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 		  Geant4 - Microdosimetry example
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                                README file
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                           CORRESPONDING AUTHOR 

S. Incerti (a, *), V. Ivantchenko (b), M. Karamitros (a)
a. Centre d'Etudes Nucleaires de Bordeaux-Gradignan 
(CENBG), IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France
b. G4AI Ltd, UK
* e-mail:incerti@cenbg.in2p3.fr 

---->0. INTRODUCTION.                                                    
                                                                       
The microdosimetry example simulates the track of two 5 MeV protons in liquid water. 
Geant4 standard EM models are used in the World volume while Geant4-DNA models
are used in a Target volume, declared as a Region.

This example is provided by the Geant4-DNA collaboration.

These processes and models are further described at:
http://geant4-dna.org

Any report or published results obtained using the Geant4-DNA software shall 
cite the following Geant4-DNA collaboration publications:
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708

We also suggest these other references related to this example:
Nucl. Instrum. and Meth. B 273 (2012) 95-97
Prog. Nucl. Sci. Tec. 2 (2011) 898-903

---->1. GEOMETRY SET-UP.
  
The geometry is a 1 mm side cube (World) made of liquid water containing a smaller cubic Target volume of liquid
water, which dimensions are twenty times smaller than the dimensions of the World volume.

--->2. SET-UP 
                                                                        
Make sure G4LEDATA points to the low energy electromagnetic libraries.

The code can be compiled with cmake.

It works in MT mode.

---->3. HOW TO RUN THE EXAMPLE                                         

Normal mode, run:

./microdosimetry -mt 2 -out microdosimetry

(or more generally
./microdosimetry -mt 2 -out myRootFile
)

The macro microdosimetry.in is executed by default; to select another one:

./microdosimetry -mac myMacro.mac

To get visualization and interactivity:

./microdosimetry -gui
( OGL used by default)

or you may use your own visualization driver, for instance:
./microdosimetry -vis "DAWNFILE"

---->4. PHYSICS

This example shows:
- how to use the Geant4-DNA processes, 
- how to count and save occurrences of processes
- how to combine them with Standard EM Physics.

A simple electron capture process is also provided in order to kill electrons 
below a chosen energy threshold, set in the Physics list.

Look at the PhyscisList.cc file.

---->5. SIMULATION OUTPUT AND RESULT ANALYSIS                                    

The output results consists in a dna.root file, containing for each simulation step:
- the type of particle for the current step
- the type of process for the current step
- the track position of the current step (in nanometers)
- the energy deposit along the current step (in eV)
- the step length (in nm)
- the total energy loss along the current step (in eV)
- the kinetic energy at PreStepPoint
- the cos of the scattering angle
- the event ID
- the track ID
- the parent track ID
- the step number

This file can be easily analyzed using for example the provided ROOT macro 
file plot.C; to do so :
* be sure to have ROOT installed on your machine
* be sure to be in the microdosimetry directory
* launch ROOT by typing root
* under your ROOT session, type in : .X plot.C to execute the macro file
* alternatively you can type directly under your session : root plot.C

The naming scheme on the displayed ROOT plots is as follows (see SteppingAction.cc),
as in the 'dnaphysics' example:

-particles:
gamma    : 0
e-       : 1    
proton   : 2
hydrogen : 3
alpha    : 4
alpha+   : 5
helium   : 6

-processes:

eCapture 				1
(only if one uses G4EmDNAPhysicsActivator in PhysicsList)

e-_G4DNAElectronSolvation 		10
e-_G4DNAElastic				11
e-_G4DNAExcitation			12
e-_G4DNAIonisation			13
e-_G4DNAAttachment			14
e-_G4DNAVibExcitation			15
msc					110
CoulombScat				120
eIoni                           	130

proton_G4DNAElastic			21
proton_G4DNAExcitation			22
proton_G4DNAIonisation			23
proton_G4DNAChargeDecrease		24
msc					210
CoulombScat				220
hIoni					230
nuclearStopping				240

hydrogen_G4DNAElastic			31
hydrogen_G4DNAExcitation		32
hydrogen_G4DNAIonisation		33
hydrogen_G4DNAChargeIncrease		35

alpha_G4DNAElastic			41
alpha_G4DNAExcitation			42
alpha_G4DNAIonisation			43
alpha_G4DNAChargeDecrease		44
msc					410
CoulombScat				420
ionIoni					430
nuclearStopping				440

alpha+_G4DNAElastic			51
alpha+_G4DNAExcitation			52
alpha+_G4DNAIonisation			53
alpha+_G4DNAChargeDecrease		54
alpha+_G4DNAChargeIncrease		55
msc					510
CoulombScat				520
hIoni					530
nuclearStopping				540

helium_G4DNAElastic			61
helium_G4DNAExcitation			62
helium_G4DNAIonisation			63
helium_G4DNAChargeIncrease		65

GenericIon_G4DNAIonisation		73
msc					710
CoulombScat				720
ionIoni					730
nuclearStopping				740

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Should you have any enquiry, please do not hesitate to contact: 
incerti@cenbg.in2p3.fr
