
///\file "medical/electronScattering2/.README.txt"
///\brief Example electronScattering2 README page

/*! \page ExampleelectronScattering2 Example electronScattering2

 Electron scattering benchmark variant 2 (Joseph Perl)

The two examples, electronScattering and electronScattering2 demonstrate how two alternate
approaches can be taken to simulating the same electron scattering benchmark experiment.

ElectronScattering2 simulates the experiment with a minimum of user code, whereas the other
version of this example shows how to do more of the work directly as the user.

In ElectronScattering2:
- Primary generation relies on the G4GeneralParticleSource.
- Material definitions are taken from the NIST database.
- Visualization uses the standard G4VisExective.
- Scoring is handled by the ready-made Geant4 scorer, G4PSCellFlux.

Both electronScattering and electronScattering2 simulate a precision electron scattering benchmark
experiment performed at NRCC Canada and published as:
"Measurement of multiple scattering of 13 and 20 MeV electrons by thin foils,"
by C. K. Ross, M. R. McEwen, A. F. McDonald, C. D. Cojocaru and B. A. Faddegon,
Med. Phys. Volume 35, Issue 9, pp. 4121-4131 (September 2008), DOI: 10.1118/1.2968095

The experiment represents the most accurate benchmark of its type.

A schematic of the experimental setup is shown in NRCC_electron_scat.pdf

The experimental data was itself published, as document number E-MPHYA6-35-034809 at http://www.aip.org/pubservs/epaps.html

The testing of three Monte Carlo simulation codes against this experimental benchmark has been
publshed as:
"The accuracy of EGSnrc, Geant4 and PENELOPE Monte Carlo systems for the simulation of electron 
scatter in external beam radiotherapy,"
by Bruce A Faddegon, Iwan Kawrakow, Yuri Kubyshin, Joseph Perl, Josep Sempau and Laszlo Urban,
Phys. Med. Biol. 54 (2009) 6151-6163, DOI:10.1088/0031-9155/54/20/008 

This present example, electronScattering2, was the Geant4 code used for this publication.

	
\section electronScattering2_s1 GEOMETRY DEFINITION
 
 The geometry is described in the enclosed documument: NRCC_electron_scat.pdf
 - A "World" volume contains an Exit Window, Primary Foil, Monitor Chamber and Helium Bag.
 - The Helium Bag contains a Gas volume, which in turn contains 2 aluminium Rings
 - A scoring cylinder is defined near the end of the World.
 	
 The default geometry is constructed in the DetectorConstruction class.
 The parameters of the Primary Foil (material and thickness) are defined from macro commands.
 

\section electronScattering2_s2 PHYSICS LIST

 Physics lists are based on modular design. Several modules are instantiated:
 1. Transportation
 2. EM physics
 3. Decays
 4. StepMax - for step limitation

 EM physics builders are from the G4 kernel physics_lists subdirectory.
  - "emstandard_opt0" recommended standard EM physics for LHC
  - "emstandard_opt1" best CPU performance standard physics for LHC
  - "emstandard_opt2" similar fast simulation
  - "emstandard_opt3" best standard EM options - analog to "local" above
  - "emstandard_opt4" best current advanced EM options standard + lowenergy
  - "emstandardSS"  standard EM physics and single scattering model
  - "emstandardWVI" standard EM physics and WentzelVI multiple scattering
  - "emstandardGS"  standard EM physics and Goudsmit-Saunderson multiple scatt.
  - "emlivermore"  low-energy EM physics using Livermore data
  - "empenelope"   low-energy EM physics implementing Penelope models
  - "emlowenergy"  low-energy EM physics implementing experimental
                   low-energy models

 Physics lists and options can be (re)set with UI commands

 Note that options set through G4EmProcessOptions are global, eg for all particle types.
 In G4 builders, it is shown how to set options per particle type.
 
       	
\section electronScattering2_s3 PRIMARY GENERATOR
 
 All of the work of the primary event generation is deferred to the G4GeneralParticleSource.
 The specific characteristics of the source are configured from the macro file, using
 /gps commands.
 - Energy is set to either 13 or 20 MeV.
 - Particle type is set to electron.
 - Direction is set exactly orthogonal to the scattering foil.
 - Source type is set to beam.
 - Spatial distribution of the beam is set as a circle gassian sigma_r of 0.042 cm

 
\section electronScattering2_s4 VISUALIZATION
 
 Visualization is controlled by the standard G4VisExecutive.
 The standard set of visualization options is supported.
 Example macros use HepRepFile. 	
  	

\section electronScattering2_s5 SCORING
  	
 All of the work of the scoring is done by the standard Geant4 scorers, G4PSCellFlux and G4PSPopulation.
 - Flux and population are scored in concentric rings at the scoring surface.
 - Flux is corrected for ring area just before output (as PSCellFlux assumes the area is the complete
 area of the face of the cylinder, not the area of the one ring).

 Because the geometry may need to be updated after various /primfoil commands,
 ElectronBenchmarkDetector is written in such a way that the sensitive detector can have its scorer ring
 logical volume updated after geometry changes. After any geometry change, ConstructSDandField is again
 called, setting the sensitive detector to use the logical volume of the updated scorer ring.
 The same sensitive detector is reused, but the manner in which the sensitive detector pointer
 is stored for this reuse is complicated by the fact that this example may be run in multi-threaded mode
 (in which each worker thread has its own sensitive detector).
 We therefore store the sensitive detector pointer in a G4Cache rather than in a direct pointer.

\section electronScattering2_s6 MACROS

 Macros are provided for all of the 37 different combinations of scattering foils and beam energies
 that were used in the actual experiment.
 Separate directories of these macros are provided for the different EM Physics options, Opt0, 1, 2 and 3.

 	
\section electronScattering2_s7 HOW TO START
 
 - Execute electornScattering2 in 'batch' mode from macro files:
\verbatim
% electronScattering2 <macro_file> <starting_seed> <output_file>
\endverbatim

   for example, to run the Al1_13MeV case with physics option 2 and a starting random seed of 1:
\verbatim
% electronScattering2 macros/Opt2/Al1_13MeV.mac 1  output/Opt2/Al1_13MeV_1
\endverbatim

 - If macro_file is not specfied, the job starts and then just waits for interactive commands
 
 - If starting_seed is not specified, it defaults to 1.
   Precision benchmark studies often involve running multiple long batch jobs and then combining the results.
   If you plan to combine more than one job with the same primary foil and energy, be sure to use different
   random seeds for each of the jobs.

 - If output_file is not specified, it defaults to output.csv in the current directory

 - To simplify batch submission of large numbers of jobs, a shell script is given called run.csh.
   The above submission could be done, for example, by:
\verbatim
run.csh Opt2/Al1_13MeV 1
\endverbatim

 - To run a basic visualization job, producing output to a HepRep file, use vis.mac, as in:
\verbatim
% electronScattering2 macros/vis.mac
\endverbatim

\section electronScattering2_s8 OUTPUT
	
  Results are given as comma-separated values (csv) files.
  - The first column gives the CellFlux for all particles.
  - The second column gives the CellFlux counting only electrons.
  - The third column gives the population for all particles.
  - The fourth column gives the populatin counting only electrons.

\section electronScattering2_s9 MULTITHREADING

  This example supports multi-threading.
  To run in multi-threaded mode, build your Geant4 with the cmake option: <br>
  -DGEANT4_BUILD_MULTITHREADED=ON
  and then set the desired number of threads by inserting the /run/numberOfThreads command
  into your macro file just before /run/initialize, as in:
\verbatim
/run/numberOfThreads 8
\endverbatim
  You may also find the output more readable if you use the following command to make output from
  each thread be collected together:
\verbatim
/control/cout/useBuffer
\endverbatim
  The visualization macro, /macros/vis.mac demonstrates use of the above two commands.
  Output from the multiple worker threads is merged by the Merge method at the end of ElectronRun.cc

*/
