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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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Figueroa, D. G., Florio, A., Torrenti, F., & Valkenburg, W. (2023). CosmoLattice: A modern code for lattice simulations of scalar and gauge field dynamics in an expanding universe. Comput. Phys. Commun., 283, 108586–13pp.
Abstract: This paper describes CosmoGattice, a modern package for lattice simulations of the dynamics of interacting scalar and gauge fields in an expanding universe. CosmoGattice incorporates a series of features that makes it very versatile and powerful: i) it is written in C++ fully exploiting the object oriented programming paradigm, with a modular structure and a clear separation between the physics and the technical details, ii) it is MPI-based and uses a discrete Fourier transform parallelized in multiple spatial dimensions, which makes it specially appropriate for probing scenarios with well -separated scales, running very high resolution simulations, or simply very long ones, iii) it introduces its own symbolic language, defining field variables and operations over them, so that one can introduce differential equations and operators in a manner as close as possible to the continuum, iv) it includes a library of numerical algorithms, ranging from O(delta t(2)) to O(delta t(10)) methods, suitable for simulating global and gauge theories in an expanding grid, including the case of 'self-consistent' expansion sourced by the fields themselves. Relevant observables are provided for each algorithm (e.g. energy densities, field spectra, lattice snapshots) and we note that, remarkably, all our algorithms for gauge theories (Abelian or non-Abelian) always respect the Gauss constraint to machine precision. Program summary Program Title:: CosmoGattice CPC Library link to program files: https://doi .org /10 .17632 /44vr5xssc6 .1 Developer's repository link: http://github .com /cosmolattice /cosmolattice Licensing provisions: MIT Programming language: C++, MPI Nature of problem: The phenomenology of high energy physics in the early universe is typically characterized by non-linear dynamics, which cannot be captured accurately with analytical techniques. In order to fully understand the non-linearities developed in a given scenario, one needs to carry out lattice simulations. A number of public packages for lattice simulations have appeared over the years, but most of them are only capable of simulating scalar fields. However, realistic models of particle physics do contain other kind of field species, such as (Abelian or non-Abelian) gauge fields, whose non-linear dynamics can also play a relevant role in the early universe. Tensor modes representing gravitational waves are also naturally expected in many scenarios. Solution method: CosmoGattice represents a modern code for lattice simulations of scalar-gauge field theories in an expanding universe. It allows for the simulation of the evolution of interacting (singlet) scalar fields, charged scalar fields under U(1) and/or SU(2) gauge groups, and the corresponding associated Abelian and/or non-Abelian gauge fields. From version 1.1 onward, CosmoGattice also allows to simulate the production of gravitational waves. Simulations can be done either in a flat space-time background, or in a homogeneous and isotropic (spatially flat) expanding FLRW background. CosmoGattice provides symplectic integrators, with accuracy ranging from O (delta t(2)) up to O(delta t(10)), to simuate the non-linear dynamics of the appropriate fields in comoving three-dimensional lattices. The code is parallelized with MPI, and uses a discrete Fourier Transform parallelized in multiple spatial dimensions, which makes it a very powerful code for probing physical problems with well-separated scales. Moreover, the code has been designed as a `platform' to implement any system of dynamical equations suitable for discretization on a lattice.
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KM3NeT Collaboration(Aiello, S. et al), Alves Garre, S., Calvo, D., Carretero, V., Garcia Soto, A., Gozzini, S. R., et al. (2024). Embedded software of the KM3NeT central logic board. Comput. Phys. Commun., 296, 109036–15pp.
Abstract: The KM3NeT Collaboration is building and operating two deep sea neutrino telescopes at the bottom of the Mediterranean Sea. The telescopes consist of latices of photomultiplier tubes housed in pressure-resistant glass spheres, called digital optical modules and arranged in vertical detection units. The two main scientific goals are the determination of the neutrino mass ordering and the discovery and observation of high-energy neutrino sources in the Universe. Neutrinos are detected via the Cherenkov light, which is induced by charged particles originated in neutrino interactions. The photomultiplier tubes convert the Cherenkov light into electrical signals that are acquired and timestamped by the acquisition electronics. Each optical module houses the acquisition electronics for collecting and timestamping the photomultiplier signals with one nanosecond accuracy. Once finished, the two telescopes will have installed more than six thousand optical acquisition nodes, completing one of the more complex networks in the world in terms of operation and synchronization. The embedded software running in the acquisition nodes has been designed to provide a framework that will operate with different hardware versions and functionalities. The hardware will not be accessible once in operation, which complicates the embedded software architecture. The embedded software provides a set of tools to facilitate remote manageability of the deployed hardware, including safe reconfiguration of the firmware. This paper presents the architecture and the techniques, methods and implementation of the embedded software running in the acquisition nodes of the KM3NeT neutrino telescopes. Program summary Program title: Embedded software for the KM3NeT CLB CPC Library link to program files: https://doi.org/10.17632/s847hpsns4.1 Licensing provisions: GNU General Public License 3 Programming language: C Nature of problem: The challenge for the embedded software in the KM3NeT neutrino telescope lies in orchestrating the Digital Optical Modules (DOMs) to achieve the synchronized data acquisition of the incoming optical signals. The DOMs are the crucial component responsible for capturing neutrino interactions deep underwater. The embedded software must configure and precisely time the operation of each DOM. Any deviation or timing mismatch could compromise data integrity, undermining the scientific value of the experiment. Therefore, the embedded software plays a critical role in coordinating, synchronizing, and operating these modules, ensuring they work in unison to capture and process neutrino signals accurately, ultimately advancing our understanding of fundamental particles in the Universe. Solution method: The embedded software on the DOMs provides a solution based on a C-based bare-metal application, operating without a real-time embedded OS. It is loaded into the RAM during FPGA configuration, consuming less than 256 kB of RAM. The software architecture comprises two layers: system software and application. The former offers OS-like features, including a multitasking scheduler, firmware updates, peripheral drivers, a UDP-based network stack, and error handling utilities. The application layer contains a state machine ensuring consistent program states. It is navigated via slow control events, including external inputs and autonomous responses. Subsystems within the application code control specific acquisition electronics components via the associated driver abstractions. Additional comments including restrictions and unusual features: Due to the operation conditions of the neutrino telescope, where access is restricted, the embedded software implements a fail-safe procedure to reconfigure the firmware where the embedded software runs.
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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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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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KM3NeT Collaboration(Aiello, S. et al), Alves Garre, S., Calvo, D., Carretero, V., Colomer, M., Corredoira, I., et al. (2020). gSeaGen: The KM3NeT GENIE-based code for neutrino telescopes. Comput. Phys. Commun., 256, 107477–15pp.
Abstract: The gSeaGen code is a GENIE-based application developed to efficiently generate high statistics samples of events, induced by neutrino interactions, detectable in a neutrino telescope. The gSeaGen code is able to generate events induced by all neutrino flavours, considering topological differences between tracktype and shower-like events. Neutrino interactions are simulated taking into account the density and the composition of the media surrounding the detector. The main features of gSeaGen are presented together with some examples of its application within the KM3NeT project. Program summary Program Title: gSeaGen CPC Library link to program files: http://dx.doi.org/10.17632/ymgxvy2br4.1 Licensing provisions: GPLv3 Programming language: C++ External routines/libraries: GENIE [1] and its external dependencies. Linkable to MUSIC [2] and PROPOSAL [3]. Nature of problem: Development of a code to generate detectable events in neutrino telescopes, using modern and maintained neutrino interaction simulation libraries which include the state-of-the-art physics models. The default application is the simulation of neutrino interactions within KM3NeT [4]. Solution method: Neutrino interactions are simulated using GENIE, a modern framework for Monte Carlo event generators. The GENIE framework, used by nearly all modern neutrino experiments, is considered as a reference code within the neutrino community. Additional comments including restrictions and unusual features: The code was tested with GENIE version 2.12.10 and it is linkable with release series 3. Presently valid up to 5 TeV. This limitation is not intrinsic to the code but due to the present GENIE valid energy range. References: [1] C. Andreopoulos at al., Nucl. Instrum. Meth. A614 (2010) 87. [2] P. Antonioli et al., Astropart. Phys. 7 (1997) 357. [3] J. H. Koehne et al., Comput. Phys. Commun. 184 (2013) 2070. [4] S. Adrian-Martinez et al., J. Phys. G: Nucl. Part. Phys. 43 (2016) 084001.
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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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Aiola, S., Amhis, Y., Billoir, P., Jashal, B. K., Henry, L., Oyanguren, A., et al. (2021). Hybrid seeding: A standalone track reconstruction algorithm for scintillating fibre tracker at LHCb. Comput. Phys. Commun., 260, 107713–5pp.
Abstract: We describe the Hybrid seeding, a stand-alone pattern recognition algorithm aiming at finding charged particle trajectories for the LHCb upgrade. A significant improvement to the charged particle reconstruction efficiency is accomplished by exploiting the knowledge of the LHCb magnetic field and the position of energy deposits in the scintillating fibre tracker detector. Moreover, we achieve a low fake rate and a small contribution to the overall timing budget of the LHCb real-time data processing.
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Consiglio, R., de Salas, P. F., Mangano, G., Miele, G., Pastor, S., & Pisanti, O. (2018). PArthENoPE reloaded. Comput. Phys. Commun., 233, 237–242.
Abstract: We describe the main features of a new and updated version of the program PArthENoPE, which computes the abundances of light elements produced during Big Bang Nucleosynthesis. As the previous first release in 2008, the new one, PArthENoPE2.0, is publicly available and distributed from the code site, http://parthenope.na.infn.it . Apart from minor changes, which will be also detailed, the main improvements are as follows. The powerful, but not freely accessible, NAG routines have been substituted by ODEPACK libraries, without any significant loss in precision. Moreover, we have developed a Graphical User Interface (GUI) which allows a friendly use of the code and a simpler implementation of running for grids of input parameters. New Version program summary Program Title: PArthENoPE2.0 Program Files doi : http://dx.doi.org/10.17632/wvgr7d8yt9.1 Licensing provisions: GPLv3 Programming language: Fortran 77 and Python Supplementary material: User Manual available on the web page http://parthenope.na.infn.it Journal reference of previous version: Comput. Phys. Commun. 178 (2008) 956 971 Does the new version supersede the previous version?: Yes Reasons for the new version: Make the code more versatile and user friendly Summary of revisions: (1) Publicly available libraries (2) GUI for configuration Nature of problem: Computation of yields of light elements synthesized in the primordial universe Solution method: Livermore Solver for Ordinary Differential Equations (LSODE) for stiff and nonstiff systems
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Gariazzo, S., de Salas, P. F., Pisanti, O., & Consiglio, R. (2022). PArthENoPE revolutions. Comput. Phys. Commun., 271, 108205–13pp.
Abstract: This paper presents the main features of a new and updated version of the program PArthENoPE, which the community has been using for many years for computing the abundances of light elements produced during Big Bang Nucleosynthesis. This is the third release of the PArthENoPE code, after the 2008 and the 2018 ones, and will be distributed from the code's website, http://parthenope.na.infn.it. Apart from minor changes, the main improvements in this new version include a revisited implementation of the nuclear rates for the most important reactions of deuterium destruction, H-2(p,gamma) He-3, H-2(d, n)He-3 and H-2(d, p)H-3, and a re-designed GUI, which extends the functionality of the previous one. The new GUI, in particular, supersedes the previous tools for running over grids of parameters with a better management of parallel runs, and it offers a brand-new set of functions for plotting the results. Program summary Program title: PArthENoPE 3.0 CPC Library link to program files: https://doi.org/10.17632/wygr7d8yt9.2 Developer's repository link: http://parthenope.na.infn.it Licensing provisions: GPLv3 Programming language: Fortran 77 and Python Nature of problem: Computation of yields of light elements synthesized in the primordial universe Solution method: Livermore Solver for Ordinary Differential Equations (LSODE) for stiff and nonstiff systems, Python GUI for running and plotting Journal reference of previous version: Comput. Phys. Commun. 233 (2018) 237-242 Does the new version supersede the previous version?: Yes Reasons for the new version: Update of the physics and improvements in the GUI Summary of revisions: Update of the physics implemented in the Fortran code and improvements in the GUI functionalities, in particular new plotting functions.
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