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=========================================================
Text version of the Hadrontherapy README file
=========================================================
=========================================================
Text version of the Hadrontherapy README file
=========================================================
Last revision: F.Romano, 5 November 2015;
Released with the Geant4 10.2 version (December 2015)
Last revision:
Released with the Geant4 10.7 version (December 2020)
------------------------------------------------------------------------------------------------
ADVERTISEMENT: this is the text version of the README file of the 'basic' hadrontherapy,
as it has been released in the official Geant4 9.6 release
as it has been released in the Geant4 10.7 release
Visit the Hadrontherapy web site (https://twiki.cern.ch/twiki/bin/view/Geant4/AdvancedExamplesHadrontherapy) to request
the complete version of this program, together with its documentation;
@@ -17,54 +16,60 @@ Institute in the framework of the MC-INFN Group
-------------------------------------------------------------------------------------------------
=========================================================
HADRONTHERAPY
=========================================================
=========================================================
HADRONTHERAPY
=========================================================
==========> MAIN AUTHORS <==========
G.A.P. Cirrone(a)*, F.Romano(a), G.Cuttone(a), L. Pandola(a), G.Milluzzo(a), J.Pipek(a)
G.A.P. Cirrone(a)*, L. Pandola(a), G.Milluzzo(a), G.Petringa(a)
==========> PAST AUTHORS <==========
R. Calcagno(a), G.Danielsen (b), F.Di Rosa(a), S.Guatelli(c), A.Heikkinen(b), P.Kaitaniemi(b),
A.Lechner(d), S.E.Mazzaglia(a), M.G.Pia(e), G.Russo(a), M.Russo(a), A.Varisano(a), A. Tramontana (a,f)
J.Pipek(a),R. Calcagno(a), G.Cuttone(a),G.Danielsen (b), F.Di Rosa(a), S.Guatelli(c), A.Heikkinen(b), P.Kaitaniemi(b),
A.Lechner(d), S.E.Mazzaglia(a), M.G.Pia(e), F.Romano(f), G.Russo(a), M.Russo(a), A.Varisano(a), A. Tramontana (a,f)
(a) Laboratori Nazionali del Sud of the INFN, Catania, Italy
(b) Helsinki Institute of Physics, Helsinki, Finland
(c) University of Wollongong, Australia
(d) CERN, (CH)
(e) INFN Section of Genova, genova, Italy
(f) Physics and Astronomy Department, Universituy of Catania, Catania, Italy
(e) INFN Section of Genova, Genova, Italy
(f) Physics and Astronomy Department, University of Catania, Catania, Italy
*Corresponding authors, email to: cirrone@lns.infn.it, francesco.romano@lns.infn.it
*Corresponding author, email to: cirrone@lns.infn.it
-------------------------------------------------------------------------------------------------
HADRONTHERAPY:
WHAT IT IS, WHAT IT DOES AND WHAT IT WILL PROVIDE
'hadrontherapy' is a Geant4-based application specifically developed to address typical needs related to the proton and ion therapy.
Its first release was in 2004. At that time 'hadrontherapy' was only capable to simulate a well specified proton therapy facility: the passive transport beam line installed at Laboratori Nazionali del Sud (INFN) in Catania, Italy.
===================================================
Today Hadrontontherapy, except that it is in continuous development, is more flexible and shows many additional capabilities with respect to the past.
Its geometrical set-up, for example, is now completely interchangeable permitting a simple switch between different geometrical configurations, which all share the same phantom (sensible detector) with the related features.
It is possible to do a simulation of a generic proton/ion transport beam line and laser-driven beam line. In this release, a module for dose average LET computations has been also included.
Deprecated ReadOutGeometry has been replaced by the use of Parallel World.
'hadrontherapy' is a Geant4-based application specifically developed to address typical needs related to proton and ion therapy.
Its first release was in 2004. At that time 'hadrontherapy' was only capable of simulating a well-specified proton therapy facility: the passive transport beam line installed at Laboratori Nazionali del Sud (INFN) in Catania, Italy.
Today Hadrontherapy, except that it is in continuous development, is more flexible and shows many additional capabilities with respect to the past.
Its geometrical set-up, for example, is now completely interchangeable permitting a simple switch between different geometrical configurations, which all share the same phantom (sensitive detector) with the related features.
It is possible to do a simulation of a generic proton/ion transport beam line and laser-driven beam line. In this release, a module for dose average LET and RBE computations have been also included.
The configurations are:
- Passive proton beam line, which is installed at the LNS-INFN facility in Catania for eye tumor treatment with protons at 62 MeV. It is simulated in PassiveProtonBeamLine.cc;
- Passive proton beam line, which is installed at the LNS-INFN facility in Catania for eye tumor treatment with protons at 62 MeV. It is simulated in PassiveProtonBeamLine.cc; (G.A.P. Cirrone et al., IEEE Nuclear Science Symposium Conference Record, 2003, 3, pp. 1756-1758, J2-5)
- Passive carbon beam line, which is the simulation of the transport beam line at LNS-INFN of Catania for experiments with carbon ion beams. It is simulated in PassiveCarbonBeamLine.cc;
- Passive carbon beam line, which is the simulation of the transport beam line at LNS-INFN of Catania for experiments with ion beams (Carbon, Oxygen and Helium). It is simulated in PassiveCarbonBeamLine.cc;
- Laser-driven beam line, which is the simulation of a beam line for the focusing, the handling and the transport of a laser-driven beam, a Faraday Cup is the eligible detector for this class. It is simulated in LaserDrivenBeamLine.cc;
- Laser-driven beam line, which is the simulation of a beam line for the focusing, the handling and the transport of a laser-driven beam, a Faraday Cup is the eligible detector for this class. It is simulated in LaserDrivenBeamLine.cc;
(A.Tramontana et al., A transport beamline solution for laser-driven proton beams
6th International Particle Accelerator Conference, IPAC 2015, 2015, pp. 2515-2518)
- TIFPA passive proton beam line, which is installed at the Protontherapy Center of Trento (Italy), used for experiments with proton beams. Geometry is implemented in HadrontherapyTIFPAPassiveProtonBeamLine.cc
(F.Tommasino et al., A new facility for proton radiobiology at the Trento proton therapy centre: Design and implementation, Physica Medica 58 (2019) 99–106)
- BEST passive proton beam line is the beamline INFN-LNS is developing for the BEST Cyclotron company for eye tumor treatment with 70 MeV protons. The geometry is implemented in BESTPassiveProtonBeamline.cc.
in PassiveProtonBeamLine.cc, in PassiveCarbonBeamLine.cc and in LaserDrivenBeamLine.cc, the user can change the geometrical characteristics of beam line elements.
Alternatively, the user can use the macro file.
In PassiveProtonBeamLine.cc, in PassiveCarbonBeamLine.cc, in LaserDrivenBeamLine.cc,in HadrontherapyTIFPAPassiveProtonBeamLine.cc and in BESTPassiveProtonBeamline.cc, the user can change the geometrical characteristics of beam line elements.
Alternatively, the user can use the macro file.
Folder structure of 'hadrontherapy'
'hadrontherapy' distribution contain different sub-folders:
\src: where source .cc files are stored
@@ -73,78 +78,86 @@ Folder structure of 'hadrontherapy'
\macro: where a set of ready-to-use macro files are provided
\field: where a set of ready-to-use .TABLE files are provided. These files are generated from OPERA & COMSOL codes for the laser-driven beam line.
\field: where a set of ready-to-use.TABLE files are provided. These files are generated from OPERA & COMSOL codes for the laser-driven beam line.
\experimentalData: in this directory, a set of reference (both experimental and analythical) data are stored. These data are then used to perform a direct comparison with simulation results that are stored in the simulationResults folder. Data stored are better described in the README file contained inside.
\experimentalData: in this directory, a set of reference (both experimental and analytical) data are stored.
\SimulationOutputs: when one of the .mac file contained in the macro folder is used, simulation results are directly stored in this directory.
\RootScripts: if the ROOT program is installed the User can use scripts contained in this directory to compare directly results from the his/her simulation with reference data provided inside the experimentalData folder.
Currently this folders structure is in development and reference data as well as ROOT scripts alongside the newly implemented features. Moreover some ROOT script can be missed. We apologize for this; please contact the authors if you need more information, clarification or useful discussion.
\data\rbe: contains the file lem1.csv including the alpha and beta values and rbe resulted from the radiobiological Local Effect Model (LEM) for three cell lines ( AG01522, U87 and HSG)
Description of the \macro folder
Inside the "macro" folder, different macro files are provided. In particular, three macro files are related to the different beam lines: hadron_therapy.mac, carbon_beamline.mac and laserDrivenBeamline.mac.
The hadron_therapy.mac permits to run a simulation with the whole proton passive beam line installed in Catania.
The carbon_beamline.mac excludes all the elements (moving the origin of the ion beam close to the water phantom) and reproduce a simple passive beam line for the use with carbon ion beams.
The laserDrivenBeamline.mac simulates a typical laser-driven proton spectrum as input for a beam line made of a quadrupole system and an energy selector.
Inside the "macro" folder, different macro files are provided.
In particular, five macro files are related to the different beam lines:
defaultMacro.mac: permits to run a simulation using the default geometry, i.e. the CATANA proton beam line in Catania. A 62 MeV gaussian proton beam with 0.25 MeV sigma and 0.028° as divergence (sigma) is launched.
You can modify by macro the range shifter thickness you
want to select. The entrance of the phantom is positioned at the isocentre ( (0,0,0)
coordinates). LET and RBE computation are activated.
carbon_beamline.mac: reproduces a simple passive beam line for the use of carbon, oxygen and helium ion beams for multidisciplinary applications (selectGeometry Carbon). A parallel 62 MeV/u carbon beam with 0.740 MeV/u sigma is simulated.
laserDrivenBeamline.mac: simulates a typical laser-driven proton spectrum as input for a beam line made of a quadrupole system, an energy selector and a Faraday Cup (selectGeometry LaserDriven)
Trento_parameters.mac: reproduces the experimental beam line installed at the Trento protontherapy centre and implements a typical source.
BestBeamLine.mac: implements the elements of the beam line developed for the BEST company and simulates a 70 MeV proton beam as input of the simulation. Dose and LET longitudinal distributions are computed at the isocentre and a native dose scorer is also added to retrieve the lateral dose profiles.
3 additional macro files are also included:
modulatorMacro.mac : allows the reconstruction of the spread out bragg peak modulating the proton beams by means of a rotating modulator wheel. The wheel is rotated of 1 degree at each run and 1000 protons are simulated in each run.
stoppingPowers.mac : calculates the stopping power of protons and alpha particles in the energy range between 1 keV up to 200 MeV
detectorGeometry.mac : example of how to modify the detector geometry
The main folder also includes an additional macro file, batch.mac which runs a simple simulation using the default geometry of the CATANA beamline.This macro is also used during the system testing process.
DOWNLOAD AND INSTALLATION
===================================================
'hadrontherapy' source code is actually released inside the official distribution of the Geant4 toolkit in the $G4INSTALL/examples/advanced folder.
'hadrontherapy' source code is released inside the distribution of the Geant4 toolkit in the $G4INSTALL/examples/advanced folder.
To run 'hadrontherapy' you must first install the Geant4 package. Once Geant4 is installed, the example must be first compiled. When compilation is completed the program can be executed.
To run 'hadrontherapy' you must first install the Geant4 package. Once Geant4 is installed, the example must be first compiled. When the compilation is completed the program can be executed.
A complete guide for the Geant4 installation in different operating systems can be found inside the official installation Geant4 pages.
If you have troubles with the Geant4 installation please send an e-mail to us.
A CMakeLists.txt file (preferred) is provided together with a standard GNUmakefile for compilation.
GEOMETRICAL SET-UP
GEOMETRIC SET-UP
===================================================
The idea of 'hadrontherapy' is to provide a tool useful for Users interested in the field of proton and ion therapy. These can include the simple calculation of dose distribution curves in water or other materials, the derivation of important transport parameters (stopping powers, ranges, etc.) in different geometrical set-ups and for different materials, up to the complete simulation of a real transport beam line for therapy.
The main component of the simulation is the phantom, a box that can be filled with different materials and where the scoring of different information (at moment the dose deposited in voxels) can be performed. A more complete description of the phantom is given in the next subsection.
The main component of the simulation is the phantom, a box that can be filled with different material and where the score of different information (at moment the dose deposited in voxels) can be performed. A more complete description of the phantom is given in the next subsection.
All these configurations will be set using macro commands.
At the moment the 'hadrontherapy' example includes the simulation of passive beam lines.
In the next future an ActiveProtonBeamLine.cc will be provided for the simulation of the active scanning treatment modality.
Moreover the possibility to add a very simple set-up (a beam, a phantom where collect the informations and some simple component) will be also provided.
All these configuration will be set using macro commands.
There is also a feature that allows the user to make a choice between alternative geometry set-ups. This can be done by using command:
There is also a feature that allows the user to make a choice between alternative geometry set-ups. This can be done by using the command:
/geometrySetup/selectGeometry <name>
where <name> is either "default" for the standard 'hadrontherapy' geometry or "Carbon" for INFN-LNS transport beam line,
normally used for interdisciplinary researches at LNS-INFN in Catania with carbon and other ion beams or "LaserDriven" for the laser-driven beam line.
At the end of the beam line a phantom (a box of uniform material) is reproduced. Inside it, a user-defined region is divided
in cubic and identical voxels. The voxels size can be varied as well as the voxelized region.
At the end of a simulation run, the dose deposited by primaries and secondaries in each voxel is collected. This information is available as an .out file or as a .root (if activated).
where <name> is either "default" for the standard 'hadrontherapy' geometry, "Carbon" for INFN-LNS transport beam line, normally used for interdisciplinary researches at LNS-INFN in Catania with carbon and other ion beams, "LaserDriven" for the laser-driven beam line, "TrentoLine" for the TIFPA beam line and "BESTBeamLine" for the beam line designed for the BEST company.
At the end of the beam line a phantom (a box of uniform material) is reproduced. Inside it, a user-defined region is divided into cubic and identical voxels. The voxel size can be varied as well as the voxelized region.
At the end of a simulation run, the dose deposited by primaries and secondaries in each voxel is collected. This information is available as an .out file.
The default size of the active voxelized region is 40x40x40 mm and actually the default voxel configuration is 200 x 1 x 1, which means 200 slices with 0.2 mm of thickness.
Of course this default can be modified in order to obtain, for example, a matrix of 80x80x80 cubic voxels each with a lateral dimension of 0.5 mm.
Of course, this default can be modified in order to obtain, for example, a matrix of 80x80x80 cubic voxels each with a lateral dimension of 0.5 mm.
Concerning the cut and stepMax values, the default configuration implies a cut value of 1 mm in the whole world (use the command /run/setCut <length> in order to set the cut for all, and the command /run/setCutForRegion <name> <length> to set the cut for the desired volume (<name>) only) and a stepMax of 0.01 mm just in the phantom and in other volumes of the laser-driven beam line (use the command /Step/waterPhantomStepMax 0.01 mm).
In any case it is strongly recommended to use a stepMax value not bigger than 5% of the dose slice thickness.
In any case, it is strongly recommended to use a stepMax value not bigger than 5% of the dose slice thickness.
THE PROTON PASSIVE LINE CLASS FILE
===================================================
The following is the description of the elements of the passive proton beam line of the Laboratori Nazionali del Sud in Catania (I). This line is completely simulated inside this class.
The following is the description of the elements of the passive proton beam line of the INFN, Laboratori Nazionali del Sud in Catania (I). This line is completely simulated inside this class.
The main elements are:
* The SCATTERING SYSTEM: to transversally enlarge the original beam
* The COLLIMATORS: placed along the beam line to collimate the beam;
* The RANGE SHIFTERS: to decrease the energy of the primary proton beam to a specific value;
* The MODULATOR WHEEL: to modulate the energy of the primary and mono-energetic beam in to a wide spectrum. The energy modulation is necessary to homogeneously irradiate a tumour volume that can extends in depth up to 20 mm;
* The MONITOR CHAMBERS: very thin ionisation chamber that permit the dose monitoring during the patient irradiation;
* The MOPI detector: microstrips, air free detector utilised for the check of the beam symmetry during the treatment;
* The PATIENT COLLIMATOR: a brass, tumour-shaped collimator able to confine the proton irradiation field in order to irradiate just the tumour mass in the transverse direction;
* The MODULATOR WHEEL: to modulate the energy of the primary and mono-energetic beam into a wide spectrum. The energy modulation is necessary to homogeneously irradiate a tumour volume that can extend in depth up to 20 mm;
* The MONITOR CHAMBERS: very thin ionisation chamber that permits the dose monitoring during the patient irradiation;
* The MOPI detector: microstrips, air-free detector utilised for the check of the beam symmetry during the treatment;
* The PATIENT COLLIMATOR: a brass, tumour-shaped collimator able to confine the proton irradiation field to irradiate just the tumour mass in the transverse direction;
The user has the possibility to vary, via messenger, almost all the geometrical characteristics of the beam line elements (i.e. their position along the beam line, their thickness, etc.).
The user can vary, via messenger, almost all the geometrical characteristics of the beam line elements (i.e. their position along the beam line, their thickness, etc.).
The elements simulated in the PassiveBeamLine.cc file are:
@@ -152,58 +165,117 @@ The elements simulated in the PassiveBeamLine.cc file are:
2. A system of collimators, to avoid the scattering radiation;
3. A modulation system that spreads the beam in energy and produces the so-called spread out Bragg peak; It is constituted by a rotating wheel of different thicknesses. The wheel rotates around its axis (parallel to the proton beam axis) and its movement can be obtained by means of a messenger between runs.
3. A modulation system that spreads the beam in energy and produces the so-called spread-out Bragg peak; It is constituted by a rotating wheel of different thicknesses. The wheel rotates around its axis (parallel to the proton beam axis) and its movement can be obtained employing a messenger between runs.
4. A set of monitor chambers (special transmission ionization chambers used to control the particle flux during the irradiation);
5. A final long collimator and a patient collimator defining the final shape of the beam before reaching the patient.
6. A water phantom: it is a box of water where the dose deposit is calculated. The use of the water phantom is required by the international protocol on the measure of dose in the case of proton and ion beams (IAEA 398, 2000).
6. A water phantom: it is a box of water where the dose deposit is calculated. The use of the water phantom is required by the international protocol on the measure of dose in the case of proton and ion beams (IAEA 398, 2000).
THE CARBON PASSIVE LINE CLASS FILE
===================================================
The PassiveCarbonBeamLine.cc class implements the Zero Degree (ZD) beamline installed at LNS-INFN and entirely dedicated to in-air irradiation with ion beams (Z > 1, E ≤ 80AMeV ).
The beam line is composed of an exit 50 um Kapton window which separates the in vacuum pipe from the in air section. The beam then hits a scattering system composed by a 20 um tantalum foil and a brass central stopper. Moreover, two different systems for the beam modulation energy are simulated reproducing the available systems at LNS-INFN: a ripple filter specifically designed for 62 AMeV carbon ion beams and a ridge filter designed for 62 AMeV helium and oxygen ion beams. A transmission monitor ionization chamber providing the on-line monitoring of the delivered dose is also simulated.
The final collimator system is then composed by a brass tube (50 cm long and 27 mm in diameter) and a brass collimator with a variable in diameter from a maximum of 27 mm to 1 mm.
RIDGE FILTER
The ridge filter consists in a 2D array of pins, whose the shape and the thickness is optimized to obtain the desired SOBP.
The developed and simulated ridge filter is composed of 900 pins, each having a square base of 1.7 x 1.7 mm2 and height of 4.72 mm. The material chosen for its realization was plastic (C21 O4 N24) with a density of 1.18 g/cm3. The filter was designed and produced thanks to a collaboration between the INFN-LNS group and the GSI, Darmstadt(D). The reconstruction of the ridge geometry was obtained by superimposed native structures (with a trapezoid shape) already presented in Geant4 (G4Trp).
RIPPLE FILTERS
===================================================
Due to the native norrower bragg peak of carbon ions with respect to protons, a configuration with two ripple filters is the most suggested for realizing a SOBP.
This solution was adopted at the ZD beam line and implemented in the simulation to obtain a flat longitudinal dose profile with carbon ions: the first filter is positioned at 7 cm from the exit window and the second one at 10 cm from the first. A single structure has a triangular section with a thin base of plexiglass (200 mm x 200 mm x 0.3 mm) and a basis 3 mm in thickness. The material density is 1.19 g/cm3.
LASER DRIVEN PROTON BEAMLINE
===================================================
Nowadays a big effort is being devoted to optically accelerate charged particles. There are several ion acceleration regimes that are being discussed in literature, but up to now the most experimentally investigated is the Target Normal Sheath Acceleration (TNSA) one.
The beam transport and focusing as well as the energy selection of these laser produced beams represents one of the critical points in order to make such beams suitable for clinical applications. In fact, in contrast to conventional accelerators, the beams produced by high intensity laser-matter interaction are typically characterized by a wide angular divergence (for example ± 25 degrees) and a 100 % energy spread.
Moreover due to the high current, conventional dosimetric systems cannot be used during the experimental sections (saturation issues) and for this reason the faraday cup detector has been proposed as the elegible absolute dosimetric device.
The following is the description of the elements of the laser-driven beam line. This line is completely simulated inside this class.
The main elements are:
* The QUADRUPOLES SYSTEM: made of four quadrupoles, to focus/defocus protons with a different energy;
* The COLLIMATORS: placed along the beam line to collimate the beam;
* The ENERGY SELECTOR SYSTEM: made of four dipoles, that provide the spatial separation of charged particles with different energies;
* The FARADAY CUP: that provide the charge measurement and the distribution of the secondary electrons;
The user can have the possibility to vary, via messenger, many characteristics of the beam line elements (i.e. their position along the beam line, their thickness, etc.).
- /LaserDriven/EnergySelector/Disable -> to disable the Energy Selector
- /LaserDriven/EnergySelector/FirstCollimator/Radius <value> -> to set the Radius of the first collimator
- /LaserDriven/EnergySelector/FirstCollimator/thickness <value> -> to set the Thickness of the first collimator
- /LaserDriven/EnergySelector/FirstCollimator/zPosizion <value> -> to set the position of the first collimator hole along the radial plane
- /LaserDriven/EnergySelector/SecondCollimator/Radius <value> -> to set the Radius of the second collimator
- /LaserDriven/EnergySelector/SecondCollimator/thickness <value> -> to set the Thickness of the second collimator
- /LaserDriven/EnergySelector/SecondCollimator/zPosizion <value> -> to set the position of the second collimator hole along the radial plane
- /LaserDriven/EnergySelector/Slit/thickness <value> -> to set the Thickness of the slit, maximum value 10mm for geometric constraintconstrain
- /LaserDriven/EnergySelector/Slit/HoleDimensionY <value> -> to set the Y dimension of the Slit Hole
- /LaserDriven/EnergySelector/Slit/HoleDimensionZ <value> -> to set the Z dimension of the Slit Hole
- /LaserDriven/EnergySelector/Slit/HolePositionZ <value> -> to set the Slit hole position in the Z direction as respect the Slit body center
- /LaserDriven/Quadrupoles/DisableQuad -> to disable the Quadrupole system
PHYSICS PROCESSES AND PHYSICS MODELS IMPLEMENTATION
===================================================
Physics models in 'hadrontherapy', following the Geant4 organization, can be definied using four different approaches:
Physics models in 'hadrontherapy', following the Geant4 organization, can be defined using four different approaches:
A particular care is addressed to the simulation of the physic processes.
Particular care is addressed to the simulation of the physics processes.
Three different approaches can be used for the choose of the physic models.
Approach 1:
Using the macro command:
/physic/addPhysics/<physics List name>.
In this case the models (for electromagnetic, hadronic elastic and hadronic inelastic) can be
In this case, the models (for electromagnetic, hadronic elastic and hadronic inelastic) can be
activated directly calling the name of the Physics Lists that are available inside the
Geant4 kernel in the directory:
$G4INSTALL/source/physics_lists/builders/include
An example of the use of the Physics List can be found in the macro files:
hadron_therapy.mac and carbon_beamline.mac
default_macro.mac and carbon_beamline.mac
Approach 2:
A set of built-in physic models are also contained inside the 'hadrontherapy' directory. These
are called Local*.cc and Local*.hh and can be activated using the macro command:
A set of built-in physic lists are also defined and included in the class HadrontherapyPhisicsList.cc and can be activated by macro command:
/physic/addPhysics/<name>.
NOTE: we do not recommend the use of local physics lists while we recommend the use of the Physics Lists or of the Reference Physics Lists (Approach 1 or 3)
Two different physics lists can be selected using this approach:
- HADRONTHERAPY_1: include HP hadronic physics models
- HADRONTHERAPY_2: HP physics models are switched off
Approach 3:
We developed this approach in order to simplify the choice of the physic models to
be used in the application.
With this approach the user must only insert a command line in his/her .mac file using the: /physics/addPackage <PACKAGE_NAME>
This permits to switch-on an already build physic package.
This permits to switch-on an already built physics package.
Various packages are already present in the Geant4 tree: they are in the directory: geant4/source/physics_lists/lists/include
Approach 4:
Directly call a reference physics list by setting the variable PHYSLIST. Ex.:
export PHYSLIST=QGSP_BIC_EMY
and the export QGSP_BIC_EMY refernce physics list will be setted
and the export QGSP_BIC_EMY reference physics list will be setted
INTERACTIVE COMMANDS
===================================================
How to change Phantom and Detector geometries
In order to let the user to change phantom and detector geometries and voxelization, some interactive commands have been provided. All parameters are mandatory, except those inside square brackets.
In order to let the user change phantom and detector geometries and voxelization, some interactive commands have been provided. All parameters are mandatory, except those inside square brackets.
Detector geometry
@@ -211,10 +283,10 @@ The user can change:
(1) The detector (box) size.
(2) The voxels sizes. Changing this parameters, and/or the detector sizes, user should choose values in order to be divisors of the detector correspondent sizes.
(2) The voxels sizes. Changing these parameters, and/or the detector sizes, users should choose values in order to be divisors of the detector correspondent sizes.
For both above commands, zero or negative values mean << don't change it >>
(3) The displacement between the phantom and the detector. Displacement parameters refer to the lower left corner of the detector respect to that of the phantom, by the point of view of the beam. In this case zero or positive values are allowed, while the negatives ones mean: << don't change it>>.
(3) The displacement between the phantom and the detector. Displacement parameters refer to the lower-left corner of the detector with respect to that of the phantom, by the point of view of the beam. In this case, zero or positive values are allowed, while the negatives ones mean: << don't change it>>.
Command synopsis:
@@ -222,14 +294,13 @@ Command synopsis:
/changeDetector/voxelSize <dimX> <dimY> <dimZ> <[unit]>
/changeDetector/displacement <dispX> <dispY> <dispZ> <[unit]>
Default size values are 4x4x4 cm for the detector, 0.2x40x40 mm for any voxel and 0x18x18 cm
for the displacement.
Default size values are 4x4x4 cm for the detector, 0.2x40x40 mm for any voxel and 0x18x18 cm for the displacement.
where the X dimension is that along the beam direction
Phantom geometry
(1) The phantom size. As usually, zero or negatives values mean: <<don't change it>>.
(2) The phantom position respect to the world. In this case specified values refer to the three components of the position of the phantom's center respect to the world's.
(1) The phantom size. As usually, zero or negative values mean: <<don't change it>>.
(2) The phantom position respects the world. In this case, specified values refer to the three components of the position of the phantom's centre respect to the world.
Command synopsis:
@@ -237,9 +308,9 @@ Command synopsis:
/changePhantom/position <posX> <posY> <posZ> <[unit]> # 20 0 0 cm
All these commands must be followed by the command /changePhantom/update
in order to check and eventually apply changes to the real geometry.
Moreover they must be issued between runs (so where you want but after the /run/initialize initialization command, or the G4State_Idle Geant4 state machine).
Obviously all the previous sizes must be set in order to maintain the detector fully inside the phantom, otherwise system complains.
to check and eventually apply changes to the real geometry.
Moreover, they must be issued between runs (so where you want but after the /run/initialize initialization command, or the G4State_Idle Geant4 state machine).
Obviously, all the previous sizes must be set in order to maintain the detector fully inside the phantom, otherwise, the system will give an error message.
Some examples follow:
@@ -254,7 +325,7 @@ Obviously all the previous sizes must be set in order to maintain the detector f
/changeDetector/size 0 8 0 cm
# Will extend the Y size to 8 cm. In this case voxel size Y doesn't change, but
# the number of voxel along Y doubles.
# the number of voxels along Y doubles.
/changePhantom/update
/changeDetector/voxelSize 100 0 0 um
@@ -268,7 +339,7 @@ Obviously all the previous sizes must be set in order to maintain the detector f
Stopping powers calculation
It is possible for the end-user to calculate, via macro command, stopping powers only for those materials inserted into G4NistMaterialBuilder class (about 300).
The end-user can calculate, via macro command, stopping powers only for those materials inserted into G4NistMaterialBuilder class (about 300).
To get stopping powers user must provide this command line on the idle interactive terminal (or into a macro file) :
/parameter/getstopping <G4_material> <Emin> <Emax> <nPoints> <[particle]> <[output_filename]>
@@ -280,7 +351,7 @@ Parameters are respectively:
The material (NIST) name (something like G4_..., the complete list of elements and materials is available into the G4NistMaterialBuilder class and can be printed to the terminal screen via the macro command: /parameter/nist )
Kinetic energy range in MeV and the number of data points to be retrieved (in a logarithmically uniform space)
The particle name (proton, e+, e-, He3, neutron,... a full list can be gotten via the macro command: /particle/list).
The particle name (proton, e+, e-, He3, neutron,... a full list can be produced via the macro command: /particle/list).
Currently, it does not work with ions.
The output filename: if users leave this blank then the standard output is used.
@@ -288,50 +359,84 @@ Below is an example in order to calculate the stopping power for alphas into Hyd
/parameter/getstopping G4_H 0.001 150 15 alpha
GEANT4 GENERAL PARTICLE SOURCE
===================================================
The General Particle Source (GPS, G4 class name: G4GeneralParticleSource) is in the current version of 'hadrontherapy': it enables the user to use standard energy, angular and spatial distributions. The GPS includes also methods to bias the sampling distribution.
The General Particle Source (GPS, G4 class name: G4GeneralParticleSource) is in the current version of 'hadrontherapy': it enables the user to use standard energy, angular and spatial distributions. The GPS also includes methods to bias the sampling distribution.
The G4GeneralParticleSource can be utilized by typing commands from the /gps command directory, or include the /gps commands in a g4macro file.
The G4GeneralParticleSource can be utilized by typing commands from the /gps command directory, or include the /gps commands in a macro file.
RADIOBIOLOGICAL QUANTITIES: DOSE, LET, RBE
===================================================
LET calculation
'hadrontherapy' application simulates and calculates the averaged dose LET.
'hadrontherapy' application simulates and calculates the averaged LET-dose and LET-track fully accounting for the contribution of secondary particles generated in the target fragmentation
Dependencies as respect to the transport parameters adopted during the Monte Carlo simulations as the production cut of secondaries particles, voxel size and the maximum steps length are minimized in the LET calculation. The first implementation of LET calculation adopted in hadrontherapy is reported in F. Romano et al.,(2014) Phys Med Biol 59(12): 2863–8. Now, in ‘hadrontherapy’ is implemented the approach reported in G. Petringa et al., (2020) Phys Med Bio. (DOI: 10.1088/1361-6560/abaeb9)
At run time, data needed to calculate LET are collected. At the end of simulation, LET mean values are calculated and stored into a file.
The Let.out file will be produced at the end of a run, where you can
find the dose average LET for each tracked particles (both primary and
find the dose and track average LET for each tracked particles (both primary and
secondary ones) and the total mean LET.
The file is structured as follows:
- The first three columns contains the voxel indexes (first index "i" refers to the beam direction);
- The fourth and fifth columns contain respectively total mean dose LET and primary mean dose LET;
- The rest of columns contain LET Dose for each single ion (whose name is in the top row of the file).
- The first three columns contain the voxel indexes (first index "i" refers to the beam direction);
- The fourth and fifth columns contain respectively total mean dose LET (LDT) and total mean track LET (LTT)
- The rest of columns contain LET Dose and Track for each single ion (whose name is in the top row of the file).
To activate the LET computation (HadrontherapyLet.cc), you have to execute
the following command:
/analysis/secondary true
/analysis/computeLet
RBE and Survival calculation
A method was developed to assess the biological damages produced by proton and ion beams in terms of survival fraction curves, i.e of the number of cells able to survive after the irradiation at different dose. The approach is based on the combined use of Monte Carlo Geant4 simulations (to calculate the doses deposited and the energy spectra of particles interacting with cells) and of the Survival analytical code (Manganaro L, Russo G, et al. Survival: a simulation toolkit introducing a modular approach for radiobiological evaluations in ion beam therapy. Phys. Med. Biol. 2018;63(8). 08–01).
The Monte Carlo simulations permit the calculation of the Edep and Ekin distributions that, coupled with the radiobiological response model, allow the final and calculation of a survival curve.
The kinetic energy and the LET value of any primary ion and of the secondaries generated in each slice of the simulated water phantom are retrieved at each simulation step. The corresponding values of αi and βi, for each specific ion i with a kinetic energy Ei and a released dose Di, are then calculated by direct linear interpolation of the Look-up-tables provided by the Survival analytical code.
(G.Petringa et al., Physica Medica 58 (2019) 72–80)
The AlphaAndBeta.out and RBE.out files are produced at the end of the run.
AlphaAndBeta.out contains the average alpha (first column) and beta (second column) parameters calculated for each slice (third column).
RBE.out contains the following quantities:
Dose (Gy): the physical dose;
ln(S): the natural log of the Survival Fraction;
Survival Fraction;
DoseB (Gy): the biological dose;
RBE: relative biological effectiveness;
depth (slice): n. of the slice;
To activate the RBE computation (HadrontherapyRBEcc), you have to execute
the following command:
#you can choose the verbosity level
/rbe/verbose 2
#you have to indicate the name of the LUT inside the rbe folder
/rbe/loadLemTable data/rbe/lem.csv
/rbe/calculation 1
/rbe/accumulate 1
#you have to indicate the name of the cell line
/rbe/cellLine ARPE19
/rbe/doseScale 7777770
SIMULATION OUTPUT
===================================================
Store results in an ASCII file
A .out ASCII file is generated at the end of each run, Dose.out is its default name that can be changed in the HadrontherapyMatrix.cc file.
The file contains four columns; the first three columns represent the voxel indexes (that univocally identify the voxel volume), while the last column represents the dose deposited in that given voxel.
Alternatively, user can force store of data to a given filename, after any BeamOn command and before the program end, by the macro command /analysis/writeDoseFile <myfile.out>.
The file contains four columns; the first three columns represent the voxel indexes (that unequivocally identify the voxel volume), while the last column represents the dose deposited in that given voxel.
Alternatively, users can force the store of data to a given filename, after any BeamOn command and before the program ends, by the macro command /analysis/writeDoseFile <myfile.out>.
Moreover, if the macro command /analysis/secondary <true> is given, before the BeamOn command, ordinated dose and fluence, for every secondary produced, is added to the file.
If the macro command /analysis/computeLet is given, an the ascii file Let.out is written, with the dose average LET computations.
If the macro command /analysis/computeLet is given, and the ascii file Let.out is written, with the dose and track average LET computations.
User must take care that any change of the phantom geometry will clear all dose data.
Setting the name of the ROOT output file
By default the name of the ROOT output file is DoseDistribution.root. The name of the file can be set by using the macro command: analysis/setAnalysisFile <filename>
Users must take care that any change of the phantom geometry will clear all dose data.
It is also possible to create multiple new output files in the same simulation session. For example:
@@ -345,56 +450,6 @@ It is also possible to create multiple new output files in the same simulation s
/run/beamOn 1000
/analysis/writeDoseFile secondRun.out
Use of the ROOT analysis
It is possible to use ROOT data analysis package directly for the production of output files.
In the last version, anyway, this functionality must be implemented by User. This can be accomplished by setting an ad-hoc environment variable (i.e. G4ANALYSIS_USE_ROOT) to 1, adding in the code lines to create outputs with the ROOT libraries and recompiling the application.
In this case you must have the ROOT framework installed in your machine.
Warning: If you plan to use ROOT analysis, please avoid compiling in the multi-threaded mode as the the ROOT library is not thread-safe.
In the next release, we plan to base the whole analysis on g4tools which will solve this issue an MT will be safe to use.
LASER DRIVEN PROTON BEAMLINE
Nowadays a big effort is being devoted for optically accelerated charged particles. There are several ion acceleration regimes that are being discussed in literature, but up to now the most experimentally investigated is the Target Normal Sheath Acceleration (TNSA) one.
The beam transport and focusing as well as the energy selection of these laser produced beams represents one of the critical points in order to make such kind of beams suitable for clinical applications. In fact, in contrast to conventional accelerators, the beams produced by high intensity laser-matter interaction are typically characterized by a wide angular divergence (for example ± 25 degrees) and a 100 % energy spread.
Moreover due to the high current, conventional dosimetric system cannot be used during the experimental sections (saturation issues) and for this reason the faraday cup detector has been proposed as the elegible absolute dosimetric device.
The following is the description of the elements of the laser-driven beam line. This line is completely simulated inside this class.
The main elements are:
* The QUADRUPOLES SYSTEM: made of four quadrupoles, to focus/defocus protons with different energy;
* The COLLIMATORS: placed along the beam line to collimate the beam;
* The ENERGY SELECTOR SYSTEM: made of four dipoles, that provide the spatial separation of charged particles with different energies;
* The FARADAY CUP: that provide the charge measurement and the distribution of the secondary electrons;
The user has the possibility to vary, via messenger, many characteristics of the beam line elements (i.e. their position along the beam line, their thickness, etc.).
- /LaserDriven/EnergySelector/Disable -> to disable the Energy Selector
- /LaserDriven/EnergySelector/FirstCollimator/Radius <value> -> to set the Radius of the first collimator
- /LaserDriven/EnergySelector/FirstCollimator/thickness <value> -> to set the Thickness of the first collimator
- /LaserDriven/EnergySelector/FirstCollimator/zPosizion <value> -> to set the position of the first collimator hole along the radial plane
- /LaserDriven/EnergySelector/SecondCollimator/Radius <value> -> to set the Radius of the second collimator
- /LaserDriven/EnergySelector/SecondCollimator/thickness <value> -> to set the Thickness of the second collimator
- /LaserDriven/EnergySelector/SecondCollimator/zPosizion <value> -> to set the position of the second collimator hole along the radial plane
- /LaserDriven/EnergySelector/Slit/thickness <value> -> to set the Thickness of the slit, maximum value 10mm for geometric constrain
- /LaserDriven/EnergySelector/Slit/HoleDimensionY <value> -> to set the Y dimension of the Slit Hole
- /LaserDriven/EnergySelector/Slit/HoleDimensionZ <value> -> to set the Z dimension of the Slit Hole
- /LaserDriven/EnergySelector/Slit/HolePositionZ <value> -> to set the Slit hole position in the Z direction as respect the Slit body center
- /LaserDriven/Quadrupoles/DisableQuad -> to disable the Quadrupole system
Please contact cirrone@lns.infn.it for more details or suggestions and feedback on this document.
FUTURE CHALLENGES AND USERS' REQUESTS
This is a list of future components and feature that will be added in 'hadrontherapy' and of main Users requests that we hope to fulfill in the next future.
- A module for the RBE (Relative Biological Effectiveness) calculation will be also delivered. The Catania Group in Collaboration with the Turin one is working on this. This module is already implemented (in a preliminary version) in an internal version of 'hadrontherapy' and can be provided, if requested. Please, contact us.
- A g4tools-compatible ROOT output from HadrontherapyAnalysisManager.
Please contact cirrone@lns.infn.it or francesco.romano@lns.infn.it for more details or suggestions and feedbacks on this document.