Gabriele Cosmo
218 lines
9.6 KiB
Plaintext
218 lines
9.6 KiB
Plaintext
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=========================================================
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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
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=========================================================
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Extended Example saxs
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--------------------
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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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1- 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 /det/setPhantomMaterial 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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/det/setComp0, /det/setComp1, /det/setComp2, /det/setComp3, 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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/det/setCustomMatDensity and /det/setCustomMatHmassfract,
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/det/setCustomMatNmassfract, /det/setCustomMatOmassfract commands,
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respectively. 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 (NH4NO3).
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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 /det/SetCustomMatFF
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command. As an example, the file myFF.dat contains the form factor of
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NH4NO3 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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2- 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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3- ACTION INITALIZATION
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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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4- 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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5- 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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6- 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 (part) - 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 (scatt) - 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 scatt ntuple, while
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the second can be used for part ntuple.
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7- HOW TO RUN
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- Execute saxs in the 'interactive mode' with visualization:
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% ./saxs
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and type in the commands line by line:
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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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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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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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- Execute saxs in the 'batch' mode from macro files
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(without visualization)
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% ./saxs saxs.in [Ncores]
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% ./saxs saxs_slits.in [Ncores]
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Ncores (optional argument) is the number of threads the user wants to use in
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MT mode.
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The following paragraphs are common to all basic examples
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A- VISUALISATION
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The visualization manager is set via the G4VisExecutive class
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in the main() function in saxs.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 an OpenGL viewer (/vis/open OGL).
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The user can change the initial viewer by commenting out this line
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and instead uncommenting one of the other /vis/open statements, such as
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HepRepFile or DAWNFILE (which produce files that can be viewed with the
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HepRApp and DAWN viewers, respectively). Note that one can always
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open new viewers at any time from the command line. For example, if
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you already have a view in, say, an OpenGL window with a name
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"viewer-0", then
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/vis/open DAWNFILE
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then to get the same view
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/vis/viewer/copyView viewer-0
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or to get the same view *plus* scene-modifications
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/vis/viewer/set/all viewer-0
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then to see the result
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/vis/viewer/flush
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The DAWNFILE, HepRepFile 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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vis.mac has additional commands that demonstrate additional functionality
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of the vis system, such as displaying text, axes, scales, date, logo and
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shows how to change viewpoint and style.
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To see even more commands use help or ls or browse the available UI commands
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in the Application Developers Guide.
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For more information on visualization, including information on how to
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install and run DAWN, OpenGL and HepRApp, see the visualization tutorials,
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for example,
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http://geant4.slac.stanford.edu/Presentations/vis/G4[VIS]Tutorial/G4[VIS]Tutorial.html
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(where [VIS] can be replaced by DAWN, OpenGL and HepRApp)
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The tracks are automatically drawn at the end of each event, accumulated
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for all events and erased at the beginning of the next run.
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B- 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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