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 		      Geant4 - Brachytherapy example
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                             README
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The brachytherapy example is currently maintained by Susanna Guatelli (1), with the support of
Pablo Cirrone (2), Dean Cutajar (1) and Stuart P. George (3)

1. Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia.
2. LNS, INFN, Catania, Italy.
3. University of Sheffield, England.
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Contact: susanna@uow.edu.au
         geant4-advanced-examples@cern.ch
        
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List of authors: 
S. Agostinelli, F. Foppiano, S. Garelli, S. Guatelli, M. G. Pia, M. Tropeano

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----> Introduction.                                                     
                                                                       
Brachytherapy example simulates  the energy deposit in a water phantom, produced by: 
1) Iridium source (endocavitary brachytherapy).                         
2) Iodium  source (interstitial brachytherapy).                         
3) Leipzig Applicator (superficial brachytherapy).                      
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----> 1.Experimental set-up.                                            

The default source is an Ir-131 source set in the center of the phantom.
The phantom is a box with size 30 cm. The phantom is set in the World volume filled 
with air.                           
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----> 2.SET-UP 
                                          
 -a standard Geant4 example GNUmakefile is provided                      

setup with:                                                              
G4SYSTEM = linux-g++                                                     

The following environment variables need to be set:                      

G4LEDATA: points to low energy database             

Setup for analysis: macro.C is provided to plot the results of the simulation, contained
in the brachytherapy.root file. If the user intends to use this macro, ROOT must be installed 
(http://root.cern.ch/drupal/).
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----> 3.How to run the example.                                         

- Batch mode:
  $G4WORKDIR/bin/Linux-g++/Brachy IridiumSourceMacro.mac                
  $G4WORKDIR/bin/Linux-g++/Brachy IodiumSourceMacro.mac       
  $G4WORKDIR/bin/Linux-g++/Brachy LeipzigSourceMacro.mac  
                                                                        
- Interative mode:                                                      
  3) $G4WORKDIR/bin/Linux-g++/Brachy
     VisualisationMacro.mac is loaded automatically. 
     WARNING: In this configuration the energy deposition is not 
              calculated. The user has to set-up the scoring mesh.
              Look at the IridiumSourceMacro.mac as example.            
   
--> Possible different configurations for interactive mode:              

1)Ir source:                                                            
idle>/run/beamOn NumberOfEvents      ...and then
idle>exit                                                               

2)Leipzig Applicator:                                                   
idle>/source/switch Leipzig                                           
idle>/run/beamOn NumberOfEvents     ...and then                         
idle> exit
                                                                        
3) Iodium  source:
idle>/source/switch Iodium                                               
idle>/primary/energy Iodium
idle>/run/beamOn NumberOfEvents     ...and then                          
idle>exit
                                                                         
* How to change the absorber material of the phantom:                                                                 
idle>/phantom/selectMaterial  materialName

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----> 4. Scoring mesh

The scoring mesh is used to calculate the energy deposition in the voxels of the phantom,
integrated over the whole run. The scoring mesh is defined in the input macro file (see IridiumSourceMacro.mac).
The user can change the default output format of the scoring in the class BrachyUserScoreWriter.
                                                                         
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----> 5. Simulation output                                               

The output is:
- ASCII file EnergyDeposition.out, with xx (mm), yy(mm), zz(mm), and energy deposition (keV), in the phantom.
- brachytherapy.root, containing an ntuple with the 3D energy deposition in the phantom. The macro macro.C is provided as example to open brachytherapy.root in ROOT interactive session and to plot the results of the simulation.                    
                                                                         
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----> 6.Visualisation                                                     

a macro is provided ad example of visualisation:  VisualisationMacro.mac 


