lars/geant4
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Import Geant4 11.0.0 source tree

Browse Source
This commit is contained in:
Gabriele Cosmo
2021-12-12 17:16:06 +01:00
parent 80e2389dd8
commit 84f33a068c
593 changed files with 68589 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
examples/advanced/brachytherapy/README
+192
View File
@@ -0,0 +1,192 @@
=========================================================
Geant4 - Brachytherapy example
=========================================================
README
---------------------
The brachytherapy example is currently maintained and upgraded by Susanna Guatelli (1), Albert Le (1) and Dean Cutajar (1), with the support of
Luciano Pandola (2)
1. Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia.
2. LNS, INFN, Catania, Italy.
------------------------------------------------------------------------
Contact: susanna@uow.edu.au
deanc@uow.edu.au
geant4-advanced-examples@cern.ch
------------------------------------------------------------------------
List of past co-authors:
S. George, S. Agostinelli, F. Foppiano, S. Garelli, M. G. Pia, M. Tropeano
-----------------------------------------------------------------
----> Introduction.
Brachytherapy example simulates the energy deposit in a water phantom, produced by:
1) Iridium sources (Flexisource and TG186).
2) Iodine sources (Bebig Isoseed and Oncura 6711 I-125).
3) Leipzig Applicator with an iridium source (model from the Istituto Tumori, Genova, Italy).
The Flexisource, an Ir-192 source manufactured by Nucletron, an Elekta company, is a source commonly used for high dose rate brachytherapy treatments.
The geometry of the Flexisource was adapted from D. Granero, J. Pérez-Calatayud, E. Casal, et al,
"A dosimetric study on the Ir-192 high dose rate Flexisource", Med. Phys. 33 (12), 2006, 4578-82.
The TG186 source is a generic Ir-192 source created to provide developers of model based dose engines with a method of validating new dose calculation techniques.
Details of the TG186 source may be obtained from Facundo Ballester, Åsa Carlsson Tedgren, Domingo Granero, et al,
"A generic high-dose rate 192Ir brachytherapy source for evaluation of model-based dose calculations beyond the TG-43 formalism", Med. Phys. 42, 2015, 3048-62
In particular in this example it is shown how to:
- model a radioactive source in terms of radiation field and geometry
- model the radiation field with the General Particle Source with two alternative methods:
1) Define the energy spectrum of photons exiting the radioactive core
2) Modelling the Radioactive decay
- calculate the energy deposition in a phantom by means of the G4 scoring mesh
- define the physics by means of a Geant4 Modular Physics List
- save results in an analysis ROOT file
- calculate the dose rate distribution along the main axis of the source
- compare the calculated dose rate distribution to reference data.
In the case of the example, the dose rate distribution of a Flexisource is compared to D. Granero,
J. Pérez-Calatayud, E. Casal, et al,"A dosimetric study on the Ir-192 high dose rate Flexisource", Med. Phys. 33 (12), 2006, 4578-82.
The dose rate distribution of the Oncura 6711 I-125 source is compared to J. Dolan, Z. Lia, J. F. Williamson, "Monte Carlo and experimental
dosimetry of an I-125 brachytherapy seed", Med. Phys. 33(12), 2006.
The example can be executed in multithreading mode.
------------------------------------------------------------------------
----> 1.Experimental set-up.
The default source is a Ir-192 Flexisource set in the center of a water phantom with size 30 cm.
The phantom is set in the World volume filled with air.
The primary radiation field is defined by means of the GeneralParticleSource
-------------------------------------------------------------------------
----> 2.SET-UP
A standard Geant4 example CMakeLists.txt is provided.
------------------------------------------------------------------------
----> 3.How to run the example.
- Batch mode:
$G4WORKDIR/bin/Linux-g++/Brachy FlexiSourceMacro.mac
$G4WORKDIR/bin/Linux-g++/Brachy LeipzigSourceMacro.mac
$G4WORKDIR/bin/Linux-g++/Brachy IridiumSourceMacro.mac
$G4WORKDIR/bin/Linux-g++/Brachy IodiumSourceMacro.mac (model of the Bebig Isoseed I-125)
$G4WORKDIR/bin/Linux-g++/Brachy OncuraIodineSourceMacro.mac (model of the Oncura 6711 I-125)
$G4WORKDIR/bin/Linux-g++/Brachy LeipzigSourceMacro.mac
- Interative mode:
3) $G4WORKDIR/bin/Linux-g++/Brachy
VisualisationMacro.mac is loaded automatically.
* How to change the absorber material of the phantom:
idle>/phantom/selectMaterial materialName
---------------------------------------------------------------------------------
----> 4. Primary radiation Field
The radiation field is defined with the General Particle Source.
Two alternative options are offered:
1) Define gamma as primary radiation field. The gamma are originated from the radioactive core.
This radiation field is defined in:
iodine_source_primary.mac and iridium_source_primary.mac
2) Model the radioactive Decay. The primary particle is the radionuclide.
This option is modelled in iodine_decay.mac and TG186_iridium_decay.mac
The GPS macros are executed in VisualisationMacro.mac by default, FlexiSourceMacro.mac, IodineSourceMacro.mac, LeipzigSourceMacro.mac
- The Flexisource is the default source of the example.
- In VisualisationMacro.mac the source is the default one. iridium_source_primary.mac is executed to define the radiation field emerging from the iridium core.
- In FlexiSourceMacro.mac the Flexi Ir source geometry is selected via interactive command. The radiation field is defined in the iridium_source_primary.mac.
- In IodineSourceMacro.mac, the Bebig Isoseed I-125 brachytherapy source is modelled. The radiation field is modelled in terms of emitted photons in iodine_source_primary.mac.
Alternatively the radioactive decay of I can be modelled using teh macro iodine_decay.mac.
- In LeipzigSourceMacro.mac, A Leipzig applicator (design provided by Istituto Tumori, Genova) is modelled. The iridium_source_leipzig_primary.mac defines the radiation field of the Ir core.
- The TG186SourceMacro.mac models the reference bIr brachytherapy source. The radiation field can be either defined with the iridium_source_primary.mac (spectrum of the emitted photons) or with TG186_iridium_decay.mac (model of the Ir decay).
- OncuraIodineSourceMacro.mac models both the geometry and the radioactive decay of the Oncura 6711 I-125 source.
--------------------------------------------------------------------------------
----> 5. Physics List
The electromagnetic Livermore Low Energy physics is active as well as the radioactive decay.
The cut is 0.05 mm.
Fluorescence and Auger electron emission are included.
------------------------------------------------------------------------
----> 6. Scoring mesh
The scoring mesh is used to calculate the energy deposition in the plane containing the source (z=0 plane)
integrated over the whole run. The scoring mesh is defined in the input macro files.
The default output format of the scoring is changed in the class BrachyUserScoreWriter.
The scoring mesh is fixed with a size of 20.025 cm along x and y. The bin size is 0.25 mm along x, y and z.
When running in interactive mode there is no scoring mesh.The user has to add it with appropriate UI
------------------------------------------------------------------------
----> 6. Analysis
G4Analysis is used to create and fill histograms in ROOT output files.
The installation of ROOT is required to plot the results of the simulation contained
in primary.root and brachytherapy.root(http://root.cern.ch/drupal/).
------------------------------------------------------------------------
----> 7. Simulation output
The output is:
- ASCII file EnergyDeposition.out, with xx (mm), yy(mm), zz(mm), and energy deposition (keV), in the phantom.
To limit the use of memory, the energy deposition is scored only in the plane containing the source, however this can be changed by the user.
By default:
EnergyDeposition_Flexi.out contains the Edep when the Flexi source is selected.
EnergyDeposition_iodine.out contains the Edep when Iodine Bebig Isoseed source is selected.
EnergyDeposition_TG186.out contains the Edep when the TG186 source is selected.
EnergyDeposition_Leipzig.out contains the Edep when the Iridium source with Leipzig applicator is selected.
EnergyDeposition_Oncura.out contains the Edep when the Iodine Oncura 6711 source is selected.
- brachytherapy.root, containing a 2D histogram with the energy deposition in the phantom. The macro macro.C is provided as example
to open brachytherapy.root in ROOT interactive session and to plot the results of the simulation.
- primary.root, with 1D histogram of the energy spectrum of photons emitted by the radionuclide (see section 4).
plot_primary.C is provided as example to open primary.root and to plot the energy spectra
-------------------------------------------------------------------------------
----> 8.Visualisation
A macro is provided ad example of visualisation: VisualisationMacro.mac.
-------------------------------------------------------------------------------
-----> 9. Comparison to reference data
The ROOT macros macro.C and plot_primary.C are provided to plot the results of the simulation, contained
in the brachytherapy.root file.
The ROOT macro TG43_relative_dose.C has brachytherapy.root as input file. It calculates the dose rate distribution along the main axis of
the brachytherapy source. The dose rate is normalised to 1 at 1 cm distance from the centre.
The output file is geant4_dose.txt with two columns:
distance from the centre (cm) dose rate distribution
The user can then compare the dose rate distribution calculated with the example to reference data.
Directory "comparison":
As an example, the dose rate distribution calculated with the Flexisource is compared to reference data from D. Granero, J. Pérez-Calatayud, E. Casal, et al, "A dosimetric study on the Ir-192 high dose rate Flexisource", Med. Phys. 33 (12), 2006, 4578-82.
The compare.C is a ROOT macro which reads the dose rate distribution calculated with the Flexisource (geant4.txt generated with the advanced example and 280 M histories ) against the reference.
The directory "comparison" contains:
- the reference data, granero.txt
- the data obtained in Geant4.10.3: geant4.txt, 280 M events. geant4.txt is obtained when executing the macro TG43_relative_dose.C
- comparison.C - macro to read geant4.txt and granero.txt and compare them in the same plot
-----> 10. Regression testing of Geant4
- the macros to run are in test_macro
- the results should be processed with analysis.C
examples/advanced/brachytherapy/test_macro/FlexiSourceMacro_livermore.mac
+30
View File
@@ -0,0 +1,30 @@
/testem/phys/addPhysics emlivermore
/run/initialize
/control/verbose 1
/tracking/verbose 0
/run/verbose 0
/event/verbose 0
#
/source/switch Flexi
###### Generation of primary field
#### Generate gamma deriving from radioactive decay
/control/execute iridium_source_primary.mac
# Scoring mesh is used to calculate
# the energy deposition in the phantom
/score/create/boxMesh boxMesh_4
#
# the voxels are 0.25 mm wide.
/score/mesh/boxSize 10.0125 10.0125 0.0125 cm
/score/mesh/nBin 801 801 1
/score/quantity/energyDeposit eDep
#
/score/close
#
/score/list
/run/beamOn 1000000000
#
# Dump scores to a file
#
/score/dumpQuantityToFile boxMesh_4 eDep EnergyDeposition_Flexi_livermore.out
#
examples/advanced/brachytherapy/test_macro/FlexiSourceMacro_opt0.mac
+30
View File
@@ -0,0 +1,30 @@
/testem/phys/addPhysics emstandard_opt0
/run/initialize
/control/verbose 1
/tracking/verbose 0
/run/verbose 0
/event/verbose 0
#
/source/switch Flexi
###### Generation of primary field
#### Generate gamma deriving from radioactive decay
/control/execute iridium_source_primary.mac
# Scoring mesh is used to calculate
# the energy deposition in the phantom
/score/create/boxMesh boxMesh_4
#
# the voxels are 0.25 mm wide.
/score/mesh/boxSize 10.0125 10.0125 0.0125 cm
/score/mesh/nBin 801 801 1
/score/quantity/energyDeposit eDep
#
/score/close
#
/score/list
/run/beamOn 1000000000
#
# Dump scores to a file
#
/score/dumpQuantityToFile boxMesh_4 eDep EnergyDeposition_Flexi_opt0.out
#
examples/advanced/brachytherapy/test_macro/FlexiSourceMacro_opt3.mac
+30
View File
@@ -0,0 +1,30 @@
/testem/phys/addPhysics emstandard_opt3
/run/initialize
/control/verbose 1
/tracking/verbose 0
/run/verbose 0
/event/verbose 0
#
/source/switch Flexi
###### Generation of primary field
#### Generate gamma deriving from radioactive decay
/control/execute iridium_source_primary.mac
# Scoring mesh is used to calculate
# the energy deposition in the phantom
/score/create/boxMesh boxMesh_4
#
# the voxels are 0.25 mm wide.
/score/mesh/boxSize 10.0125 10.0125 0.0125 cm
/score/mesh/nBin 801 801 1
/score/quantity/energyDeposit eDep
#
/score/close
#
/score/list
/run/beamOn 1000000000
#
# Dump scores to a file
#
/score/dumpQuantityToFile boxMesh_4 eDep EnergyDeposition_Flexi_opt3.out
#
examples/advanced/brachytherapy/test_macro/FlexiSourceMacro_opt4.mac
+30
View File
@@ -0,0 +1,30 @@
/testem/phys/addPhysics emstandard_opt4
/run/initialize
/control/verbose 1
/tracking/verbose 0
/run/verbose 0
/event/verbose 0
#
/source/switch Flexi
###### Generation of primary field
#### Generate gamma deriving from radioactive decay
/control/execute iridium_source_primary.mac
# Scoring mesh is used to calculate
# the energy deposition in the phantom
/score/create/boxMesh boxMesh_4
#
# the voxels are 0.25 mm wide.
/score/mesh/boxSize 10.0125 10.0125 0.0125 cm
/score/mesh/nBin 801 801 1
/score/quantity/energyDeposit eDep
#
/score/close
#
/score/list
/run/beamOn 1000000000
#
# Dump scores to a file
#
/score/dumpQuantityToFile boxMesh_4 eDep EnergyDeposition_Flexi_opt4.out
#
examples/advanced/brachytherapy/test_macro/FlexiSourceMacro_penelope.mac
+29
View File
@@ -0,0 +1,29 @@
/testem/phys/addPhysics empenelope
/run/initialize
/control/verbose 1
/tracking/verbose 0
/run/verbose 0
/event/verbose 0
#
/source/switch Flexi
###### Generation of primary field
#### Generate gamma deriving from radioactive decay
/control/execute iridium_source_primary.mac
# Scoring mesh is used to calculate
# the energy deposition in the phantom
/score/create/boxMesh boxMesh_4
#
# the voxels are 0.25 mm wide.
/score/mesh/boxSize 10.0125 10.0125 0.0125 cm
/score/mesh/nBin 801 801 1
/score/quantity/energyDeposit eDep
#
/score/close
#
/score/list
/run/beamOn 1000000000
#
# Dump scores to a file
#
/score/dumpQuantityToFile boxMesh_4 eDep EnergyDeposition_Flexi_penelope.out
#
examples/advanced/brachytherapy/test_macro/iridium_source_primary.mac
+129
View File
@@ -0,0 +1,129 @@
/gps/ene/type Arb
/gps/hist/type arb
/gps/hist/point 0.0614 1e-8
/gps/hist/point 0.0615 0.412
/gps/hist/point 0.0616 1e-8
/gps/hist/point 0.0629 1e-8
/gps/hist/point 0.063 0.7039
/gps/hist/point 0.0631 1e-8
/gps/hist/point 0.0650 1e-8
/gps/hist/point 0.0651 1.1309
/gps/hist/point 0.0652 1e-8
/gps/hist/point 0.0667 1e-8
/gps/hist/point 0.0668 1.9178
/gps/hist/point 0.0669 1e-8
/gps/hist/point 0.0710 1e-8
/gps/hist/point 0.0711 0.0827
/gps/hist/point 0.0712 1e-8
/gps/hist/point 0.0713 1e-8
/gps/hist/point 0.0714 0.1600
/gps/hist/point 0.0715 1e-8
/gps/hist/point 0.0733 1e-8
/gps/hist/point 0.0734 0.0560
/gps/hist/point 0.0735 1e-8
/gps/hist/point 0.0753 1e-8
/gps/hist/point 0.0754 0.2292
/gps/hist/point 0.0755 1e-8
/gps/hist/point 0.0756 1e-8
/gps/hist/point 0.0757 0.4408
/gps/hist/point 0.0758 1e-8
/gps/hist/point 0.0777 1e-8
/gps/hist/point 0.0778 0.1570
/gps/hist/point 0.0779 1e-8
/gps/hist/point 0.1103 1e-8
/gps/hist/point 0.1104 0.0042
/gps/hist/point 0.1105 1e-8
/gps/hist/point 0.1362 1e-8
/gps/hist/point 0.1363 0.0860
/gps/hist/point 0.1364 1e-8
/gps/hist/point 0.1769 1e-8
/gps/hist/point 0.1770 0.0018
/gps/hist/point 0.1771 1e-8
/gps/hist/point 0.2012 1e-8
/gps/hist/point 0.2013 0.1624
/gps/hist/point 0.2014 1e-8
/gps/hist/point 0.2057 1e-8
/gps/hist/point 0.2058 1.1468
/gps/hist/point 0.2059 1e-8
/gps/hist/point 0.2802 1e-8
/gps/hist/point 0.2803 0.0039
/gps/hist/point 0.2804 1e-8
/gps/hist/point 0.2832 1e-8
/gps/hist/point 0.2833 0.0913
/gps/hist/point 0.2834 1e-8
/gps/hist/point 0.2959 1e-8
/gps/hist/point 0.2960 12.3498
/gps/hist/point 0.2961 1e-8
/gps/hist/point 0.3084 1e-8
/gps/hist/point 0.3085 12.7626
/gps/hist/point 0.3086 1e-8
/gps/hist/point 0.3164 1e-8
/gps/hist/point 0.3165 35.5660
/gps/hist/point 0.3166 1e-8
/gps/hist/point 0.3291 1e-8
/gps/hist/point 0.3292 0.0060
/gps/hist/point 0.3293 1e-8
/gps/hist/point 0.3744 1e-8
/gps/hist/point 0.3745 0.2493
/gps/hist/point 0.3746 1e-8
/gps/hist/point 0.4164 1e-8
/gps/hist/point 0.4165 0.2877
/gps/hist/point 0.4166 1e-8
/gps/hist/point 0.4204 1e-8
/gps/hist/point 0.4205 0.0237
/gps/hist/point 0.4206 1e-8
/gps/hist/point 0.4680 1e-8
/gps/hist/point 0.4681 20.5587
/gps/hist/point 0.4682 1e-8
/gps/hist/point 0.4845 1e-8
/gps/hist/point 0.4846 1.0942
/gps/hist/point 0.4847 1e-8
/gps/hist/point 0.4852 1e-8
/gps/hist/point 0.4853 0.0010
/gps/hist/point 0.4854 1e-8
/gps/hist/point 0.4890 1e-8
/gps/hist/point 0.4891 0.1504
/gps/hist/point 0.4892 1e-8
/gps/hist/point 0.5885 1e-8
/gps/hist/point 0.5886 1.9423
/gps/hist/point 0.5887 1e-8
/gps/hist/point 0.5934 1e-8
/gps/hist/point 0.5935 0.0181
/gps/hist/point 0.5936 1e-8
/gps/hist/point 0.5993 1e-8
/gps/hist/point 0.5994 0.0017
/gps/hist/point 0.5995 1e-8
/gps/hist/point 0.6043 1e-8
/gps/hist/point 0.6044 3.5361
/gps/hist/point 0.6045 1e-8
/gps/hist/point 0.6124 1e-8
/gps/hist/point 0.6125 2.2962
/gps/hist/point 0.6126 1e-8
/gps/hist/point 0.7038 1e-8
/gps/hist/point 0.7039 0.0018
/gps/hist/point 0.7040 1e-8
/gps/hist/point 0.7657 1e-8
/gps/hist/point 0.7658 0.0006
/gps/hist/point 0.7659 1e-8
/gps/hist/point 0.8844 1e-8
/gps/hist/point 0.8845 0.1251
/gps/hist/point 0.8846 1e-8
/gps/hist/point 1.0614 1e-8
/gps/hist/point 1.0615 0.0228
/gps/hist/point 1.0616 1e-8
/gps/hist/point 1.0898 1e-8
/gps/hist/point 1.0899 0.0005
/gps/hist/point 1.0890 1e-8
/gps/hist/point 1.3781 1e-8
/gps/hist/point 1.3782 0.0005
/gps/hist/point 1.3783 1e-8
/gps/hist/inter Lin
/gps/particle gamma
/gps/pos/type Volume
/gps/pos/shape Cylinder
/gps/pos/radius 0.30 mm
/gps/pos/halfz 1.75 mm
/gps/pos/centre 0. 0. 0. mm
/gps/ang/type iso