
///\file "medical/dna/UHDR/.README.txt"
///\brief Example (UHDR) Ultra High Dose Rate README page

/*! \page ExampleUHDR Example UHDR

\ This example is provided by the Geant4-DNA collaboration
  (http://geant4-dna.org).

  Any report or published results obtained using the Geant4-DNA software
  shall cite the following Geant4-DNA collaboration publications:\n
  Med. Phys. 45 (2018) e722-e739\n
  Phys. Med. 31 (2015) 861-874\n
  Med. Phys. 37 (2010) 4692-4708\n
  Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178\n


\section UHDR_s0 INTRODUCTION

 This example shows how to activate the mesoscopic model in chemistry and
 combine with SBS model (Tran et al.,Int. J. Mol. Sci. 22 (2021) 6023).
 It allows to simulate chemical reactions longtime (beyond 1 us) of post-irradiation.

 To run the example:
\verbatim
mkdir UHRD-build
cd UHRD-build
cmake ../pathToExamples/UHRD
make
\endverbatim

In batch mode, the macro beam.in can be used as follows:
\verbatim
./UHRD beam.in
\endverbatim
 or
\verbatim
./UHRD beam.in 123
   # 123 is the user's seed number
\endverbatim

\section UHDR_s1 GEOMETRY DEFINITION


 The world volume is a simple water box 3.2 x 3.2 x 3.2 um3 for 0.01 Gy of cut-off
 absorbed dose and 1.6 x 1.6 x 1.6 um3 for 1 Gy. This example is limited to these geometries.
 The choice of simulation volume is a compromise between a sufficient number of chemical species a
 nd an achievable computation time.

 Two parameters define the geometry :
 - the material of the box for the physical stage is water.
 - for the chemistry stage, the concentration of scavengers in [mole/l]
   is added. This concentration is supposed to have no effect on the
   physical stage. pH is defined as scavengers of H3O^1, OH^-1.
   In this example, we consider that chemical molecules diffuse and react in a
   bounded volume (that is, limited by geometrical boundaries) which is also
   the irradiated water box volume of the physical stage.
   The bouncing of chemical molecules on the volume border is applied
   for both SBS and mesoscopic models.
   The bouncing is not applied for physical stage.

\section UHDR_s2 PHYSICS LIST

 PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option2
 and EmDNAChemistry constructors (the chemistry constructor uses the
 Step-by-step method).

\section UHDR_s3  CHEMISTRY WORLD

 This object is controlled by DetectorContruction. It defines the chemistry volume,
 scavengers and pH of water.

\section UHDR_s4 AN EVENT: PRIMARY GENERATOR

This example utilizes the G4SingleParticleSource.
Each event consists of multiple incident particles.
A large number has been chosen to ensure that the stack remains non-empty until the desired
energy deposition is achieved (which is then converted to a cutoff dose).
With each /run/beamOn command, a group of particles is emitted. The cutoff dose
(dose threshold) determined by users.
The actual dose is calculated based on the real energy deposited in the volume.

\section UHDR_s5 DETECTOR RESPONSE : Scorer

There is one G4MultiFunctionalDetector object which computes the
energy deposition and the number of species along time in order to
extract the G-value:
(Number of species X) / (100 eV of deposited energy).

These two macro commands can be used to control the scoring time:
\verbatim
/scorer/species/addTimeToRecord 1 ps
   # user can select time bin to score G values.
/scorer/species/nOfTimeBins
   # or user can automatically select time bin logarithmically.
\endverbatim

\section UHDR_s6 PULSE ACTION

This functionality is not available for this version.

\section UHDR_s7 OUTPUT

G-value

\section UHDR_s8 RELEVANT MACRO COMMANDS AND MACRO FILE

The user macro file is: beam.in

\section UHDR_s9 REACTION BUILDER

 Reaction lists are collected by builders for specific applications.
 ChemNO2_NO3ScavengerBuilder is to build the reaction list with NO2-/NO3-.
 ChemPureWaterBuilder is to build the reaction list with pH.
 ChemOxygenWaterBuilder is to build the reaction list with ROS.
 ChemFrickeReactionBuilder is to build the reaction list of Fricke Dosimeter.

\section UHDR_s10 PLOT

The information about all the molecular species is scored in a ROOT
(https://root.cern) ntuple file Dose_xxx.root (xxx is seed number).
The ROOT program plot_time.C
can be used to plot the G values vs time for each species.

Execute plot_time as:
\verbatim
root plot_time.C
\endverbatim

or print G values to scorer.txt
\verbatim
root plot_time.C > scorer.txt
\endverbatim

The results show the molecular species (G values) as a function of
time (ns). Please correct the dose in the
\verbatim
TTree *tree = (TTree *) dir->Get("0.010000");
\endverbatim

Funding: FNS Synergia grant MAGIC-FNS CRSII5_186369.
Contact: H. Tran (tran@cenbg.in2p3.fr)
CNRS, lp2i, UMR 5797, Université de Bordeaux, F-33170 Gradignan, France
*/
