Software/Geant4/Tutorials/Advanced/High-Precision Dosimetry

From PBTWiki
Jump to navigation Jump to search

Introduction

This tutorial is based on the Geant4-DNA project tutorials. We chose to show three of the examples:

  • dnaphysics : This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class G4EmDNAPhysics. Here you can find more information about the different physics process that are used to build class G4EmDNAPhysics . 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.
  • dnageometry : This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. 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.
  • microbeam : This example simulates the cellular irradiation beam line installed on the AIFIRA electrostatic accelerator facility located at 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.

How to run the tutorials

Connect to the HEP cluster

ssh -X username@plus1.hep.ucl.ac.uk 

username@plus1.hep.ucl.ac.uk's password: type your password here

Setup your environment

[username@plus1 ~]$ source /unix/pbt/software/scripts/pbt.sh

Copy the code to your working directory

[username@plus1 ~]$ cp -r /unix/pbt/tutorials/advanced/DNAProject .
  
[username@plus1 ~]$ cd DNAProject

dnaphysics:

Inside /home/username/DNAProject/ create a directory

[username@plus1 DNAProject]$ mkdir dnaphysics_build

Compile the code with make and cmake

[username@plus1 DNAProject]$ cd dnaphysics_build 

[username@plus1 dnaphysics_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnaphysics 

[username@plus1 dnaphysics_build]$ make

Run macro dna.mac

[username@plus1 dnaphysics_build]$ ./dnaphysics dna.mac

dnageometry:

Inside /home/username/DNAProject/ create a directory

[username@plus1 DNAProject]$ mkdir dnageometry_build

Compile the code with make and cmake

[username@plus1 DNAProject]$ cd dnageometry_build 

[username@plus1 dnageometry_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnageometry 

[username@plus1 dnageometry_build]$ make

Run macro dnageometry.mac

[username@plus1 dnageometry_build]$ ./dnageometry dnageometry.mac

microbeam:

Inside /home/username/DNAProject/ create a directory

[username@plus1 DNAProject]$ mkdir microbeam_build

Compile the code with make and cmake

[username@plus1 DNAProject]$ cd microbeam_build 

[username@plus1 microbeam_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/microbeam 

[username@plus1 microbeam_build]$ make

Run macro microbeam.mac

[username@plus1 microbeam_build]$ ./microbeam microbeam.mac

How to analyze the data

dnaphysics

This is a link to the official dnaphysics tutorial explanation notes. We recommend to read it before proceeding with this tutorial.

Root file

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 physics process
  • x, y and z coordinates of the beginning of the step
  • total energy deposit alo[eV]
  • step length [nm]
  • kinetic energy difference along the step [eV]

You can open the first root file and see the different ntuples: 

[username@plus1 dnaphysics_build]$ root -l dna_t0.root

root [1] new TBrowser

Select ROOT Files, dna_t0.root and Folder dna

Click on the different leafs

You can analyze the root files using plot.C macro. 

[username@plus1 dnaphysics_build]$ root -l

root [1] .x plot.C

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. Here you can find the codes for flagParticle and flagProcess. The root macro produces the following plots:

plot.png

Run with different settings

You can change the type and the energy of the incident particle by modifying the macro dna.mac. Open the macro with editor pico: 

[username@plus1 dnaphysics_build]$ pico dna.mac

This is the content of the macro: 

#/control/execute vis.mac
/tracking/verbose 0
/run/verbose 2
#/dna/det/setMat G4_WATER_MODIFIED
/dna/det/setMat G4_WATER
/gun/particle e-
#/gun/particle proton
#/gun/particle hydrogen
#/gun/particle alpha
#/gun/particle alpha+
#/gun/particle helium
/gun/energy 1 keV
/run/initialize
/process/em/auger true
/run/beamOn 100

Visualisation

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.

dnageometry

This is a link to the official dnageometry tutorial explanation notes.

Root file

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:

  • type of particle
  • type of physics process
  • the two DNA strands
  • x, y and z coordinates of the post step [nm]
  • total energy deposit alo[eV]
  • step length [nm]

You can analyze the root files using plot.C macro. First, copy this macro to your directory, then run the root macro. 

[username@plus1 dnaphysics_build]$ cp /home/username/DNAProject/dnageometry/plot.C .

[username@plus1 dnaphysics_build]$ root -l

root [1] .x plot.C

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).

plot.png

You can modify root macro plot.C and plot the other ntuples.

microbeam

This is a link to the official microbeam tutorial explanation notes.

Root file

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. 

[username@plus1 dnaphysics_build]$ root -l

root [1] .x plot.C

plot.png

Retrieved from "https://www.hep.ucl.ac.uk/pbt/pbtWiki/index.php?title=Software/Geant4/Tutorials/Advanced/High-Precision_Dosimetry&oldid=1100"