High-precision dosimetry

== <span style="color:#000080"> Introduction </span> ==

This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show two of these tutorials:

* <span style="color:#ff0000"> dnaphysics </span>: This example shows how to simulate track structures in 100-micron side cube made of liquid water. Different type of particles are shot from the center of the volume. The physics processes are defined using class '''G4EmDNAPhysics'''. You can find more information about the different physics process which are used to build the class '''G4EmDNAPhysics''' [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html here]. [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. The output of this tutorial is the type of particle, type of process, energy deposit and energy loss for every simulation step.  

* <span style="color:#ff0000"> dnageometry </span>: This example simulates the track structure of different charge particles within a simplified geometrical model of the DNA molecule contained in a cell nucleus. The output is type of particle, type of process, energy deposit and energy loss for every simulation step. 

== <span style="color:#000080"> Setting up the environment </span> ==

; Connect to HEP cluster 

<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk 

password: type your password here

cd /home/username/ 
</pre>

; Setup your environment

<pre style="color: #800000; background-color: #dcdcdc">
source /unix/pbt/software/dev/bin/pbt-dev.sh  
</pre>

== <span style="color:#000080"> How to get the code </span> ==

; Copy the code to your working directory 

<pre style="color: #800000; background-color: #dcdcdc">
cp -r /unix/pbt/tutorials/advanced/DNAProject .
  
cd DNAProject
</pre>
 
== <span style="color:#000080"> How to run the codes </span> == 

* <span style="color:#ff0000"> dnaphysics </span>:

; Inside /home/username/DNAProject/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
mkdir dnaphysics_build  
</pre>

; To compile the code enter this directory and run cmake and make 

<pre style="color: #800000; background-color: #dcdcdc">
cd dnaphysics_build 

cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnaphysics 

make  
</pre>