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== Introduction ==
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== <span style="color:#000080"> Introduction </span> ==
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----
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This is a tutorial about applications of GEANT4 to medical physics. The GEANT4 is installed on the HEP Linux cluster at UCL. You will need an account on that cluster to be able to use this software, run example tutorials and create your own applications.
This is a tutorial about applications of GEANT4 to medical physics. The GEANT4 is installed on the HEP Linux cluster at UCL. You will need an account on that cluster to be able to use this software, run example tutorials and create your own applications.
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== Accounts and Registration ==
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== <span style="color:#000080"> Accounts and Discussion forum </span> ==
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=== Getting a computing account ===
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Apply for a computing account on the HEP Linux cluster by sending e-mail to [mailto:support@hep.ucl.ac.uk HEPComputingSupport]. In your e-mail you have to state the reason for your application (e.g. medical physics student who will use GEANT4 on the HEP cluster).
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You will receive an e-mail from the HEP computing support with your username and password. Now you can log in to the HEP cluster “plus1” via  ssh username@plus1.hep.ucl.ac.uk.
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* Getting a computing account
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Apply for a computing account on the HEP Linux cluster by sending e-mail to UCL HEP Computing Support. In your e-mail you have to state the reason for your application (e.g. medical physics student who will use GEANT4 on the HEP cluster).
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=== Where to get help ===
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You will receive an e-mail from the HEP computing support with your ''username'' and ''password''. Now you can log in to the HEP cluster plus1 via  ssh ''username''@plus1.hep.ucl.ac.uk. Your personal area on plus1 cluster will be at /home/''username''/.
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You can write to the discussion section.
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== The basics of GEANT4 ==
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* Discussion about the tutorials 
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GEANT4 is a toolkit for simulating the passage of particles through matter. The user creates his/her own simulation application using GEANT4 tools. The tools are base classes. There are eight base classes. 
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* Three classes are mandatory  
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You can write to the discussion forum by clicking the <span style="color:#0000ff"> discussion </span> tab at the top of the page.
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== <span style="color:#000080"> The basics of GEANT4 </span> ==
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; G4VUserDetectorConstruction
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GEANT4 is a toolkit for simulating the passage of particles through matter. You can use GEANT4 by creating your own simulation applications using the available GEANT4 tools.
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: Describe the experimental setup, geometry and materials
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; G4VUserPhysicsList
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: Define particles, physics processes and range cuts
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; G4UserPrimaryGeneratorAction
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: Describe particle source, source dimensions, initial position, energy spectrum, angular distributions
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* The rest are optional
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* [[Introduction to GEANT4]] will help you understand the basics of GEANT4 and the necessary ingredients to write your own application. 
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* Useful links:
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** [http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ Geant4 User's Guide for Application Developers]
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** [http://geant4.web.cern.ch/geant4/G4UsersDocuments/UsersGuides/PhysicsReferenceManual/html/PhysicsReferenceManual.html Physics Reference Manual]
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** [http://www-geant4.kek.jp/Reference/10.00/index.html GEANT4 Classes]
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** [http://hypernews.slac.stanford.edu/HyperNews/geant4/cindex GEANT4 hypernews]
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** [http://www-geant4.kek.jp/LXR/ Geant4 Cross Reference]
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** [http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/FAQ/html/index.html Frequently Asked Questions]
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; G4UserRunAction
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== <span style="color:#000080"> Data analysis software </span> ==
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: Define and store histograms
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; G4UserEventAction
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: Event selection and analysis of simulation data
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; G4UserStackingAction
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: Customize priority of tracks
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; G4UserTrackingAction
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: Decide whether a trajectory should be stored or not
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; G4UserSteppingAction
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: Kill, suspend, postpone a track
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You can create your own classes which are derived from the base classes. All of them should be registered with the G4RunManager. In function main() which is the skeleton of your simulation code you instantiate G4RunManager and notify it of your mandatory and optional classes.
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These tutorials use ROOT to analyse data. Useful links:
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* [http://root.cern.ch/drupal/content/root-users-guide-534 ROOT User's Guide]
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* [http://root.cern.ch/root/html534/guides/primer/ROOTPrimer.html ROOT Primer]
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* [http://root.cern.ch/root/html/tutorials/ ROOT tutorials]
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== Basic tutorials ==
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Similarly, data can be analysed using MATLAB. This is a link to interactive introduction to MATLAB:
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* [http://www.see.ed.ac.uk/teaching/courses/matlab/ MATLAB introduction]
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This section includes several basic tutorials:
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* [[Monoenergetic photon pencil beam]] is a simple code which shows the dose distribution in water along the incident monoenergetic photon beam.
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== <span style="color:#000080"> Basic tutorials </span> ==
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* [[Monoenergetic proton pencil beam]] is a simple code which shows the dose distribution in water along the incident monoenergetic proton beam.
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* [[Proton beam with realistic geometry]] is a more complex code with realistic geometry of the proton beam. It shows the dose distribution in water along the beam. There are two options for the beam geometry:  
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** Gaussian beam profile
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** Beam profile from phase space files
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* [[Several proton beams with spread out Bragg peaks]] is a complex code which shows the dose distribution in water with several incident monoenergetic proton beams. 
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This section includes several basic tutorials:
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=== Monoenergetic photon pencil beam incident on a water cube ===
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* [[Monoenergetic photon pencil beam]] is a simple code which shows the dose deposition in water along the incident monoenergetic photon beam.
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* [[Monoenergetic proton pencil beam]] is a simple code which shows the dose deposition in water along the incident monoenergetic proton beam.  
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* Introduction
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* [[Proton beam with realistic geometry]] is a simple code with realistic geometry of the proton beam. The primary particles are generated with initial energy, position and direction described by Gaussian distributions. Computed is the dose deposition in water along the beam.  
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* [[Several proton beams with spread out Bragg peaks]] is a simple code which shows the dose deposition in water from several incident monoenergetic proton beams.
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This example shows the dose distribution in water along the incident photon beam. The beam hits the water cube surface and deposits a dose under the surface of the water. The volume of the water cube is divided into voxels. At each voxel the dose contribution from the pencil beams is summed up and yields the total dose along the beam axis.  
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* [[Electron beam using phase-space files]] is a simple code which shows the dose deposition in water along the incident electron beam using phase-space data files.
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* Setting up the environment
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; Connect to plus1 cluster and create folder PhotonPencilBeam in your area
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<blockquote>
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<span style="color:#800000"> ssh username@plus1.hep.ucl.ac.uk </span> <br/>
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<span style="color:#800000"> cd /home/username/ </span> <br/>
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<span style="color:#800000"> mkdir PhotonPencilBeam </span> <br/>
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<span style="color:#800000"> cd PhotonPencilBeam </span>
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</blockquote>
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; Setup GEANT4 environment
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<blockquote>
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<span style="color:#800000"> source GEANT4 script </span>
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</blockquote>
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* How to get the code
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; Copy the code to your area
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<blockquote>
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<span style="color:#800000"> cp -r /vasileva/BasicExamples/PhotonPencilBeam_source /username/PhotonPencilBeam/ </span>
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</blockquote>
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* How to run the code  
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; Inside /username/PhotonPencilBeam/ create directory
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<blockquote>
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<span style="color:#800000"> mkdir PhotonPencilBeam_build </span>
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</blockquote>
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; Change to this directory and run cmake and make to build the PhotonPencilBeam tutorial
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<blockquote>
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<span style="color:#800000"> cd PhotonPencilBeam_build </span> <br/>
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<span style="color:#800000"> cmake -DGeant4_DIR=/unix/pbt/Software/..../ /username/PhotonPencilBeam_source/ </span> <br/>
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<span style="color:#800000"> make </span>
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</blockquote>
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* How to analyze data
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=== Monoenergetic proton pencil beam incident on a water cube ===
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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* Comparison with data from The Clatterbridge Cancer Centre
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=== Proton beam with realistic geometry incident on a water cube ===
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==== Gaussian beam profile ====
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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* Comparison with data from The Clatterbridge Cancer Centre
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==== Beam profile from phase space files ====
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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* Comparison with data from The Clatterbridge Cancer Centre
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=== Several proton beams with spread out Bragg peaks ===
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== <span style="color:#000080"> Advanced tutorials </span> ==
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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== Advanced tutorials ==
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This section includes several advanced tutorials:
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=== Cherenkov simulation ===
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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=== Computed tomography ===
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* [[Computed tomography]]
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* [[High-precision dosimetry]]
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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=== High-precision dosimetry ===
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== <span style="color:#000080"> Installing GEANT4 locally </span> ==
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* Introduction
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* Setting up the environment
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* How to get the code
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* How to run the code
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* How to analyze data
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== Installing GEANT4 software locally ==
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* [[Downloading the Geant4 package]]
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* [[Linux terminal]]
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* [[Installing Geant4]]
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* [[Updating Geant4]]
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* [[Running an example]]

Latest revision as of 10:21, 26 May 2016

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