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


/*! \page ExampleDnaphysics Example dnaphysics

\author S. Incerti (a, *), , H. Tran (a, *), V. Ivantchenko (b), M. Karamitros\n
a. LP2i, IN2P3 / CNRS / Bordeaux 1 University, 33175 Gradignan, France \n
b. G4AI Ltd., UK
* e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr \n

\section dnaphysics_s1 INTRODUCTION.

The dnaphysics example shows how to simulate track structures in liquid water
using the Geant4-DNA physics models and processes.

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, (2018) e722-e739
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 in DetectorConstruction.
The material can be changed directly in dnaphysics.in macro file.

\section dnaphysics_s3 SET-UP

Make sure $G4LEDATA points to the low energy electromagnetic data files.

\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.

\section dnaphysics_s5 PHYSICS

The PhysicsList uses Geant4-DNA Physics constructors or activator.
Activator can be used to apply Geant4-DNA to a specific Region only.

1) Geant4-DNA Physics constructors can be selected using the command:

\verbatim
/dna/test/addPhysics DNA_OptX
\endverbatim

where X is 0 to 8 (2, 4 or 6 are recommended).

2) Alternatively, Geant4-DNA activator for World Region can be selected using the command:

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

where X = 0, 2, 4, or 6.

3) In addition to 1) or 2), to enable radioactive decay, one can use:

\verbatim
/dna/test/addPhysics raddecay
\endverbatim

4) Warning regarding ions: when the incident particle type is ion
(/gun/particle ion), specified with Z and A numbers (/gun/ion A Z),
the Rudd ionisation extended model is used. The particles are tracked
by default down to 0.5 MeV/u. This tracking cut can be bypassed using :

\verbatim
/dna/test/addIonsTrackingCut false
\endverbatim

\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 step PostStepPoint coordinates (in nm)
- 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 (in eV)
- the cos of the scattering angle
- the event ID
- the track ID
- the parent track ID
- the step number

This information is extracted from the SteppingAction class.

The ROOT 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):

- 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

Capture: 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

phot: 81 \n
compt: 82 \n
conv: 83 \n
Rayl: 84 \n

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

Should you have any enquiry, please do not hesitate to contact:
incerti@cenbg.in2p3.fr or tran@lp2ib.in2p3.fr

*/
