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 		  Geant4 - dnaphysics example
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                                README file
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                           CORRESPONDING AUTHOR 

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

---->0. INTRODUCTION.                                                    
                                                                       
The dnaphysics example shows how to simulate track structures in liquid water
using the Geant4-DNA physics processes and models. 

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 publication:
Med. Phys. 37 (2010) 4692-4708

---->1. GEOMETRY SET-UP.
 
The geometry is a 100-micron side cube (World) made of liquid water (G4_WATER
material). Particles are shot from the center of the volume.

The variable density feature of materials is illustrated. 
Material can be changed directly in dna.mac macro file.

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

The variable G4ANALYSIS_USE must be set to 1.

The code can be compiled with cmake.

It works in MT mode.

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

In interactive mode, run:

./dnaphysics

The macro dna.mac is executed by default. It shows how to shoot different 
particle types.

To get visualization, make sure to uncomment the #/control/execute vis.mac
 line in the macro (not recommended).

---->4. PHYSICS

This example shows:
- how to use the Geant4-DNA processes, using the G4EmDNAPhysics constructor
(look at the PhysicsList.cc file)
- how to affect them a number
(look at the SteppingAction.cc file)

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

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 enery loss along the current step (in eV)

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 directory containing the ROOT files created by dnaphysics
* copy plot.C into this directory
* from there, 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):

This is the same naming scheme as in the "microdosimetry" advanced example.

-particles:

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

-processes:

e-_G4DNAElastic			11
e-_G4DNAExcitation		12
e-_G4DNAIonisation		13
e-_G4DNAAttachment		14
e-_G4DNAVibExcitation		15

proton_G4DNAExcitation		17
proton_G4DNAIonisation		18
proton_G4DNAChargeDecrease	19

hydrogen_G4DNAExcitation	20
hydrogen_G4DNAIonisation	21
hydrogen_G4DNAChargeIncrease	22

alpha_G4DNAExcitation		23
alpha_G4DNAIonisation		24
alpha_G4DNAChargeDecrease	25

alpha+_G4DNAExcitation		26
alpha+_G4DNAIonisation		27
alpha+_G4DNAChargeDecrease	28
alpha+_G4DNAChargeIncrease	29

helium_G4DNAExcitation		30
helium_G4DNAIonisation		31
helium_G4DNAChargeIncrease	32

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