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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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----
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=== Getting a computing account ===
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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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Apply for a computing account on the HEP Linux cluster by sending e-mail to support@hep.ucl.ac.uk. In your e-mail you have to state the reason for your application (i.e. medical physics student who will use the GEANT4 software).
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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 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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* Discussion about the tutorials  
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=== Where to get help ===
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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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== The basics of GEANT4 ==
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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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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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* [[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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* Three classes are mandatory:
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== <span style="color:#000080"> Data analysis software </span> ==
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; G4VUserDetectorConstruction
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These tutorials use ROOT to analyse data. Useful links:
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: Describe the experimental setup, geometry and materials
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* [http://root.cern.ch/drupal/content/root-users-guide-534 ROOT User's Guide]
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; G4VUserPhysicsList
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* [http://root.cern.ch/root/html534/guides/primer/ROOTPrimer.html ROOT Primer]
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: Define particles, physics processes and range cuts
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* [http://root.cern.ch/root/html/tutorials/ ROOT tutorials]
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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 classes:
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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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; G4UserRunAction
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== <span style="color:#000080"> Basic tutorials </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 the user simulation code you instantiate G4RunManager and notify it of your mandatory and optional classes.
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This section includes several basic tutorials:
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== Basic examples ==
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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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* [[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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* [[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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=== Monoenergetic photon pencil beam incident on a water cube ===
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== <span style="color:#000080"> Advanced tutorials </span> ==
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* Introduction
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This section includes several advanced tutorials:
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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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* [[Computed tomography]]
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* [[High-precision dosimetry]]
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* Setting up the environment
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== <span style="color:#000080"> Installing GEANT4 locally </span> ==
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** Connect to plus1 cluster and create a folder PhotonPencilBeam in your local area:
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* [[Downloading the Geant4 package]]
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* [[Linux terminal]]
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<blockquote>
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* [[Installing Geant4]]
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ssh username@plus1.hep.ucl.ac.uk
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* [[Updating Geant4]]
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mkdir PhotonPencilBeam
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* [[Running an example]]
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cd PhotonPencilBeam
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</blockquote>
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** Setup GEANT4 environment:
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<blockquote>
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source ... (GEANT4 script)
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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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cp /vasileva/BasicExamples/PhotonPencilBeam_source /username/PhotonPencilBeam/
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</blockquote>
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* How to run the code
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** Inside /username/PhotonPencilBeam/ create a folder:
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<blockquote>
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mkdir PhotonPencilBeam_build
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</blockquote>
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** Change to this build directory and run cmake and make to build the PhotonPencilBeam example:
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<blockquote>
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cd PhotonPencilBeam_build
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cmake -DGeant4_DIR=/unix/pbt/Software/..../ /username/PhotonPencilBeam_source/
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make
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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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* 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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* 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 examples ==
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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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* 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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* 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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Latest revision as of 10:21, 26 May 2016

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