//$Id$

///\file "medical/dna/dnaphysics/.README.txt"
///\brief Example dnaphysics README page


/*! \page ExampleDnaphysics Example dnaphysics

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

\section dnaphysics_s1 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 publications: \n
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708 \n

\section dnaphysics_s2 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.

\section dnaphysics_s3 SET-UP 
                                                                        
Make sure G4LEDATA points to the low energy electromagnetic data files.

The code can be compiled with cmake.

It works in MT mode.

\section dnaphysics_s4 HOW TO RUN THE EXAMPLE                                         

In interactive mode, run:

\verbatim
./dnaphysics
\endverbatim

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).

\section dnaphysics_s5 PHYSICS

This example shows:
- how to use the Geant4-DNA processes, which are activated automatically at low energy,
below the applicability range of G4EmStandardPhysics_option4 constructor
(look at the PhysicsList.cc file)
- how to count and save occurrences of processes
(look at the SteppingAction.cc file)

\section dnaphysics_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 enery loss along the current step (in eV)
- the event ID

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: \n
e-       : 1    \n 
proton   : 2 \n
hydrogen : 3 \n
alpha    : 4 \n
alpha+   : 5 \n
helium   : 6 \n
\n
- processes: \n
Capture or e-_G4DNAElectronSolvation 	1 \n
e-_G4DNAElastic				11 \n
e-_G4DNAExcitation			12 \n
e-_G4DNAIonisation			13 \n
e-_G4DNAAttachment			14 \n
e-_G4DNAVibExcitation			15 \n
eCapture				16 \n \n
proton_G4DNAExcitation			17 \n
proton_G4DNAIonisation			18 \n
proton_G4DNAChargeDecrease		19 \n \n
hydrogen_G4DNAExcitation		20 \n
hydrogen_G4DNAIonisation		21 \n
hydrogen_G4DNAChargeIncrease		22 \n \n
alpha_G4DNAExcitation			23 \n
alpha_G4DNAIonisation			24 \n
alpha_G4DNAChargeDecrease		25 \n \n
alpha+_G4DNAExcitation			26 \n
alpha+_G4DNAIonisation			27 \n
alpha+_G4DNAChargeDecrease		28 \n
alpha+_G4DNAChargeIncrease		29 \n \n
helium_G4DNAExcitation			30 \n
helium_G4DNAIonisation			31 \n
helium_G4DNAChargeIncrease		32 \n \n
\n
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Should you have any enquiry, please do not hesitate to contact: 
incerti@cenbg.in2p3.fr

*/
