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


/*! \page Examplesvalue Example svalue

\author S. Incerti et al. (a, *) \n
a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
* e-mail: incerti@lp2ib.in2p3.fr

\section svalue_s1 INTRODUCTION.

The svalue example shows how to calculate monoenergetic S values in liquid water
using the Geant4-DNA physics processes and models.

It is adapted from TestEm12.

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:
Med. Phys. 51 (2024) 5873–5889
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 svalue_s2 GEOMETRY SET-UP

The geometry is a spherical nucleus surrounded by a spherical shell
representing the cytoplasm. Nucleus radius and shell thickness can be selected
from the provided macro file svalue.in, as well as materials
(G4_WATER or G4_Galactic). The world is a sphere with radius 1e3 larger than
the radius of the nucleus

Particles are shot randomly inside the cytoplasm.

Particle type and energy can be controlled by the
svalue.in macro file.

The PrimaryGeneratorAction class is adapted (G4 state dependent)
in order to enable generic physics list usage
(empty modular physics list).

An alternative MyPrimaryGeneratorActionFromFile class is provided as an example
for reading input data from a file in MT mode for the generation of primaries.
The MyFileReader class is provided as well. They are document in:
https://twiki.cern.ch/twiki/bin/view/Geant4/QuickMigrationGuideForGeant4V10

\section svalue_s3 SET-UP

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

Set the variable MYFILE as 1 in MyFile.hh if you wish to use a spectrum file
of incident energies. By default, this variable is not defined. The file name and
number of lines to read can be specified in MyFile.cc. A spectrum.txt file is provided
as example.

The code can be compiled with cmake.

It works in MT mode.

\section svalue_s4 HOW TO RUN THE EXAMPLE

In interactive mode, run:

\verbatim
./svalue svalue.in
\endverbatim

The svalue.in macro allows a full control of the simulation.

Two alternative macros, svalue-iodine125.in and svalue-iodine131.in
are provided for the simulation of radioactive sources.

The svalue-spectrum.in macro shows how to shoot particles
from the spectrum.txt file of energies (unit: eV), which has been created
using the spectrum.C sample ROOT macro.

\section svalue_s5 PHYSICS

You can select Geant4-DNA physics constructor in svalue.in.

A tracking cut can be applied if requested.

\section svalue_s6 SIMULATION OUTPUT AND RESULT ANALYSIS

The output results consist in a text file (s.txt), containing :
- the radius of the nucleus (in nm)
- the thickness of the cytoplasm (in nm)
- the energy of incident particles (in eV)
- the S value for the cytoplasm (in Gy/Bq.s)
- the rms on S value for the cytoplasm (in Gy/Bq.s)
- the S value for the nucleus (in Gy/Bq.s)
- the rms on S value for the nucleus (in Gy/Bq.s)

One can use the plot.C ROOT macro file to display results.

Note: rms values correspond to standard deviation.
