High-precision dosimetry

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== <span style="color:#000080"> Introduction </span> ==
== <span style="color:#000080"> Introduction </span> ==
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This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show two of these tutorials:
+
This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show three of the examples:
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* <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"> dnaphysics </span>: This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class '''G4EmDNAPhysics'''. [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html Here] you can find more information about the different physics process that are used to build class '''G4EmDNAPhysics''' . [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. Simulated is a an electron beam using class '''G4ParticleGun'''. The beam is shot from the center of the cube. The output of this tutorial is a root ntuple with type of particle, type of physics process, energy deposit, energy loss and step length for every simulation step.   
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* <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.  
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* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. [http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html Here] you can read more about the DNA structure. Simulated are 6109 DNA pairs with the following structures: double helix, nucleosome, chromatine fibres, chromatine fibre loops and chromosome territories. Proton beam is simulated using class '''G4ParticleGun'''. The physics processes are defined using class '''G4EmDNAPhysics'''. The output is a root ntuple with type of particle, type of physics process, energy deposit and step length for every simulation step.  
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== <span style="color:#000080"> Setting up the environment </span> ==
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* <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output among other things is the dose deposited in the cell cytoplasm and in the cell nucleus.
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; Connect to HEP cluster  
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== <span style="color:#000080"> How to run the tutorial </span> ==
 +
 
 +
; Connect to the HEP cluster  
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk  
ssh -X username@plus1.hep.ucl.ac.uk  
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password: type your password here
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username@plus1.hep.ucl.ac.uk's password: type your password here
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cd /home/username/
 
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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source /unix/pbt/software/dev/bin/pbt-dev.sh   
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[username@plus1 ~]$ source /unix/pbt/software/dev/bin/pbt-dev.sh   
</pre>
</pre>
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== <span style="color:#000080"> How to get the code </span> ==
 
; Copy the code to your working directory  
; Copy the code to your working directory  
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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cp -r /unix/pbt/tutorials/advanced/DNAProject .
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[username@plus1 ~]$ cp -r /unix/pbt/tutorials/advanced/DNAProject .
    
    
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cd DNAProject
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[username@plus1 ~]$ cd DNAProject
</pre>
</pre>
   
   
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== <span style="color:#000080"> How to run the codes </span> ==
 
-
 
* <span style="color:#ff0000"> dnaphysics </span>:
* <span style="color:#ff0000"> dnaphysics </span>:
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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mkdir dnaphysics_build   
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[username@plus1 DNAProject]$ mkdir dnaphysics_build   
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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cd dnaphysics_build  
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[username@plus1 DNAProject]$ cd dnaphysics_build  
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cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnaphysics  
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[username@plus1 dnaphysics_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnaphysics  
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make   
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[username@plus1 dnaphysics_build]$ make   
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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./dnaphysics dna.mac
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[username@plus1 dnaphysics_build]$ ./dnaphysics dna.mac
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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mkdir dnageometry_build   
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[username@plus1 DNAProject]$ mkdir dnageometry_build   
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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cd dnageometry_build  
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[username@plus1 DNAProject]$ cd dnageometry_build  
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cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnageometry  
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[username@plus1 dnageometry_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnageometry  
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make   
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[username@plus1 dnageometry_build]$ make   
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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./dnageometry dna.mac
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[username@plus1 dnageometry_build]$ ./dnageometry dna.mac
 +
</pre>
 +
 
 +
* <span style="color:#ff0000"> microbeam </span>:
 +
 
 +
; Inside /home/username/DNAProject/ create a directory
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DNAProject]$ mkdir microbeam_build 
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</pre>
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 +
; To compile the code enter this directory and run cmake and make
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DNAProject]$ cd microbeam_build
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[username@plus1 microbeam_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/microbeam
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[username@plus1 microbeam_build]$ make 
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</pre>
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; Run macro microbeam.mac.
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 microbeam_build]$ ./microbeam microbeam.mac
</pre>
</pre>
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=== <span style="color:#ff0000"> dnaphysics </span> ===
=== <span style="color:#ff0000"> dnaphysics </span> ===
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The macro dna.mac produces root file '''dna.root''' with ntuples containing the following information for every step:
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This is a [http://geant4advancedexampleswg.wikispaces.com/DNAPhysics link] to the official dnaphysics tutorial explanation notes. We recommend to read it before proceeding with this tutorial.
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==== <span style="color:#000080"> Root file </span> ====
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The macro dna.mac produces two root files '''dna_t0.root''' and '''dna_t1.root''' with ntuples containing the following information for every step:  
* type of particle
* type of particle
* type of physics process
* type of physics process
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* x, y and z coordinates of the step  
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* x, y and z coordinates of the beginning of the step  
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* total energy deposit [eV]
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* total energy deposit alo[eV]
* step length [nm]
* step length [nm]
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* kinetic energy difference along the step[eV]  
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* kinetic energy difference along the step [eV]  
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You can open the first root file and see the different ntuples:
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 dnaphysics_build]$ root -l dna_t0.root
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root [1] new TBrowser
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Select ROOT Files, dna_t0.root and Folder dna
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Click on the different leafs
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</pre>
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You can analyze the root files using '''plot.C''' macro.
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 dnaphysics_build]$ root -l
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root [1] .x plot.C
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</pre>
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The macro produces two plots. The first plot shows the distribution of the different physics plrocesses. The second plot shows the trajectory of the incident particle. [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/flags.txt Here] you can find the codes for '''flagParticle''' and '''flagProcess'''. The root macro produces the following plots: 
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http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/plot.png
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==== <span style="color:#000080"> Run with different settings </span> ====
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You can change the type and the energy of the incident particle by modifying the macro dna.mac. Open the macro with editor pico:
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 +
<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 dnaphysics_build]$ pico dna.mac
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</pre>
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This is the content of the macro:
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<pre style="color: #800000; background-color: #dcdcdc">
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#/control/execute vis.mac
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/tracking/verbose 0
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/run/verbose 2
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#/dna/det/setMat G4_WATER_MODIFIED
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/dna/det/setMat G4_WATER
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/gun/particle e-
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#/gun/particle proton
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#/gun/particle hydrogen
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#/gun/particle alpha
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#/gun/particle alpha+
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#/gun/particle helium
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/gun/energy 1 keV
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/run/initialize
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/process/em/auger true
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/run/beamOn 100
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</pre>
 +
 
 +
==== <span style="color:#000080"> Visualisation </span> ====
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There is an option to run dna.mac with visualisation (in dna.mac uncomment line /control/execute vis.mac). However, runing with visualisation is very slow and it is not recommended. 
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 +
=== <span style="color:#ff0000"> dnageometry </span> ===
 +
 
 +
This is a [http://geant4advancedexampleswg.wikispaces.com/DNAGeometry link] to the official dnageometry tutorial explanation notes.
 +
 
 +
==== <span style="color:#000080"> Root file </span> ====
 +
 
 +
The macro dnageometry.mac produces a root file '''dnageometry.root''' with ntuples. The ntuples contain information for those geant4 steps for which the deposited energy in the DNA backbone is different from zero:
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 +
* type of particle
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* type of physics process
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* the two DNA strands
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* x, y and z coordinates of the post step [nm]
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* total energy deposit alo[eV]
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* step length [nm]
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You can analyze the root files using '''plot.C''' macro. First, copy this macro to your directory, then run the root
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macro.
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 dnaphysics_build]$ cp /home/username/DNAProject/dnageometry/plot.C .
 +
 
 +
[username@plus1 dnaphysics_build]$ root -l
 +
 
 +
root [1] .x plot.C
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</pre>
 +
 
 +
The macro produces a plot that shows the position of the two DNA strands in two colors. The spheres represent the amino bases. The plot shows only the DNA pairs with deposited energy (see the ntuple deffinition in SteppingAction.cc).   
 +
 
 +
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png
 +
 
 +
You can modify root macro '''plot.C''' and plot the other ntuples.
 +
 +
=== <span style="color:#ff0000"> microbeam </span> ===
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 +
This is a [http://geant4advancedexampleswg.wikispaces.com/MicrobeamExample link] to the official microbeam tutorial explanation notes.
 +
 
 +
==== <span style="color:#000080"> Root file </span> ====
 +
 
 +
The macro microbeam.mac produces root files '''microbeam_t0.root''' and '''microbeam_t1.root''' with ntuples grouped in five folders.
 +
 
 +
You can analyze the root ntuples using the '''plot.C''' macro.
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 dnaphysics_build]$ root -l
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 +
root [1] .x plot.C
 +
</pre>
 +
 
 +
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/microbeam/plot.png
 +
 
 +
== <span style="color:#000080"> Files </span> ==
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You can analyze the '''dna.root''' file using '''plot.C''' macro. The macro produces two plots. The first plot shows the distribution of the different physics plrocesses when the incident particle interacts with the water cube. The second plot shows the trajectory of the incident particle. [Here] you can find the codes for '''flagParticle''' and '''flagProcess'''.
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[[List of high-precision dosimetry files with brief description]]

Latest revision as of 17:29, 2 September 2014

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