//$Id$

///\file "medical/dna/microdosimetry/.README.txt"
///\brief ExampleMicrodosimetry README page


/*! \page ExampleMicrodosimetry Example microdosimetry

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

\section microdosimetry_s1  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: \n
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708

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

\section microdosimetry_s2 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.

\section microdosimetry_s3 SET-UP 
                                                                        
Make sure G4LEDATA points to the low energy electromagnetic libraries.

The code can be compiled with cmake.

It works in MT mode.

\section microdosimetry_s4 HOW TO RUN THE EXAMPLE                                         
Normal mode, run:

\verbatim
./microdosimetry -mt 2 -out microdosimetry
\endverbatim

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

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

\verbatim
./microdosimetry -mac myMacro.mac
\endverbatim

To get visualization and interactivity:

\verbatim
./microdosimetry -gui
\endverbatim
( OGL used by default)

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

\section microdosimetry_s5 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.

\section microdosimetry_s6 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: \n
gamma    : 0 \n 
e-       : 1 \n 
proton   : 2 \n
hydrogen : 3 \n
alpha    : 4 \n
alpha+   : 5 \n
helium   : 6 \n
\n
- processes: \n

eCapture				1 \n
(only if one uses G4EmDNAPhysicsActivator in PhysicsList)

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

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

hydrogen_G4DNAElastic		31 \n
hydrogen_G4DNAExcitation	32 \n
hydrogen_G4DNAIonisation	33 \n
hydrogen_G4DNAChargeIncrease	35 \n \n

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

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

helium_G4DNAElastic             61 \n
helium_G4DNAExcitation		62 \n
helium_G4DNAIonisation		63 \n
helium_G4DNAChargeIncrease	65 \n \n

GenericIon_G4DNAIonisation      73 \n
msc				710 \n
msc				710 \n
CoulombScat			720 \n
ionIoni				730 \n
nuclearStopping			740 \n \n

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

*/
