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Author |
Gimenez-Alventosa, V.; Gimenez, V.; Oliver, S. |
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Title |
PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE |
Type |
Journal Article |
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Year |
2021 |
Publication |
Computer Physics Communications |
Abbreviated Journal |
Comput. Phys. Commun. |
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Volume |
267 |
Issue |
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Pages |
108065 - 12pp |
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Keywords |
Radiation transport; Monte Carlo simulation; Electron-photon showers; Parallel computing; MPI; Medical physics |
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Abstract |
Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts their applicability. To help solve these current limitations, we present PenRed, a general-purpose, standalone, extensible and modular framework code based on PENELOPE for parallel Monte Carlo simulations of electron-photon transport through matter. It has been implemented in C++ programming language and takes advantage of modern object-oriented technologies. In addition, PenRed offers the capability to read and process DICOM images as well as to construct and simulate image-based voxelized geometries, so as to facilitate its usage in medical applications. Our framework has been successfully verified against the original PENELOPE Fortran code. Furthermore, the implemented parallelism has been tested showing a significant improvement in the simulation time without any loss in precision of results. Program summary Program title: PenRed: Parallel Engine for Radiation Energy Deposition. CPC Library link to program files: https://doi .org /10 .17632/rkw6tvtngy.1 Licensing provision: GNU Affero General Public License (AGPL). Programming language: C++ standard 2011. Nature of problem: Monte Carlo simulations usually require a huge amount of computation time to achieve low statistical uncertainties. In addition, many applications necessitate particular characteristics or the extraction of specific quantities from the simulation. However, most available Monte Carlo codes do not provide an efficient parallel and truly modular structure which allows users to easily customise their code to suit their needs without an in-depth knowledge of the code system. Solution method: PenRed is a fully parallel, modular and customizable framework for Monte Carlo simulations of the passage of radiation through matter. It is based on the PENELOPE [1] code system, from which inherits its unique physics models and tracking algorithms for charged particles. PenRed has been coded in C++ following an object-oriented programming paradigm restricted to the C++11 standard. Our engine implements parallelism via a double approach: on the one hand, by using standard C++ threads for shared memory, improving the access and usage of the memory, and, on the other hand, via the MPI standard for distributed memory infrastructures. Notice that both kinds of parallelism can be combined together in the same simulation. Moreover, both threads and MPI processes, can be balanced using the builtin load balance system (RUPER-LB [30]) to maximise the performance on heterogeneous infrastructures. In addition, PenRed provides a modular structure with methods designed to easily extend its functionality. Thus, users can create their own independent modules to adapt our engine to their needs without changing the original modules. Furthermore, user extensions will take advantage of the builtin parallelism without any extra effort or knowledge of parallel programming. Additional comments including restrictions and unusual features: PenRed has been compiled in linux systems withg++ of GCC versions 4.8.5, 7.3.1, 8.3.1 and 9; clang version 3.4.2 and intel C++ compiler (icc) version 19.0.5.281. Since it is a C++11-standard compliant code, PenRed should be able to compile with any compiler with C++11 support. In addition, if the code is compiled without MPI support, it does not require any non standard library. To enable MPI capabilities, the user needs to install whatever available MPI implementation, such as openMPI [24] or mpich [25], which can be found in the repositories of any linux distribution. Finally, to provide DICOM processing support, PenRed can be optionally compiled using the dicom toolkit (dcmtk) [32] library. Thus, PenRed has only two optional dependencies, an MPI implementation and the dcmtk library. |
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Address |
[Gimenez-Alventosa, V] Univ Politecn Valencia, Inst Instrumentac Imagen Mol I3M, Ctr Mixto CSIC, Cami Vera S-N, Valencia 46022, Spain, Email: vicent.gimenez@i3m.upv.es; |
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Elsevier |
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English |
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0010-4655 |
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Notes |
WOS:000678508900001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ pastor @ |
Serial |
4907 |
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Author |
Oliver, S.; Rodriguez Bosca, S.; Gimenez-Alventosa, V. |
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Title |
Enabling particle transport on CAD-based geometries for radiation simulations with penRed |
Type |
Journal Article |
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Year |
2024 |
Publication |
Computer Physics Communications |
Abbreviated Journal |
Comput. Phys. Commun. |
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Volume |
298 |
Issue |
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Pages |
109091 - 11pp |
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Keywords |
Radiation transport; PENELOPE physics; Monte Carlo simulation; PenRed; CAD; Triangular surface mesh |
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Abstract |
Geometry construction is a fundamental aspect of any radiation transport simulation, regardless of the Monte Carlo code being used. Typically, this process is tedious, time-consuming, and error-prone. The conventional approach involves defining geometries using mathematical objects or surfaces. However, this method comes with several limitations, especially when dealing with complex models, particularly those with organic shapes. Furthermore, since each code employs its own format and methodology for defining geometries, sharing and reproducing simulations among researchers becomes a challenging task. Consequently, many codes have implemented support for simulating over geometries constructed via Computer-Aided Design (CAD) tools. Unfortunately, this feature is lacking in penRed and other PENELOPE physics-based codes. Therefore, the objective of this work is to implement such support within the penRed framework. New version program summary Program Title: Parallel Engine for Radiation Energy Deposition (penRed) CPC Library link to program files: https://doi.org/10.17632/rkw6tvtngy.2 Developer's repository link: https://github.com/PenRed/PenRed Code Ocean capsule: https://codeocean.com/capsule/1041417/tree Licensing provisions: GNU Affero General Public License v3 Programming language: C++ standard 2011. Journal reference of previous version: V. Gimenez-Alventosa, V. Gimenez Gomez, S. Oliver, PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE, Computer Physics Communications 267 (2021) 108065. doi:https://doi.org/10.1016/j.cpc.2021.108065. Does the new version supersede the previous version?: Yes Reasons for the new version: Implements the capability to simulate on CAD constructed geometries, among many other features and fixes. Summary of revisions: All changes applied through the code versions are summarized in the file CHANGELOG.md in the repository package. Nature of problem: While Monte Carlo codes have proven valuable in simulating complex radiation scenarios, they rely heavily on accurate geometrical representations. In the same way as many other Monte Carlo codes, penRed employs simple geometric quadric surfaces like planes, spheres and cylinders to define geometries. However, since these geometric models offer a certain level of flexibility, these representations have limitations when it comes to simulating highly intricate and irregular shapes. Anatomic structures, for example, require detailed representations of organs, tissues and bones, which are difficult to achieve using basic geometric objects. Similarly, complex devices or intricate mechanical systems may have designs that cannot be accurately represented within the constraints of such geometric models. Moreover, when the complexity of the model increases, geometry construction process becomes more difficult, tedious, time-consuming and error-prone [2]. Also, as each Monte Carlo geometry library uses its own format and construction method, reproducing the same geometry among different codes is a challenging task. Solution method: To face the problems stated above, the objective of this work is to implement the capability to simulate using irregular and adaptable meshed geometries in the penRed framework. This kind of meshes can be constructed using Computer-Aided Design (CAD) tools, the use of which is very widespread and streamline the design process. This feature has been implemented in a new geometry module named “MESH_BODY” specific for this kind of geometries. This one is freely available and usable within the official penRed package1. It can be used since penRed version 1.9.3b and above. |
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Address |
[Oliver, S.] Univ Politecn Valencia, Inst Seguridad Ind Radiofis & Medioambiental ISIRY, Cami Vera S-N, Valencia 46022, Spain |
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Elsevier |
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English |
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0010-4655 |
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Notes |
WOS:001172840800001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
6077 |
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Author |
Gimenez-Alventosa, V.; Antunes, P.C.G.; Vijande, J.; Ballester, F.; Perez-Calatayud, J.; Andreo, P. |
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Title |
Collision-kerma conversion between dose-to-tissue and dose-to-water by photon energy-fluence corrections in low-energy brachytherapy |
Type |
Journal Article |
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Year |
2017 |
Publication |
Physics in Medicine and Biology |
Abbreviated Journal |
Phys. Med. Biol. |
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Volume |
62 |
Issue |
1 |
Pages |
146-164 |
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Keywords |
Monte Carlo; dosimetry; low-energy seed; collision-kerma; mass energy-absorption coefficients; energy-fluence correction factor |
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Abstract |
The AAPM TG-43 brachytherapy dosimetry formalism, introduced in 1995, has become a standard for brachytherapy dosimetry worldwide; it implicitly assumes that charged-particle equilibrium (CPE) exists for the determination of absorbed dose to water at different locations, except in the vicinity of the source capsule. Subsequent dosimetry developments, based on Monte Carlo calculations or analytical solutions of transport equations, do not rely on the CPE assumption and determine directly the dose to different tissues. At the time of relating dose to tissue and dose to water, or vice versa, it is usually assumed that the photon fluence in water and in tissues are practically identical, so that the absorbed dose in the two media can be related by their ratio of mass energy-absorption coefficients. In this work, an efficient way to correlate absorbed dose to water and absorbed dose to tissue in brachytherapy calculations at clinically relevant distances for low-energy photon emitting seeds is proposed. A correction is introduced that is based on the ratio of the water-to-tissue photon energy-fluences. State-of-the art Monte Carlo calculations are used to score photon fluence differential in energy in water and in various human tissues (muscle, adipose and bone), which in all cases include a realistic modelling of low-energy brachytherapy sources in order to benchmark the formalism proposed. The energy-fluence based corrections given in this work are able to correlate absorbed dose to tissue and absorbed dose to water with an accuracy better than 0.5% in the most critical cases (e.g. bone tissue). |
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Address |
[Gimenez-Alventosa, Vicent; Antunes, Paula C. G.; Vijande, Javier; Ballester, Facundo] Univ Valencia, Dept Atom Mol & Nucl Phys, E-46100 Burjassot, Spain, Email: vijande@uv.es |
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Publisher |
Iop Publishing Ltd |
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English |
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0031-9155 |
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Notes |
WOS:000391567700001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
2923 |
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Author |
Gimenez-Alventosa, V.; Gimenez, V.; Ballester, F.; Vijande, J.; Andreo, P. |
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Title |
Correction factors for ionization chamber measurements with the 'Valencia' and 'large field Valencia' brachytherapy applicators |
Type |
Journal Article |
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Year |
2018 |
Publication |
Physics in Medicine and Biology |
Abbreviated Journal |
Phys. Med. Biol. |
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Volume |
63 |
Issue |
12 |
Pages |
125004 - 10pp |
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Keywords |
skin applicator; Valencia applicator; large field Valencia applicator; HDR brachytherap; brachytherapy dosimetry; Monte Carlo |
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Abstract |
Treatment of small skin lesions using HDR brachytherapy applicators is a widely used technique. The shielded applicators currently available in clinical practice are based on a tungsten-alloy cup that collimates the source-emitted radiation into a small region, hence protecting nearby tissues. The goal of this manuscript is to evaluate the correction factors required for dose measurements with a plane-parallel ionization chamber typically used in clinical brachytherapy for the 'Valencia' and 'large field Valencia' shielded applicators. Monte Carlo simulations have been performed using the PENELOPE-2014 system to determine the absorbed dose deposited in a water phantom and in the chamber active volume with a Type A uncertainty of the order of 0.1%. The average energies of the photon spectra arriving at the surface of the water phantom differ by approximately 10%, being 384 keV for the 'Valencia' and 343 keV for the 'large field Valencia'. The ionization chamber correction factors have been obtained for both applicators using three methods, their values depending on the applicator being considered. Using a depth-independent global chamber perturbation correction factor and no shift of the effective point of measurement yields depth-dose differences of up to 1% for the 'Valencia' applicator. Calculations using a depth-dependent global perturbation factor, or a shift of the effective point of measurement combined with a constant partial perturbation factor, result in differences of about 0.1% for both applicators. The results emphasize the relevance of carrying out detailed Monte Carlo studies for each shielded brachytherapy applicator and ionization chamber. |
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Address |
[Gimenez-Alventosa, V.] Univ Politecn Valencia, CSIC, Ctr Mixto, Inst Instrumentac Imagen Mol I3M, E-46022 Valencia, Spain, Email: Javier.vijande@uv.es |
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Publisher |
Iop Publishing Ltd |
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English |
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0031-9155 |
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Notes |
WOS:000434682500004 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
3609 |
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Author |
Gimenez-Alventosa, V.; Gimenez, V.; Ballester, F.; Vijande, J.; Andreo, P. |
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Title |
Monte Carlo calculation of beam quality correction factors for PTW cylindrical ionization chambers in photon beams |
Type |
Journal Article |
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Year |
2020 |
Publication |
Physics in Medicine and Biology |
Abbreviated Journal |
Phys. Med. Biol. |
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Volume |
65 |
Issue |
20 |
Pages |
205005 - 11pp |
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Keywords |
TRS 398; Monte Carlo; dosimetry; ionization chambers; MV photon beams |
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Abstract |
The beam quality correction factork(Q)for megavoltage photon beams has been calculated for eight PTW (Freiburg, Germany) ionization chambers (Farmer chambers PTW30010, PTW30011, PTW30012, and PTW30013, Semiflex 3D chambers PTW31021, PTW31010, and PTW31013, and the PinPoint 3D chamber PTW31016). Simulations performed on the widely used NE-2571 ionization chamber have been used to benchmark the results. The Monte Carlo code PENELOPE/penEasy was used to calculate the absorbed dose to a point in water and the absorbed dose to the active air volume of the chambers for photon beams in the range 4 to 24 MV. Of the nine ionization chambers analysed, only five are included in the current version of the International Code of Practice for dosimetry based on standards of absorbed dose to water (IAEA TRS 398). The values reported in this work agree with those in the literature within the uncertainty estimates and are to be included in the average values of the data obtained by different working groups for the forthcoming update of TRS 398. |
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Address |
[Gimenez-Alventosa, Vicent] Univ Politecn Valencia, CSIC, Ctr Mixto, Inst Instrumentac Imagen Mol I3M, Valencia, Spain, Email: javier.vijande@uv.es |
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Publisher |
Iop Publishing Ltd |
Place of Publication |
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English |
Summary Language |
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Original Title |
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Abbreviated Series Title |
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ISSN |
0031-9155 |
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Notes |
WOS:000576070000001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ pastor @ |
Serial |
4556 |
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