Example saxs

Author

Gianfranco Paternò - INFN and University Ferrara (Italy)
pater.nosp@m.no@f.nosp@m.e.inf.nosp@m.n.it

The example saxs implements the typical setup of a Small Angle X-ray Scattering (SAXS) experiment. It is meant to illustrate the usage of molecular interference (MI) of Rayleigh (coherent) scattering of photons inside the matter, which is implemented in the G4PenelopeRayleighModelMI model.

Geometry

The setup consists of a phantom/sample under investigation, slits to collimate the photon beam and a shielded detector to collect the photons scattered by the phantom (see SAXSDetectorConstruction).

The geometry is scalable through the interactive commands defined in the SAXSDetectorConstructionMessenger class. All the significant quantities, such as the setup (scattering) rotation angle, the position and size of all the volumes, as well as the phantom material can be set via macro commands.

Two macro files come with this example: saxs.in and saxs_slits.in.

1. In the saxs.in macro, the phantom is a cylinder with a diameter and a height of 10 mm made of a mixture of 80% fat and 20% water. In general, if the argument of /det/setPhantomMaterial command is 2, as in this case, the material is a biological tissue ("MedMat") defined as a mixture of fat, water, collagen and hydroxyapatite. The weight fraction of the mixture components can be set through commands

    /det/setComp0
    /det/setComp1
    /det/setComp2
    /det/setComp3
   

   respectively. The tissue form factor (including MI) is automatically calculated as a weighed sum of the form factors of the basis components.
   In this case, no slits are foreseen and the sensitive detector positioned 400 mm downstream of the phantom collects all the photons transmitted and scattered by the phantom, which is irradiated by a pencil beam with an energy of 20 keV.
2. In the saxs_slits.in macro, the phantom is again a cylinder with a diameter and a height of 10 mm. The phantom is made of a custom material ("CustomMat") whose density and composition is set through

    /det/setCustomMatDensity
    /det/setCustomMatHmassfract,
    /det/setCustomMatNmassfract
    /det/setCustomMatOmassfract
   

   commands. In general, a custom material can be defined by specifying the mass fraction of H, C, N, O, Na, P, S, Cl, K, and Ca via commands analogous to those mentioned above. In this case, the material composition corresponds to that of ammonium nitrate (NH₄NO₃). For a custom material, the user can provide the path of the file with the material form factor (with MI) through the

    /det/SetCustomMatFF
   

   command. As an example, the file myFF.dat contains the form factor of NH₄NO₃ measured by Harding in 1999. In this case the slits upstream and downstream the phantom are present. This setup is suitable for both monochromatic and polychromatic beams. To speed-up the simulation, a monochromatic photon beam was chosen, but a polychromatic beam can be easily defined.
   

Physics

In this example, only electromagnetic processes and decays are considered.

They are defined in a custom physics list that allows the user to choose among various EM PhysicsList constructors. In particular, by choosing G4EmPenelopePhysicsMI and setting fUseMIFlag as true, it is possible to enable the molecular interference effects. This is the default configuration.

Action Initialization

SAXSActionInitialization class instantiates and registers to Geant4 kernel all user action classes. While in sequential mode the action classes are instatiated just once, by invoking the method: SAXSActionInitialization::Build(), in multi-threading mode the same method is invoked for each thread worker and so all user action classes are defined thread-local.

A run action class is instantiated both thread-local and global. That's why its instance is created also in the method SAXSActionInitialization::BuildForMaster(), which is invoked only in multi-threading mode.

Primary generator

The primary generator action class employs the G4GeneralParticleSource (GPS) generator. The primary beam has to be defined via the G4 built-in commands of the G4GeneralParticleSource in a input macro file. In particular, a photon beam directed toward the phantom must be defined to test the MI effects. The X-ray beam can be monochromatic or polychromatic, parallel or divergent.

Event and Detector Response

An event consists of the generation of a single particle which is transported through the phantom and then to the sensitive detector.

The interactions of the photons inside the phantom, and in particular, the scattering events, are scored in a dedicated ntuple through the SAXSSteppingAction class.

The hits of the particles on the sensitive detector positioned downstream of the phantom (SAXSSensitiveDetectorHit) are recorded in a dedicated ntuple through the SAXSSensitiveDetector class.

Analysis

The analysis tools are used to accumulate statistics. ntuple are created in SAXSRunAction::SAXSRunAction() constructor for the following quantities:

Ntuple1 (part) - Particles impinging on the Sensitive Detector (SD):

• energy of the particles
• position of the hits
• momentum of the particles
• time of the hits
• type of impinging particles
• ID number of the impinging particles
• number of scattering events a primary had before hitting the SD
• event number of the hits

Ntuple2 (scatt) - Interactions of photons inside the phantom:

• ID of the process occurred (0-> transportation, 1->Rayleigh, 2->Compton, 3->Photoelectic)
• initial energy of the particles
• scattering angle

The ntuples are saved in the output file in the Root format. When running in multi-threading mode, the ntuples accumulated on threads are automatically merged in a single output file.

The default output format is root. Two root scripts come with this example to analyze the output file: scattAnalysis.C and ADXRD.C. The first can be used to analyze the scatt ntuple, while the second can be used for part ntuple.

How to run

Execute saxs in the 'interactive mode' with visualization:

  % ./saxs

and type in the commands line by line:

  Idle> /control/verbose 2
  Idle> /tracking/verbose 1
  Idle> ...
  Idle> /run/beamOn 10 
  Idle> ...
  Idle> exit

or it is possible to run a macro file (test.in is a simple macro where the primary beam is defined through the usual GPS commands):

  Idle> /control/execute test.in
  Idle> /run/beamOn 10 
  ....
  Idle> exit

Execute saxs in the 'batch' mode from macro files (without visualization)

  % ./saxs saxs.in [Ncores]   
  % ./saxs saxs_slits.in [Ncores]

Ncores (optional argument) is the number of threads the user wants to use in MT mode.

Appendix

The following paragraphs are common to all basic examples

Visualization

The visualization manager is set via the G4VisExecutive class in the main() function in saxs.cc.
The initialisation of the drawing is done via a set of /vis/ commands in the macro vis.mac. This macro is automatically read from the main function when the example is used in interactive running mode.

By default, vis.mac opens an OpenGL viewer (/vis/open OGL). The user can change the initial viewer by commenting out this line and instead uncommenting one of the other /vis/open statements, such as HepRepFile or DAWNFILE (which produce files that can be viewed with the HepRApp and DAWN viewers, respectively). Note that one can always open new viewers at any time from the command line. For example, if you already have a view in, say, an OpenGL window with a name "viewer-0", then

  /vis/open DAWNFILE

then to get the same view

  /vis/viewer/copyView viewer-0

or to get the same view plus scene-modifications

  /vis/viewer/set/all viewer-0

then to see the result

  /vis/viewer/flush

The DAWNFILE, HepRepFile drivers are always available (since they require no external libraries), but the OGL driver requires that the Geant4 libraries have been built with the OpenGL option.

vis.mac has additional commands that demonstrate additional functionality of the vis system, such as displaying text, axes, scales, date, logo and shows how to change viewpoint and style. To see even more commands use help or ls or browse the available UI commands in the Application Developers Guide.

For more information on visualization, including information on how to install and run DAWN, OpenGL and HepRApp, see the visualization tutorials, for example, http://geant4.slac.stanford.edu/Presentations/vis/G4[VIS]Tutorial/G4[VIS]Tutorial.html (where [VIS] can be replaced by DAWN, OpenGL and HepRApp)

The tracks are automatically drawn at the end of each event, accumulated for all events and erased at the beginning of the next run.

User Interfaces

The user command interface is set via the G4UIExecutive class in the main() function in saxs.cc The selection of the user command interface is then done automatically according to the Geant4 configuration or it can be done explicitly via the third argument of the G4UIExecutive constructor (see exampleB4a.cc).