Gabriele Cosmo
265 lines
9.9 KiB
Markdown
265 lines
9.9 KiB
Markdown
\page Examplesaxs Example saxs
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\author Gianfranco Paternò - INFN and University Ferrara (Italy) \n
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paterno@fe.infn.it
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The example saxs implements the typical setup of a Small Angle X-ray
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Scattering (SAXS) experiment. It is meant to illustrate the
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usage of molecular interference (MI) of Rayleigh (coherent) scattering
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of photons inside the matter, which is implemented in the
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G4PenelopeRayleighModelMI model.
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## Geometry
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The setup consists of a phantom/sample under investigation, slits
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to collimate the photon beam and a shielded detector to collect
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the photons scattered by the phantom (see SAXSDetectorConstruction).
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The geometry is scalable through the interactive commands defined
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in the SAXSDetectorConstructionMessenger class. All the significant
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quantities, such as the setup (scattering) rotation angle, the position
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and size of all the volumes, as well as the phantom material can be
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set via macro commands.
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Two macro files come with this example: saxs.in and saxs_slits.in.
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-# In the saxs.in macro, the phantom is a cylinder with a diameter and
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a height of 10 mm made of a mixture of 80% fat and 20% water.
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In general, if the argument of <code>/det/setPhantomMaterial</code> command is 2,
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as in this case, the material is a biological tissue ("MedMat")
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defined as a mixture of fat, water, collagen and hydroxyapatite.
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The weight fraction of the mixture components can be set through commands
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```
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/det/setComp0
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/det/setComp1
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/det/setComp2
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/det/setComp3
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```
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respectively.
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The tissue form factor (including MI) is automatically calculated as a
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weighed sum of the form factors of the basis components.
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In this case, no slits are foreseen and the sensitive detector
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positioned 400 mm downstream of the phantom collects all the photons
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transmitted and scattered by the phantom, which is irradiated
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by a pencil beam with an energy of 20 keV.
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-# In the saxs_slits.in macro, the phantom is again a cylinder with a
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diameter and a height of 10 mm. The phantom is made of a custom
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material ("CustomMat") whose density and composition is set through
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```
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/det/setCustomMatDensity
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/det/setCustomMatHmassfract,
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/det/setCustomMatNmassfract
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/det/setCustomMatOmassfract
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```
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commands. In general, a custom material can be defined by
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specifying the mass fraction of H, C, N, O, Na, P, S, Cl, K, and Ca via
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commands analogous to those mentioned above. In this case, the material
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composition corresponds to that of ammonium nitrate
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(NH<sub>4</sub>NO<sub>3</sub>).
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For a custom material, the user can provide the path of the file with
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the material form factor (with MI) through the
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```
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/det/SetCustomMatFF
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```
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command. As an example, the file myFF.dat contains the form factor of
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NH<sub>4</sub>NO<sub>3</sub> measured by Harding in 1999.
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In this case the slits upstream and downstream the phantom
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are present. This setup is suitable for both monochromatic and
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polychromatic beams. To speed-up the simulation, a monochromatic
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photon beam was chosen, but a polychromatic beam can be easily defined.
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## Physics
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In this example, only electromagnetic processes and decays are considered.
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They are defined in a custom physics list that allows the user to
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choose among various EM PhysicsList constructors. In particular,
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by choosing G4EmPenelopePhysicsMI and setting fUseMIFlag as true,
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it is possible to enable the molecular interference effects. This
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is the default configuration.
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## Action Initialization
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SAXSActionInitialization class instantiates and registers to
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Geant4 kernel all user action classes. While in sequential mode
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the action classes are instatiated just once, by invoking the
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method: SAXSActionInitialization::Build(),
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in multi-threading mode the same method is invoked for each thread
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worker and so all user action classes are defined thread-local.
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A run action class is instantiated both thread-local and global.
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That's why its instance is created also in the method
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SAXSActionInitialization::BuildForMaster(), which is
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invoked only in multi-threading mode.
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## Primary generator
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The primary generator action class employs the G4GeneralParticleSource (GPS)
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generator. The primary beam has to be defined via the G4 built-in
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commands of the G4GeneralParticleSource in a input macro file.
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In particular, a photon beam directed toward the phantom must be defined
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to test the MI effects. The X-ray beam can be monochromatic or
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polychromatic, parallel or divergent.
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## Event and Detector Response
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An event consists of the generation of a single particle which is
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transported through the phantom and then to the sensitive detector.
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The interactions of the photons inside the phantom, and in particular,
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the scattering events, are scored in a dedicated ntuple through the
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SAXSSteppingAction class.
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The hits of the particles on the sensitive detector positioned
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downstream of the phantom (SAXSSensitiveDetectorHit) are recorded
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in a dedicated ntuple through the SAXSSensitiveDetector class.
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## Analysis
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The analysis tools are used to accumulate statistics.
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ntuple are created in SAXSRunAction::SAXSRunAction()
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constructor for the following quantities:
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Ntuple1 (<code>part</code>) - Particles impinging on the Sensitive Detector (SD):
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- energy of the particles
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- position of the hits
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- momentum of the particles
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- time of the hits
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- type of impinging particles
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- ID number of the impinging particles
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- number of scattering events a primary had before hitting the SD
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- event number of the hits
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Ntuple2 (<code>scatt</code>) - Interactions of photons inside the phantom:
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- ID of the process occurred
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(0-> transportation, 1->Rayleigh, 2->Compton, 3->Photoelectic)
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- initial energy of the particles
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- scattering angle
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The ntuples are saved in the output file in the Root format.
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When running in multi-threading mode, the ntuples accumulated
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on threads are automatically merged in a single output file.
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The default output format is root. Two root scripts come with
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this example to analyze the output file: scattAnalysis.C and
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ADXRD.C. The first can be used to analyze the <code>scatt</code> ntuple, while
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the second can be used for <code>part</code> ntuple.
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## How to run
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Execute <code>saxs</code> in the 'interactive mode' with visualization:
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```
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% ./saxs
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```
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and type in the commands line by line:
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```
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Idle> /control/verbose 2
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Idle> /tracking/verbose 1
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Idle> ...
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Idle> /run/beamOn 10
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Idle> ...
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Idle> exit
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```
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or it is possible to run a macro file (test.in is a simple macro where the
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primary beam is defined through the usual GPS commands):
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```
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Idle> /control/execute test.in
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Idle> /run/beamOn 10
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....
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Idle> exit
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```
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Execute saxs in the 'batch' mode from macro files (without visualization)
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```
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% ./saxs saxs.in [Ncores]
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% ./saxs saxs_slits.in [Ncores]
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```
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<code>Ncores</code> (optional argument) is the number of threads the user wants
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to use in MT mode.
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## Appendix
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The following paragraphs are common to all basic examples
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## VISUALISATION
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The visualization manager is set via the G4VisExecutive class
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in the main() function in exampleB1.cc.
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The initialisation of the drawing is done via a set of /vis/ commands
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in the macro vis.mac. This macro is automatically read from
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the main function when the example is used in interactive running mode.
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By default, vis.mac opens the default viewer (/vis/open).
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This chooses a graphics system (in order of priority):
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- by argument in G4VisExecutive construction.
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- by environment variable, G4VIS_DEFAULT_DRIVER.
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- by information in ~/.g4session.
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- by mode (batch/interactive) and if interactive, by your build flags.
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The user can change the initial viewer
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- with environment variable G4VIS_DEFAULT_DRIVER. The format is
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```
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<graphics-system> [<window-size-hint>]
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```
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Set this, e.g:
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- (bash) export G4VIS_DEFAULT_DRIVER=TSG
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- (tcsh) setenv G4VIS_DEFAULT_DRIVER OI
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- The window-size-hint can optionally be added, e.g:
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- (bash) export G4VIS_DEFAULT_DRIVER="RayTracerQt 1000x1000-0+0"
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- on the command line, precede the app invocation, e.g:
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- ```
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G4VIS_DEFAULT_DRIVER=Vtk ./<application-name>
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```
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- with ~/.g4session.
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For other suggestions for G4VIS_DEFAULT_DRIVER (see list of registered
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graphics systems printed at the start):
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- DAWNFILE: to create a .prim file suitable for viewing in DAWN.
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- VRML2FILE: to create a .wrl file suitable for viewing in a VRML viewer.
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- "TSG_OFFSCREEN 1200x1200": to create an image file with TSG.
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- See the tsg_offscreen.mac in examples/basic/B5 for more commands
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to change the file format, file name, picture size, etc.
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See "Choosing a graphics viewer" in the Application Guide for details.
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Of course you can change the viewer by editing the /vis/open line in vis.mac.
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Also, after the initial viewer opens, you may open a different viewer by typing
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on the command line, e.g:
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```
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/vis/open DAWNFILE
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```
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or
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```
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/vis/open RayTraceQt
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```
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(if you are using the Qt GUI).
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The view parameters of the existing viewer are copied.
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The DAWNFILE and similar drivers are always available
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(since they require no external libraries), but the OGL driver requires
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that the Geant4 libraries have been built with the OpenGL option.
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The vis.mac macro in example B1 has additional commands
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that demonstrate additional functionality of the vis system, such as
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displaying text, axes, scales, date, logo and shows how to change
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viewpoint and style. Consider copying these to other examples or
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your application. To see even more commands use help or
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ls or browse the available UI commands in the Application
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Developers Guide, "Controlling Visualization from Commands".
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### User Interfaces
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The user command interface is set via the G4UIExecutive class
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in the main() function in saxs.cc.
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The selection of the user command interface is then done automatically
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according to the Geant4 configuration or it can be done explicitly via
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the third argument of the G4UIExecutive constructor (see exampleB4a.cc).
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