in macro, the phantom is a cylinder with a diameter and
30 a height of 10 mm made of a mixture of 80% fat and 20% water.
31 In general, if the argument of /det/setPhantomMaterial command is 2,
32 as in this case, the material is a biological tissue ("MedMat")
33 defined as a mixture of fat, water, collagen and hydroxyapatite.
34 The weight fraction of the mixture components can be set through commands
35 /det/setComp0, /det/setComp1, /det/setComp2, /det/setComp3, respectively.
36 The tissue form factor (including MI) is automatically calculated as a
37 weighed sum of the form factors of the basis components.
38 In this case, no slits are foreseen and the sensitive detector
39 positioned 400 mm downstream of the phantom collects all the photons
40 transmitted and scattered by the phantom, which is irradiated
41 by a pencil beam with an energy of 20 keV.
42
43 In the saxs_slits.in macro, the phantom is again a cylinder with a
44 diameter and a height of 10 mm. The phantom is made of a custom
45 material ("CustomMat") whose density and composition is set through
46 /det/setCustomMatDensity and /det/setCustomMatHmassfract,
47 /det/setCustomMatNmassfract, /det/setCustomMatOmassfract commands,
48 respectively. In general, a custom material can be defined by
49 specifying the mass fraction of H, C, N, O, Na, P, S, Cl, K, and Ca via
50 commands analogous to those mentioned above. In this case, the material
51 composition corresponds to that of ammonium nitrate (NH4NO3).
52 For a custom material, the user can provide the path of the file with
53 the material form factor (with MI) through the /det/SetCustomMatFF
54 command. As an example, the file myFF.dat contains the form factor of
55 NH4NO3 measured by Harding in 1999.
56 In this case the slits upstream and downstream the phantom
57 are present. This setup is suitable for both monochromatic and
58 polychromatic beams. To speed-up the simulation, a monochromatic
59 photon beam was chosen, but a polychromatic beam can be easily defined.
60
61 2- PHYSICS
62
63 In this example, only electromagnetic processes and decays are considered.
64 They are defined in a custom physics list that allows the user to
65 choose among various EM PhysicsList constructors. In particular,
66 by choosing G4EmPenelopePhysicsMI and setting fUseMIFlag as true,
67 it is possible to enable the molecular interference effects. This
68 is the default configuration.
69
70 3- ACTION INITALIZATION
71
72 SAXSActionInitialization class instantiates and registers to
73 Geant4 kernel all user action classes. While in sequential mode
74 the action classes are instatiated just once, by invoking the
75 method: SAXSActionInitialization::Build(),
76 in multi-threading mode the same method is invoked for each thread
77 worker and so all user action classes are defined thread-local.
78
79 A run action class is instantiated both thread-local and global.
80 That's why its instance is created also in the method
81 SAXSActionInitialization::BuildForMaster(), which is
82 invoked only in multi-threading mode.
83
84 4- PRIMARY GENERATOR
85
86 The primary generator action class employs the G4GeneralParticleSource (GPS)
87 generator. The primary beam has to be defined via the G4 built-in
88 commands of the G4GeneralParticleSource in a input macro file.
89 In particular, a photon beam directed toward the phantom must be defined
90 to test the MI effects. The X-ray beam can be monochromatic or
91 polychromatic, parallel or divergent.
92
93 5- EVENT AND DETECTOR RESPONSE
94
95 An event consists of the generation of a single particle which is
96 transported through the phantom and then to the sensitive detector.
97
98 The interactions of the photons inside the phantom, and in particular,
99 the scattering events, are scored in a dedicated ntuple through the
100 SAXSSteppingAction class.
101
102 The hits of the particles on the sensitive detector positioned
103 downstream of the phantom (SAXSSensitiveDetectorHit) are recorded
104 in a dedicated ntuple through the SAXSSensitiveDetector class.
105
106 6- ANALYSIS:
107
108 The analysis tools are used to accumulate statistics.
109 ntuple are created in SAXSRunAction::SAXSRunAction()
110 constructor for the following quantities:
111
112 Ntuple1 (part) - Particles impinging on the Sensitive Detector (SD):
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 before hitting the SD
120 - event number of the hits
121
122 Ntuple2 (scatt) - Interactions of photons inside the phantom:
123 - ID of the process occurred
124 (0-> transportation, 1->Rayleigh, 2->Compton, 3->Photoelectic)
125 - initial energy of the particles
126 - scattering angle
127
128 The ntuples are saved in the output file in the Root format.
129
130 When running in multi-threading mode, the ntuples accumulated
131 on threads are automatically merged in a single output file.
132
133 The default output format is root. Two root scripts come with
134 this example to analyze the output file: scattAnalysis.C and
135 ADXRD.C. The first can be used to analyze the scatt ntuple, while
136 the second can be used for part ntuple.
137
138 7- HOW TO RUN
139
140 - Execute saxs in the 'interactive mode' with visualization:
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 (test.in is a simple macro where the
150 primary beam is defined through the usual GPS commands):
151 Idle> /control/execute test.in
152 Idle> /run/beamOn 10
153 ....
154 Idle> exit
155
156 - Execute saxs in the 'batch' mode from macro files
157 (without visualization)
158 % ./saxs saxs.in [Ncores]
159 % ./saxs saxs_slits.in [Ncores]
160 Ncores (optional argument) is the number of threads the user wants to use in
161 MT mode.
162
163
164 The following paragraphs are common to all basic examples
165
166 A- VISUALISATION
167
168 The visualization manager is set via the G4VisExecutive class
169 in the main() function in saxs.cc.
170 The initialisation of the drawing is done via a set of /vis/ commands
171 in the macro vis.mac. This macro is automatically read from
172 the main function when the example is used in interactive running mode.
173
174 By default, vis.mac opens an OpenGL viewer (/vis/open OGL).
175 The user can change the initial viewer by commenting out this line
176 and instead uncommenting one of the other /vis/open statements, such as
177 HepRepFile or DAWNFILE (which produce files that can be viewed with the
178 HepRApp and DAWN viewers, respectively). Note that one can always
179 open new viewers at any time from the command line. For example, if
180 you already have a view in, say, an OpenGL window with a name
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-modifications
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 available
191 (since they require no external libraries), but the OGL driver requires
192 that the Geant4 libraries have been built with the OpenGL option.
193
194 vis.mac has additional commands that demonstrate additional functionality
195 of the vis system, such as displaying text, axes, scales, date, logo and
196 shows how to change viewpoint and style.
197 To see even more commands use help or ls or browse the available UI commands
198 in the Application Developers Guide.
199
200 For more information on visualization, including information on how to
201 install and run DAWN, OpenGL and HepRApp, see the visualization tutorials,
202 for example,
203 http://geant4.slac.stanford.edu/Presentations/vis/G4[VIS]Tutorial/G4[VIS]Tutorial.html
204 (where [VIS] can be replaced by DAWN, OpenGL and HepRApp)
205
206 The tracks are automatically drawn at the end of each event, accumulated
207 for all events and erased at the beginning of the next run.
208
209 B- USER INTERFACES
210
211 The user command interface is set via the G4UIExecutive class
212 in the main() function in saxs.cc
213 The selection of the user command interface is then done automatically
214 according to the Geant4 configuration or it can be done explicitly via
215 the third argument of the G4UIExecutive constructor (see exampleB4a.cc).
216
217
