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== Introduction ==
== Geant4 ==
 
This is a tutorial about applications of GEANT4 to medical physics.
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.
 
== Accounts ==
 
* Getting a computing account
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).
 
You will receive an e-mail from the HEP computing support with your <code>username</code> 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''/.
 
== The basics of GEANT4 ==


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.  
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.  


* [[Software/Geant4/Introduction|Introduction to GEANT4]] will help you understand the basics of GEANT4 and the necessary ingredients to write your own application.   
* [[/Introduction|Introduction to GEANT4]] will help you understand the basics of GEANT4 and the necessary ingredients to write your own application.   
* Useful links:  
* Useful links:  
** [http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ Geant4 User's Guide for Application Developers]  
** [http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ Geant4 User's Guide for Application Developers]  
Line 25: Line 12:
** [http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/FAQ/html/index.html Frequently Asked Questions]  
** [http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/FAQ/html/index.html Frequently Asked Questions]  


== Data Analysis Software ==
This is a tutorial about applications of GEANT4 to medical physics.
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.
 
== Running Geant4 Simulations ==
 
In order to run Geant4 simulations, you will either need to download and install the software yourself or source Geant4 over CVMFS via he UCL HEP Linux cluster. (There is an existing installation on the UCL HEP Linux cluster, however this version 10.3). 
 
In order to use the UCL HEP Linux cluster, you will need a HEP account: please contact Prof. Simon Jolly for more details. 
 
For more information on using Geant4 on the HEP Linux cluster, see the [[/UCL HEP Cluster|UCL HEP Linux Cluster page]]. 
 
Input files for Geant4 are simply plain text files than can be edited with your preferred text editor. 
For remote editing on multiple platforms, it is possible to use the [http://www.eclipse.org Eclipse IDE]:
for instructions on using Eclipse to edit files over SSH, [[/Eclipse|see the PBTWiki Eclipse page]].


These tutorials use ROOT to analyse data. Useful links:
To submit Geant4 jobs to the HEP Linux cluster, see the [[/UCL HEP Batch Farm|UCL HEP Batch Farm page]].
* [http://root.cern.ch/drupal/content/root-users-guide-534 ROOT User's Guide]
* [http://root.cern.ch/root/html534/guides/primer/ROOTPrimer.html ROOT Primer]
* [http://root.cern.ch/root/html/tutorials/ ROOT tutorials]


Similarly, data can be analysed using MATLAB. This is a link to interactive introduction to MATLAB:
In order to install your own version of Geant4, you will need to download and compile the course code from the [http://geant4.web.cern.ch/geant4/ CERN Geant4 website]. 
* [http://www.see.ed.ac.uk/teaching/courses/matlab/ MATLAB introduction]


== Tutorials ==
Extensive instructions have been put together describing how to compile the code yourself. The best place to start is the [[/Installation|Geant4 Installation page]].


There are two sets of tutorials available to help you getting started in running simulations with Geant4:
'''Full instructions for installing Geant4 on MacOS can be found [https://www.hep.ucl.ac.uk/pbt/wiki/Proton_Calorimetry/Detector_Simulation here].'''


=== Basic ===
== [[/Tutorials|Tutorials]] ==


There are several basic tutorials that introduce the rudiments of Geant4 simulations for proton therapy:
A number of tutorials are available to help you get started running your own simulations. 
It is recommended that novice users make use of these simulations as templates to construct their own.


* [[Software/Geant4/Tutorials/Basic/Monoenergetic Photon Pencil Beam|Monoenergetic Photon Pencil Beam]] is a simple code which shows the dose deposition in water along the incident monoenergetic photon beam.
There are tutorials available to help you getting started in running simulations with Geant4 over the UCL HEP Linux Cluster via CVMFS (recommended):
* [[Software/Geant4/Tutorials/Basic/Monoenergetic Proton Pencil Beam|Monoenergetic Proton Pencil Beam]] is a simple code which shows the dose deposition in water along the incident monoenergetic proton beam.
* [[Software/Geant4/Tutorials/Basic/Proton Beam With Realistic Geometry|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.
* [[Software/Geant4/Tutorials/Basic/Spread Out Bragg Peaks|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. 
* [[Software/Geant4/Tutorials/Basic/Electron Beam Using Phase-Space Files|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.


=== Advanced ===
* [[/Tutorials/PBTCVMFS|Basic PBT Tutorials]] introduce the rudiments of Geant4 for proton therapy simulations: these are described in more detail on the [[/Tutorials/PBTCVMFS|Basic PBT Tutorials]].


There are two more advanced tutorials available:
There are also two sets of tutorials available using the older version Geant4 (10.2) that's installed on the  UCL HEP Linux Cluster (only use if absolutely necessary):


* [[Software/Geant4/Tutorials/Advanced/Computed Tomography|Computed Tomography]]
* [[/Tutorials/Basic|The Basic Tutorials]] introduce the rudiments of Geant4 for proton therapy simulations: these are described in more detail on the [[/Tutorials/Basic|Basic Tutorials page]].
* [[Software/Geant4/Tutorials/Advanced/High-Precision Dosimetry|High-Precision Dosimetry]]
* [[/Tutorials/Advanced|The Advanced Tutorials]] describe more sophisticated proton therapy simulations in Geant4: more information can be found on the [[/Tutorials/Advanced|Advanced Tutorials page]].


== Installing GEANT4 locally ==
== Data Analysis Software ==


* [[Downloading the Geant4 package]]
These tutorials use ROOT to analyse data. Useful links:
* [[Linux terminal]]
* [http://root.cern.ch/drupal/content/root-users-guide-534 ROOT User's Guide]
* [[Installing Geant4]]
* [http://root.cern.ch/root/html534/guides/primer/ROOTPrimer.html ROOT Primer]
* [[Updating Geant4]]
* [http://root.cern.ch/root/html/tutorials/ ROOT tutorials]  
* [[Running an example]]
 
Similarly, data can be analysed using MATLAB. This is a link to interactive introduction to MATLAB:
* [http://www.see.ed.ac.uk/teaching/courses/matlab/ MATLAB introduction]

Latest revision as of 16:00, 13 November 2024

Geant4

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.

This is a tutorial about applications of GEANT4 to medical physics. 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.

Running Geant4 Simulations

In order to run Geant4 simulations, you will either need to download and install the software yourself or source Geant4 over CVMFS via he UCL HEP Linux cluster. (There is an existing installation on the UCL HEP Linux cluster, however this version 10.3).

In order to use the UCL HEP Linux cluster, you will need a HEP account: please contact Prof. Simon Jolly for more details.

For more information on using Geant4 on the HEP Linux cluster, see the UCL HEP Linux Cluster page.

Input files for Geant4 are simply plain text files than can be edited with your preferred text editor. For remote editing on multiple platforms, it is possible to use the Eclipse IDE: for instructions on using Eclipse to edit files over SSH, see the PBTWiki Eclipse page.

To submit Geant4 jobs to the HEP Linux cluster, see the UCL HEP Batch Farm page.

In order to install your own version of Geant4, you will need to download and compile the course code from the CERN Geant4 website.

Extensive instructions have been put together describing how to compile the code yourself. The best place to start is the Geant4 Installation page.

Full instructions for installing Geant4 on MacOS can be found here.

Tutorials

A number of tutorials are available to help you get started running your own simulations. It is recommended that novice users make use of these simulations as templates to construct their own.

There are tutorials available to help you getting started in running simulations with Geant4 over the UCL HEP Linux Cluster via CVMFS (recommended):

There are also two sets of tutorials available using the older version Geant4 (10.2) that's installed on the UCL HEP Linux Cluster (only use if absolutely necessary):

Data Analysis Software

These tutorials use ROOT to analyse data. Useful links:

Similarly, data can be analysed using MATLAB. This is a link to interactive introduction to MATLAB:

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