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Ayala, C., & Cvetic, G. (2016). anQCD: Fortran programs for couplings at complex momenta in various analytic QCD models. Comput. Phys. Commun., 199, 114–117.
Abstract: We provide three Fortran programs which evaluate the QCD analytic (holomorphic) couplings A(v)(Q(2)) for complex or real squared momenta Q(2). These couplings are holomorphic analogs of the powers a(Q(2))(v) of the underlying perturbative QCD (pQCD) coupling a(Q(2)) equivalent to alpha(s)(Q(2))/pi, in three analytic QCD models (anQCD): Fractional Analytic Perturbation Theory (FAPT), Two-delta analytic QCD (2 delta anQCD), and Massive Perturbation Theory (MPT). The index v can be noninteger. The provided programs do basically the same job as the Mathematica package anQCD.m published by us previously (Ayala and Cvetic, 2015), but are now written in Fortran. Program summary Program title: AanQCDext Catalogue identifier: AEYKv10 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYICv1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 12105 No. of bytes in distributed program, including test data, etc.: 98822 Distribution format: tar.gz Programming language: Fortran. Computer: Any work-station or PC where Fortran 95/200312008 (gfortran) is running. Operating system: Operating system Linux (Ubuntu and Scientific Linux), Windows (in all cases using gfortran). Classification: 11.1, 11.5. Nature of problem: Calculation of values of the running analytic couplings A(v)(Q(2); N-f) for general complex squared momenta Q(2) equivalent to -q(2), in three analytic QCD models, where A(v)(Q(2); N-f) is the analytic (holomorphic) analog of the power (alpha(s)(Q(2); N-f)/pi)(v). Here, A(v)(Q(2); N-f) is a holomorphic function in the Q(2) complex plane, with the exception of the negative semiaxis (-infinity, -M-thr(2)], reflecting the analyticity properties of the spacelike renormalization invariant quantities D(Q(2)) in QCD. In contrast, the perturbative QCD power (alpha(s)(Q(2); N-f)/pi)(v) has singularities even outside the negative semiaxis (Landau ghosts). The three considered models are: Analytic Perturbation theory (APT); Two-delta analytic QCD (2 delta anQCD); Massive Perturbation Theory (MPT). We refer to Ref. [1] for more details and literature. Solution method: The Fortran programs for FAPT and 2 delta anQCD models contain routines and functions needed to perform two-dimensional numerical integrations involving the spectral function, in order to evaluate A(v)(Q(2)) couplings. In MPT model, one-dimensional numerical integration involving A(1)(Q(2)) is sufficient to evaluate any A(v)(Q(2)) coupling. Restrictions: For unphysical choices of the input parameters the results are meaningless. When Q(2) is close to the cut region of the couplings (Q(2) real negative), the calculations can take more time and can have less precision. Running time: For evaluation of a set of about 10 related couplings, the times vary in the range t similar to 10(1)-10(2) s. MPT requires less time, t similar to 1-10(1) s. References: [1] C. Ayala and G. Cvetic, anQCD: a Mathematica package for calculations in general analytic QCD models, Comput. Phys. Commun. 190 (2015) 182.
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Allanach, B. C., Bednyakov, A., & Ruiz de Austri, R. (2015). Higher order corrections and unification in the minimal supersymmetric standard model: SOFTSUSY3.5. Comput. Phys. Commun., 189, 192–206.
Abstract: We explore the effects of three-loop minimal supersymmetric standard model renormalisation group equation terms and some leading two-loop threshold corrections on gauge and Yukawa unification: each being one loop higher order than current public spectrum calculators. We also explore the effect of the higher order terms (often 2-3 GeV) on the lightest CP even Higgs mass prediction. We illustrate our results in the constrained minimal supersymmetric standard model. Neglecting threshold corrections at the grand unified scale, the discrepancy between the unification scale alpha(s) and the other two unified gauge couplings changes by 0.1% due to the higher order corrections and the difference between unification scale bottom-tau Yukawa couplings neglecting unification scale threshold corrections changes by up to 1%. The difference between unification scale bottom and top Yukawa couplings changes by a few percent. Differences due to the higher order corrections also give an estimate of the size of theoretical uncertainties in the minimal supersymmetric standard model spectrum. We use these to provide estimates of theoretical uncertainties in predictions of the dark matter relic density (which can be of order one due to its strong dependence on sparticle masses) and the LHC sparticle production cross-section (often around 30%). The additional higher order corrections have been incorporated into SOFTSUSY, and we provide details on how to compile and use the program. We also provide a summary of the approximations used in the higher order corrections. Program Summary Nature of problem: Calculating supersymmetric particle spectrum and mixing parameters in the minimal supersymmetric standard model. The solution to the renormalisation group equations must be consistent with boundary conditions on supersymmetry breaking parameters, as well as the weak-scale boundary condition on gauge couplings, Yukawa couplings and the Higgs potential parameters. Program title: SOFTSUSY Catalogue identifier: ADPMv50 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADPMv50.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 240528 No. of bytes in distributed program, including test data, etc.: 2597933 Distribution format: tar.gz Programming language: C++, Fortran. Computer: Personal computer. Operating system: Tested on Linux 3.4.6. Word size: 64 bits. Classification: 11.1, 11.6. External routines: At least GiNaC1.3.5 [1] and CLN1.3.1 (both freely obtainable from http://www.ginac.de). Does the new version supersede the previous version?: Yes Catalogue identifier of previous version: ADPMv40 Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 2322 Solution method: Nested iterative algorithm. Reasons for new version: Extension to include additional two and three-loop terms. Summary of revisions: All quantities in the minimal supersymmetric standard model are extended to have three-loop renormalisation group equations (including 3-family mixing) in the limit of real parameters and some leading two-loop threshold corrections are incorporated to the third family Yukawa couplings and the strong gauge coupling. Restrictions: SOFTSUSY will provide a solution only in the perturbative regime and it assumes that all couplings of the model are real (i.e. CP-conserving). If the parameter point under investigation is non-physical for some reason (for example because the electroweak potential does not have an acceptable minimum), SOFTSUSY returns an error message. The higher order corrections included are for the real R-parity conserving minimal supersymmetric standard model (MSSM) only. Running time: A minute per parameter point. The tests provided with the package only take a few seconds to run.
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Athron, P., Park, J. H., Stockinger, D., & Voigt, A. (2015). FlexibleSUSY-A spectrum generator generator for supersymmetric models. Comput. Phys. Commun., 190, 139–172.
Abstract: We introduce FlexibleSUSY, a Mathematica and C++ package, which generates a fast, precise C++ spectrum generator for any SUSY model specified by the user. The generated code is designed with both speed and modularity in mind, making it easy to adapt and extend with new features. The model is specified by supplying the superpotential, gauge structure and particle content in a SARAH model file; specific boundary conditions e.g. at the GUT, weak or intermediate scales are defined in a separate FlexibleSUSY model file. From these model files, FlexibleSUSY generates C++ code for self-energies, tadpole corrections, renormalization group equations (RGEs) and electroweak symmetry breaking (EWSB) conditions and combines them with numerical routines for solving the RGEs and EWSB conditions simultaneously. The resulting spectrum generator is then able to solve for the spectrum of the model, including loop-corrected pole masses, consistent with user specified boundary conditions. The modular structure of the generated code allows for individual components to be replaced with an alternative if available. FlexibleSUSY has been carefully designed to grow as alternative solvers and calculators are added. Predefined models include the MSSM, NMSSM, E6SSM, USSM, R-symmetric models and models with right-handed neutrinos. Program Summary Program title: FlexibleSUSY Catalogue identifier: AEVIv10 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEVIv10.html obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 129406 No. of bytes in distributed program, including test data, etc.: 854831 Distribution format: tar.gz Programming language: C++, Wolfram/Mathematica, FORTRAN, Bourne shell. Computer: Personal computer. Operating system: Tested on Linux 3.x, Mac OS X. Classification: 11.1, 11.6, 6.5. External routines: SARAH 4.0.4, Boost library, Eigen, LAPACK Nature of problem: Determining the mass spectrum and mixings for any supersymmetric model. The generated code must find simultaneous solutions to constraints which are specified at two or more different renormalization scales, which are connected by renormalization group equations forming a large set of coupled first-order differential equations. Solution method: Nested iterative algorithm and numerical minimization of the Higgs potential. Restrictions: The couplings must remain perturbative at all scales between the highest and the lowest boundary condition. FlexibleSUSY assumes that all couplings of the model are real (i.e. CP-conserving). Due to the modular nature of the generated code, adaption and extension to overcome restrictions in scope is quite straightforward. Running time: 0.06-0.2 seconds per parameter point.
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Basso, L., Belyaev, A., Chowdhury, D., Hirsch, M., Khalil, S., Moretti, S., et al. (2013). Proposal for generalised supersymmetry Les Houches Accord for see-saw models and PDG numbering scheme. Comput. Phys. Commun., 184(3), 698–719.
Abstract: The SUSY Les Houches Accord (SLHA) 2 extended the first SLHA to include various generalisations of the Minimal Supersymmetric Standard Model (MSSM) as well as its simplest next-to-minimal version. Here, we propose further extensions to it, to include the most general and well-established see-saw descriptions (types I/II/III, inverse, and linear) in both an effective and a simple gauged extension of the MSSM framework. In addition, we generalise the PDG numbering scheme to reflect the properties of the particles. (c) 2012 Elsevier B.V. All rights reserved.
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Oliver, S., Rodriguez Bosca, S., & Gimenez-Alventosa, V. (2024). Enabling particle transport on CAD-based geometries for radiation simulations with penRed. Comput. Phys. Commun., 298, 109091–11pp.
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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Gimenez-Alventosa, V., Gimenez, V., & Oliver, S. (2021). PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE. Comput. Phys. Commun., 267, 108065–12pp.
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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