High-precision dosimetry
From UCL HEP PBT Wiki
for
High-precision dosimetry
Jump to:
navigation
,
search
== <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> ; Run macro dna.mac. <pre style="color: #800000; background-color: #dcdcdc"> ./dnaphysics dna.mac </pre> * <span style="color:#ff0000"> dnageometry </span>: ; Inside /home/username/DNAProject/ create a directory <pre style="color: #800000; background-color: #dcdcdc"> mkdir dnageometry_build </pre> ; To compile the code enter this directory and run cmake and make <pre style="color: #800000; background-color: #dcdcdc"> cd dnageometry_build cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DNAProject/dnageometry make </pre> ; Run macro dna.mac. <pre style="color: #800000; background-color: #dcdcdc"> ./dnageometry dna.mac </pre> == <span style="color:#000080"> How to analyze data </span> == === <span style="color:#000080"> dnaphysics </span> === ==== <span style="color:#000080"> Root file </span> ==== The macro dna.mac produces root file '''dna.root''' with ntuples containing the following information for every step: * type of particle * type of physics process * x, y and z coordinates of the step * total energy deposit [eV] * step length [nm] * kinetic energy difference along the step[eV] 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. [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'''. ==== <span style="color:#000080"> Changes in macro dna.mac </span> ==== You can change the type and the energy of the incident particle by modifying the macro dna.mac. Open the macro with editor pico: #/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 ==== <span style="color:#000080"> Visualisation </span> ====
Return to
High-precision dosimetry
.
Views
Page
Discussion
View source
History
Personal tools
Log in
Navigation
Main page
Community portal
Current events
Recent changes
Random page
Help
Search
Toolbox
What links here
Related changes
Special pages