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$Id: README,v 1.6 2009/04/29 14:17:03 sincerti Exp $
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 		  Geant4 - Microdosimetry example
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                                README file
                          ----------------------

                           CORRESPONDING AUTHOR 

S. Incerti (a, *) et al.
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 microdosimetry example simulates the track of a 10 keV Helium+ (positive
charge is +e) particle in liquid water using only Geant4-DNA processes.

---->1. GEOMETRY SET-UP.
 
The geometry is a 1 mm side cube of liquid water.

---->2. SET-UP 
                                                                        
- a standard Geant4 example GNUmakefile is provided                     

setup with:                                                             
compiler = gcc-3.4.6
G4SYSTEM = linux-g++                                                    

The following section gives the necessary environment variables.                     

------->>2.1  ENVIRONMENT VARIABLES

All variables are defined with their default value.

 - G4SYSTEM = Linux-g++

 - G4INSTALL              points to the installation directory of GEANT4;

 - G4LIB                  point to the compiled libraries of GEANT4;

 - G4WORKDIR              points to the work directory;

 - CLHEP_BASE_DIR         points to the installation directory of CHLEP; 

 - G4LEDATA               points to the low energy electromagnetic libraries;

 - LD_LIBRARY_PATH = $CLHEP_BASE_DIR/lib

 - G4LEVELGAMMADATA       points to the photoevaporation library;

 - NeutronHPCrossSections points to the neutron data files;

 - G4RADIOACTIVEDATA      points to the libraries for radio-active decay 
                          hadronic processes;
 
However, the $G4LEVELGAMMADATA, $NeutronHPCrossSections and $G4RADIOACTIVEDATA
variables do not need to be defined for this example.

Once these variables have been set, simply type gmake to compile the
Microdosimetry example. 

------->>2.2  VISUALIZATION

Visualization is not activated by default.

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

In interactive mode, run:

> $G4WORDIR/bin/$G4SYSTEM/Microdosimetry

The macro microdosimetry.mac is executed by default. 

To get visualization, make sure to uncomment the /vis/... lines in the macro.

---->4. PHYSICS

This example shows how to use the Geant4-DNA processes AND how to affect them a
name.

Look at the PhyscisList.cc file.

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

This example does not need any external analysis package. 
The output results consists in a track.txt file, containing at each line :
- 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)

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):

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

-processes:
e-_G4DNAElastic			: 11
e-_G4DNAExcitation		: 12
e-_G4DNAIonisation		: 13
proton_G4DNAExcitation		: 14
proton_G4DNAIonisation		: 15
proton_G4DNAChargeDecrease	: 16
hydrogen_G4DNAIonisation	: 17
hydrogen_G4DNAChargeIncrease	: 18
alpha_G4DNAExcitation		: 19
alpha_G4DNAIonisation 		: 20
alpha_G4DNAChargeDecrease	: 21
alpha+_G4DNAExcitation		: 22
alpha+_G4DNAIonisation		: 23
alpha+_G4DNAChargeDecrease	: 24
alpha+_G4DNAChargeIncrease	: 25
helium_G4DNAExcitation		: 26
helium_G4DNAIonisation		: 27
helium_G4DNAChargeIncrease  	: 28


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