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== Introduction ==
== Introduction ==
 +
----
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.
== Accounts and Registration ==
== Accounts and Registration ==
 +
----
=== Getting a computing account ===
=== Getting a computing account ===
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== The basics of GEANT4 ==
== The basics of GEANT4 ==
 +
----
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:   
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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== Basic examples ==
== Basic examples ==
 +
----
 +
 +
=== Monoenergetic photon pencil beam incident on a water cube ===
 +
 +
* Introduction
 +
 +
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.
 +
 +
* Setting up the environment
 +
 +
** Connect to plus1 cluster and create a folder PhotonPencilBeam in your local area:
 +
 +
<blockquote>
 +
ssh username@plus1.hep.ucl.ac.uk
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mkdir PhotonPencilBeam
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cd PhotonPencilBeam
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</blockquote>
 +
 +
** Setup GEANT4 environment:
 +
 +
<blockquote>
 +
source ... (GEANT4 script)
 +
</blockquote>
 +
 +
* How to get the code
 +
 +
** Copy the code to your area:
 +
 +
<blockquote>
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cp /vasileva/BasicExamples/PhotonPencilBeam_source /username/PhotonPencilBeam/
 +
</blockquote>
 +
 +
* How to run the code
 +
 +
** Inside /username/PhotonPencilBeam/ create a folder:
 +
 +
<blockquote>
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mkdir PhotonPencilBeam_build
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</blockquote>
 +
 +
** Change to this build directory and run cmake and make to build the PhotonPencilBeam example:
 +
 +
<blockquote>
 +
cd PhotonPencilBeam_build
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cmake -DGeant4_DIR=/unix/pbt/Software/..../ /username/PhotonPencilBeam_source/
 +
make
 +
</blockquote>
 +
 +
* How to analyze data
 +
 +
=== Monoenergetic proton pencil beam incident on a water cube ===
 +
 +
* Introduction
 +
* Setting up the environment
 +
* How to get the code
 +
* How to run the code
 +
* How to analyze data
 +
* Comparison with data from The Clatterbridge Cancer Centre
 +
 +
=== Proton beam with realistic geometry incident on a water cube ===
 +
 +
* Introduction
 +
* Setting up the environment
 +
* How to get the code
 +
* How to run the code
 +
* How to analyze data
 +
* Comparison with data from The Clatterbridge Cancer Centre
 +
 +
=== Several proton beams with spread out Bragg peaks ===
 +
 +
* Introduction
 +
* Setting up the environment
 +
* How to get the code
 +
* How to run the code
 +
* How to analyze data
== Advanced examples ==
== Advanced examples ==
 +
----
-
== Installing GEANT4 software locally ==
+
=== Cherenkov simulation ===
 +
* Introduction
 +
* Setting up the environment
 +
* How to get the code
 +
* How to run the code
 +
* How to analyze data
 +
=== Computed tomography ===
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* Introduction
 +
* Setting up the environment
 +
* How to get the code
 +
* How to run the code
 +
* How to analyze data
-
Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
+
=== High-precision dosimetry ===
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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
+
 
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* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
+
* Introduction
-
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
+
* Setting up the environment
 +
* How to get the code
 +
* How to run the code
 +
* How to analyze data
 +
 
 +
== Installing GEANT4 software locally ==
 +
----

Revision as of 12:11, 2 July 2014

Contents

Introduction


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.

Accounts and Registration


Getting a computing account

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).

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.

Where to get help

The basics of GEANT4


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:

  • Three classes are mandatory:
G4VUserDetectorConstruction
Describe the experimental setup, geometry and materials
G4VUserPhysicsList
Define particles, physics processes and range cuts
G4UserPrimaryGeneratorAction
Describe particle source, source dimensions, initial position, energy spectrum, angular distributions
  • The rest are optional classes:
G4UserRunAction
Define and store histograms
G4UserEventAction
Event selection and analysis of simulation data
G4UserStackingAction
Customize priority of tracks
G4UserTrackingAction
Decide whether a trajectory should be stored or not
G4UserSteppingAction
Kill, suspend, postpone a track

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.

Basic examples


Monoenergetic photon pencil beam incident on a water cube

  • Introduction

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.

  • Setting up the environment
    • Connect to plus1 cluster and create a folder PhotonPencilBeam in your local area:
ssh username@plus1.hep.ucl.ac.uk mkdir PhotonPencilBeam cd PhotonPencilBeam
    • Setup GEANT4 environment:
source ... (GEANT4 script)
  • How to get the code
    • Copy the code to your area:
cp /vasileva/BasicExamples/PhotonPencilBeam_source /username/PhotonPencilBeam/
  • How to run the code
    • Inside /username/PhotonPencilBeam/ create a folder:
mkdir PhotonPencilBeam_build
    • Change to this build directory and run cmake and make to build the PhotonPencilBeam example:
cd PhotonPencilBeam_build cmake -DGeant4_DIR=/unix/pbt/Software/..../ /username/PhotonPencilBeam_source/ make
  • How to analyze data

Monoenergetic proton pencil beam incident on a water cube

  • Introduction
  • Setting up the environment
  • How to get the code
  • How to run the code
  • How to analyze data
  • Comparison with data from The Clatterbridge Cancer Centre

Proton beam with realistic geometry incident on a water cube

  • Introduction
  • Setting up the environment
  • How to get the code
  • How to run the code
  • How to analyze data
  • Comparison with data from The Clatterbridge Cancer Centre

Several proton beams with spread out Bragg peaks

  • Introduction
  • Setting up the environment
  • How to get the code
  • How to run the code
  • How to analyze data

Advanced examples


Cherenkov simulation

  • Introduction
  • Setting up the environment
  • How to get the code
  • How to run the code
  • How to analyze data

Computed tomography

  • Introduction
  • Setting up the environment
  • How to get the code
  • How to run the code
  • How to analyze data

High-precision dosimetry

  • Introduction
  • Setting up the environment
  • How to get the code
  • How to run the code
  • How to analyze data

Installing GEANT4 software locally


Personal tools