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


/*! \page ExampleDnaphysics Example dnaphysics

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

Below 1 MeV, Geant4-DNA models are used while, above this energy, 
G4EmStandardPhysics_option4 models are used.

The Geant4-DNA 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:
Med. Phys. 45, e722-e739 (2018)
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708
Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178

\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

In batch, the macro dnaphysics.in can be used. It shows how to shoot different 
particle types.

The combination of G4EmStandardPhysics_option4 and Geant4-DNA models in the World
is activated thanks to the following UI command in dnaphysics.in: 

\verbatim
/process/em/AddDNARegion World DNA_Opt0
\endverbatim

For now, only the "DNA_Opt0" configuration is allowed.

\section dnaphysics_s5 PHYSICS

This example shows:
- how to use the Geant4-DNA models, which are activated automatically at low energy,
below 1 MeV, and G4EmStandardPhysics_option4 models above
(look at the PhysicsList.cc file)
- how to count and save occurrences of processes
(look at the SteppingAction.cc file)

Alternatively, the direct usage of Geant4-DNA physics constructors is also shown 
in comment in the PhysicsList.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 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 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
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
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
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

*/
