     =========================================================
 		  Geant4 - dnaphysics example
     =========================================================

                                README file
                          ----------------------

                           CORRESPONDING AUTHOR 

S. Incerti (a,*), V. Ivantchenko (b), 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. 

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

Geant4-DNA models for electrons are based on a combination of default models with option4 models.

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

---->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 code can be compiled with cmake.

It works in MT mode.

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

In interactive mode, run:

./dnaphysics

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: 

/process/em/AddDNARegion World DNA_Opt0

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

---->4. 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.

---->5. 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:

gamma    : 0
e-       : 1    
proton   : 2
hydrogen : 3
alpha    : 4
alpha+   : 5
helium   : 6

-processes:

Capture 				1
(only if one uses G4EmDNAPhysicsActivator in PhysicsList)

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

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

hydrogen_G4DNAElastic			31
hydrogen_G4DNAExcitation		32
hydrogen_G4DNAIonisation		33
hydrogen_G4DNAChargeIncrease		35

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

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

helium_G4DNAElastic			61
helium_G4DNAExcitation			62
helium_G4DNAIonisation			63
helium_G4DNAChargeIncrease		65

GenericIon_G4DNAIonisation		73
msc					710
CoulombScat				720
ionIoni					730
nuclearStopping				740

---------------------------------------------------------------------------

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