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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
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Extended Example saxs
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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.
1- 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.
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.
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 and /det/setCustomMatHmassfract,
/det/setCustomMatNmassfract, /det/setCustomMatOmassfract commands,
respectively. 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.
2- 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.
3- ACTION INITALIZATION
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.
4- 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.
5- 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.
6- 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 a format
selected in SAXSAnalysis.hh.
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.
7- 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.
The following paragraphs are common to all basic examples
A- VISUALISATION
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.
B- 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).
Gabriele Cosmo