Computer Physics Communications最新文献

{"title":"ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data","authors":"W. Haeck,&nbsp;N. Gibson,&nbsp;P. Talou","doi":"10.1016/j.cpc.2024.109245","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109245","url":null,"abstract":"<div><p><span>ENDFtk</span> is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. <span>ENDFtk</span> offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. In this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. <span>ENDFtk</span> is open source and available for download via GitHub (<span>https://github.com/njoy/ENDFtk</span><svg><path></path></svg>).</p></div><div><h3>Program summary</h3><p><em>Program title:</em> <span>ENDFtk</span> 1.0</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/9p4kxc2cvd.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/njoy/ENDFtk</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> BSD-3 clause</p><p><em>Programming language:</em> C++ and Python</p><p><em>External routines/libraries:</em> pybind11, ranges-v3, spdlog</p><p><em>Nature of problem:</em> Provide an interface to read, write and manipulate nuclear data files using the ENDF-6 format. This interface can be integrated into other libraries requiring access to nuclear data, or be used directly using the Python interface.</p><p><em>Solution method:</em> Library of C++ routines, with their Python bindings, to be integrated in higher-level codes and scripts</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141291808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An unconditionally-stable well-posed relativistic particle pusher","authors":"Xiang-Ren Zhou,&nbsp;Li Zhang","doi":"10.1016/j.cpc.2024.109263","DOIUrl":"10.1016/j.cpc.2024.109263","url":null,"abstract":"<div><p>Particle pushers widely used in Particle-in-Cell(PIC) simulations are commonly required to be unconditionally stable and meet the basic physical laws. In this work, basing on central difference, we propose an unconditionally stable and well posed particle pusher. By mathematical deduction, the high-dimensional non-linear problem for solving tensor-form relativistic Lorentz force law equation is transformed to a quartic scalar problem and a following linear problem. Some practical suggestions for programming and some numerical results are also given.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FIRE 6.5: Feynman integral reduction with new simplification library","authors":"Alexander V. Smirnov ,&nbsp;Mao Zeng","doi":"10.1016/j.cpc.2024.109261","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109261","url":null,"abstract":"<div><p>FIRE is a program which performs integration-by-parts (IBP) reductions of Feynman integrals. Originally, the C++ version of FIRE relies on the computer algebra system Fermat by Robert Lewis to simplify rational functions. We present an upgrade of FIRE which incorporates a new library FUEL initially described in a separate publication, which enables a flexible choice of third-party computer algebra systems as simplifiers, as well as efficient communications with some of the simplifiers as C++ libraries rather than through Unix pipes. We achieve significant speedups for IBP reductions of Feynman integrals involving many kinematic variables, when using an open source backend based on FLINT newly added in this work, or the Symbolica backend developed by Ben Ruijl as a potential successor of FORM.</p></div><div><h3>Program summary</h3><p><em>Program title:</em> FIRE, version 6.5 (FIRE 6.5)</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/cy6k69pb3y.2</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://gitlab.com/feynmanintegrals/fire.git</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> GPLv2</p><p><em>Programming language:</em> <span>Wolfram Mathematica</span> 8.0 or higher, <span>C++17</span></p><p><em>Supplementary material:</em> See linked repository for installation instructions.</p><p><em>Journal reference of previous version:</em> Comput. Phys. Commun. 247 (2020) 106877</p><p><em>Does the new version supersede the previous version?:</em> Yes.</p><p><em>Reasons for the new version:</em> The new version no longer relies on a single computer algebra system, <span>Fermat</span> [1], but instead allows a flexible choice of several systems, some of which offer higher performance, especially when the number of variables is large.</p><p><em>Summary of revisions:</em> A new library <span>FUEL</span> [2] is used as a core component of the new version of <span>FIRE</span> to access different computer algebra systems as simplifiers of rational function expressions. Since the first release of <span>FUEL</span> described elsewhere, <span>FUEL</span> version 1.0 here has been enhanced with a new backend based on the open source library <span>FLINT</span> [3] that provides highly performant simplification of rational functions.</p><p><em>Nature of problem:</em> Feynman integrals of a given family are reduced to a finite set of master integrals, by solving linear equations arising from integration by parts, using Gaussian elimination. The coefficients of the linear equations are generally rational functions in kinematic variables and the spacetime dimension, and the simplification of such rational functions during Gaussian elimination is a key task that is improved in this upgrade of <span>FIRE</span>.</p><p><em>Solution method:</em> Computer algebra systems with state-of-the-art capabilities for polynomial GCD computations are used as simplification backends, or simp","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CNUCTRAN: A program for computing final nuclide concentrations using a direct simulation approach","authors":"K.A. Bala,&nbsp;M.R. Omar,&nbsp;John Y.H. Soo,&nbsp;W.M.H. Wan Mokhtar","doi":"10.1016/j.cpc.2024.109258","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109258","url":null,"abstract":"<div><p>It is essential to precisely determine the evolving concentrations of radioactive nuclides within transmutation problems. It is also a crucial aspect of nuclear physics with widespread applications in nuclear waste management and energy production. This paper introduces <span>CNUCTRAN</span>, a novel computer program that employs a probabilistic approach to estimate nuclide concentrations in transmutation problems. <span>CNUCTRAN</span> directly simulates nuclei transformations arising from various nuclear reactions, diverging from the traditional deterministic methods that solve the Bateman equation using matrix exponential approximation. This approach effectively addresses numerical challenges associated with solving the Bateman equations, therefore, circumventing the need for matrix exponential approximations that risk producing nonphysical concentrations. Our sample calculations using <span>CNUCTRAN</span> shows that the concentration predictions of <span>CNUCTRAN</span> have a relative error of less than 0.001% compared to the state-of-the-art method, CRAM, in different test cases. This makes <span>CNUCTRAN</span> a valuable alternative tool for transmutation analysis.</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> <span>CNUCTRAN</span></p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/b484w2vx52.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/rabieomar92/cnuctran/releases</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> MIT</p><p><em>Programming language:</em> C++</p><p><em>Nature of problem:</em> <span>CNUCTRAN</span> simulates the transmutation of various nuclides such as decays, fissions, and neutron induced reactions using a direct simulation approach. It has the capability of predicting the final concentration of a large system of nuclides altogether after a specified time step, <span><math><msub><mrow><mi>t</mi></mrow><mrow><mi>f</mi></mrow></msub></math></span>.</p><p><em>Solution method:</em> <span>CNUCTRAN</span> works based on the novel probabilistic method such that it does not compute the final nuclide concentrations by solving Bateman equations. Instead, it statistically tracks nuclide transformations into one another in a transmutation problem. The technique encapsulates various possible nuclide transformations into a sparse transfer matrix, <span><math><mi>T</mi></math></span>, whose elements are made up of various nuclear reaction probabilities. Next, <span><math><mi>T</mi></math></span> serves as a matrix operator acting on the initial nuclide concentrations, <span><math><mi>y</mi><mo>(</mo><mn>0</mn><mo>)</mo></math></span>, producing the final nuclide concentrations, <strong>y</strong>.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Jiezi: an open-source Python software for simulating quantum transport based on non-equilibrium Green's function formalism","authors":"Junyan Zhu ,&nbsp;Jiang Cao ,&nbsp;Chen Song ,&nbsp;Bo Li ,&nbsp;Zhengsheng Han","doi":"10.1016/j.cpc.2024.109251","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109251","url":null,"abstract":"<div><p>We present a Python-based open-source library named <span>Jiezi</span>, which provides the means of simulating the electronic transport properties of nanoscaled devices on the atomistic level. The key feature of <span>Jiezi</span> lies in its core algorithm, i.e., self-consistent orchestration between the non-equilibrium Green's function (NEGF) method and a Poisson's equation solver. Beyond the construction of the tight-binding (TB) Hamiltonian with empirical parameters for conventional materials, the package offers a comprehensive framework for constructing the Wannier-based Hamiltonian matrix, enabling the investigation of novel materials and their heterostructures. To expedite the solution of NEGF systems, a methodology based on renormalization theory is proposed for reducing the dimension of the Hamiltonian matrix. Additionally, we adopt a non-linear Poisson equation solver with no analytical approximation in this software. The software facilitates seamless integration with external tools for geometry and mesh generation and post-processing. In this paper, we present the main capabilities and workflow by demonstrating with a simulation for the carbon nanotube field-effect transistor (CNTFET).</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> Jiezi</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/nk79kbtww4.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/Jiezi-negf/Jiezi</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> GPLv3</p><p><em>Programming language:</em> Python</p><p><em>Nature of problem:</em> Simulates the quantum transport property of nano-scaled transistors based on the predefined device structure and the material composition.</p><p><em>Solution method:</em> Solves the coupled Schrödinger equation and Poisson equation by NEGF and finite element method.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001747/pdfft?md5=ab8916061cc89c6369f91c496a5a9fcc&pid=1-s2.0-S0010465524001747-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141084302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive framework to enhance numerical simulations in the spectral-element code Nek5000","authors":"D. Massaro ,&nbsp;A. Peplinski ,&nbsp;R. Stanly ,&nbsp;S. Mirzareza ,&nbsp;V. Lupi ,&nbsp;T. Mukha ,&nbsp;P. Schlatter","doi":"10.1016/j.cpc.2024.109249","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109249","url":null,"abstract":"<div><p>A framework is presented for the spectral-element code <span>Nek5000</span>, which has been, and still is, widely used in the computational fluid dynamics (CFD) community to perform high-fidelity numerical simulations of transitional and high Reynolds number flows. Despite the widespread usage, there is a deficiency in having a comprehensive set of tools specifically designed for conducting simulations using <span>Nek5000</span>. To address this issue, we have created a unique framework that allows, <em>inter alia</em>, to perform stability analysis and compute statistics of a turbulent flow. The framework encapsulates modules that provide tools, run-time parameters and memory structures, defining interfaces and performing different tasks. First, the framework architecture is described, showing its non-intrusive approach. Then, the modules are presented, explaining the main tools that have been implemented and describing some of the test cases. The code is open-source and available online, with proper documentation, to-run instructions and related examples.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001723/pdfft?md5=0bdec44d85699e37935d33c0c56bc54d&pid=1-s2.0-S0010465524001723-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141084301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DeHNSSo: The delft harmonic Navier-Stokes solver for nonlinear stability problems with complex geometric features","authors":"S. Westerbeek ,&nbsp;S. Hulshoff ,&nbsp;H. Schuttelaars ,&nbsp;M. Kotsonis","doi":"10.1016/j.cpc.2024.109250","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109250","url":null,"abstract":"<div><p>A nonlinear Harmonic Navier-Stokes (HNS) framework is introduced for simulating instabilities in laminar spanwise-invariant shear layers, featuring sharp and smooth wall surface protuberances. While such cases play a critical role in the process of laminar-to-turbulent transition, classical stability theory analyses such as parabolized or local stability methods fail to provide (accurate) results, due to their underlying assumptions. The generalized incompressible Navier-Stokes (NS) equations are expanded in perturbed form, using a spanwise and temporal Fourier ansatz for flow perturbations. The resulting equations are discretized using spectral collocation in the wall-normal direction and finite-difference methods in the streamwise direction. The equations are then solved using a direct sparse-matrix solver. The nonlinear mode interaction terms are converged iteratively. The solution implementation makes use of a generalized domain transformation to account for geometrical smooth surface features, such as humps. No-slip conditions can be embedded in the interior domain to account for the presence of sharp surface features such as forward- or backward-facing steps. Common difficulties with Navier-Stokes solvers, such as the treatment of the outflow boundary and convergence of nonlinear terms, are considered in detail. The performance of the developed solver is evaluated against several cases of representative boundary layer instability growth, including linear and nonlinear growth of Tollmien-Schlichting waves in a Blasius boundary layer and stationary crossflow instabilities in a swept flat-plate boundary layer. The latter problem is also treated in the presence of a geometrical smooth hump and a sharp forward-facing step at the wall. HNS simulation results, such as perturbation amplitudes, growth rates, and shape functions, are compared to benchmark flow stability analysis methods such as Parabolized Stability Equations (PSE), Adaptive Harmonic Linearized Navier-Stokes (AHLNS), or Direct Numerical Simulations (DNS). Good agreement is observed in all cases. The HNS solver is subjected to a grid convergence study and a simple performance benchmark, namely memory usage and computational cost. The computational cost is found to be considerably lower than high-fidelity DNS at comparable grid resolutions.</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> DeHNSSo</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/9bnms99kk2.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/SvenWesterbeek/DeHNSSo</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> GPLv3</p><p><em>Programming language:</em> Matlab</p><p><em>Supplementary material:</em> The supplementary material contains the code as well as a user manual.</p><p><em>Nature of problem:</em> Fluid flows are subject to laminar-to-turbulent transition following the growth of instabilities.","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001735/pdfft?md5=d004601e2b52d69146119eda014b888d&pid=1-s2.0-S0010465524001735-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141077921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MISTER-T: An open-source software package for quantum optimal control of multi-electron systems on arbitrary geometries","authors":"Yuan Chen ,&nbsp;Mahmut Sait Okyay ,&nbsp;Bryan M. Wong","doi":"10.1016/j.cpc.2024.109248","DOIUrl":"10.1016/j.cpc.2024.109248","url":null,"abstract":"<div><p>We present an open-source software package, MISTER-T (Manipulating an Interacting System of Total Electrons in Real-Time), for the quantum optimal control of interacting electrons within a time-dependent Kohn-Sham formalism. In contrast to other implementations restricted to simple models on rectangular domains, our method enables quantum optimal control calculations for multi-electron systems (in the effective mass formulation) on nonuniform meshes with arbitrary two-dimensional cross-sectional geometries. Our approach is enabled by forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency. We provide several examples of the versatility and efficiency of the MISTER-T code in handling complex geometries and quantum control mechanisms. The capabilities of the MISTER-T code provide insight into the implications of varying propagation times and local control mechanisms to understand a variety of strategies for manipulating electron dynamics in these complex systems.</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> MISTER-T</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/psymy4ddnw.1</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> GNU General Public License 3</p><p><em>Programming language:</em> MATLAB</p><p><em>Supplementary material:</em> animated movies of total electron densities under the influence of optimal control fields for (1) an asymmetric double-well potential for long propagation times, (2) an asymmetric double-well potential for short propagation times, and (3) a triple-well potential with a position-dependent effective mass.</p><p><em>Nature of problem:</em> The MISTER-T code solves quantum optimal control problems for interacting electrons within a time-dependent Kohn-Sham formalism. It can handle two-dimensional systems with arbitrary cross-sectional geometries within the effective mass formulation. The user-friendly code uses forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency.</p><p><em>Solution method:</em> iterative solution of the quantum optimal control equations using finite element methods, effective mass formulation, pseudoskeleton decomposition, sparse matrix linear algebra, and nonuniform fast Fourier transforms.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001711/pdfft?md5=ef74cd15cf84bf6ac30afe3a9868240b&pid=1-s2.0-S0010465524001711-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141048809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An unstructured body-of-revolution electromagnetic particle-in-cell algorithm with radial perfectly matched layers and dual polarizations","authors":"Dong-Yeop Na ,&nbsp;Fernando L. Teixeira ,&nbsp;Yuri A. Omelchenko","doi":"10.1016/j.cpc.2024.109247","DOIUrl":"10.1016/j.cpc.2024.109247","url":null,"abstract":"<div><p>A novel electromagnetic particle-in-cell algorithm has been developed for fully kinetic plasma simulations on unstructured (irregular) meshes in complex body-of-revolution geometries. The algorithm, implemented in the BORPIC++ code, utilizes a set of field scalings and a coordinate mapping, reducing the Maxwell field problem in a cylindrical system to a Cartesian finite element Maxwell solver in the meridian plane. The latter obviates the cylindrical coordinate singularity in the symmetry axis. The choice of an unstructured finite element discretization enhances the geometrical flexibility of the BORPIC++ solver compared to the more traditional finite difference solvers. Symmetries in Maxwell's equations are explored to decompose the problem into two dual polarization states with isomorphic representations that enable code reuse. The particle-in-cell scatter and gather steps preserve charge-conservation at the discrete level. Our previous algorithm (BORPIC+) discretized the <strong>E</strong> and <strong>B</strong> field components of TE^<em>ϕ</em> and TM^<em>ϕ</em> polarizations on the finite element (primal) mesh <span>[1]</span>, <span>[2]</span>. Here, we employ a new field-update scheme. Using the same finite element (primal) mesh, this scheme advances two sets of field components independently: (1) <strong>E</strong> and <strong>B</strong> of TE^<em>ϕ</em> polarized fields, (<span><math><msub><mrow><mi>E</mi></mrow><mrow><mi>z</mi></mrow></msub><mo>,</mo><msub><mrow><mi>E</mi></mrow><mrow><mi>ρ</mi></mrow></msub><mo>,</mo><msub><mrow><mi>B</mi></mrow><mrow><mi>ϕ</mi></mrow></msub></math></span>) and (2) <strong>D</strong> and <strong>H</strong> of TM^<em>ϕ</em> polarized fields, (<span><math><msub><mrow><mi>D</mi></mrow><mrow><mi>ϕ</mi></mrow></msub><mo>,</mo><msub><mrow><mi>H</mi></mrow><mrow><mi>z</mi></mrow></msub><mo>,</mo><msub><mrow><mi>H</mi></mrow><mrow><mi>ρ</mi></mrow></msub></math></span>). Since these field updates are not explicitly coupled, the new field solver obviates the coordinate singularity, which otherwise arises at the cylindrical symmetric axis, <span><math><mi>ρ</mi><mo>=</mo><mn>0</mn></math></span> when defining the discrete Hodge matrices (generalized finite element mass matrices). A cylindrical perfectly matched layer is implemented as a boundary condition in the radial direction to simulate open space problems, with periodic boundary conditions in the axial direction. We investigate effects of charged particles moving next to the cylindrical perfectly matched layer. We model azimuthal currents arising from rotational motion of charged rings, which produce TM^<em>ϕ</em> polarized fields. Several numerical examples are provided to illustrate the first application of the algorithm.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141043901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking massively parallel spectral proper orthogonal decompositions in the PySPOD package","authors":"Marcin Rogowski ,&nbsp;Brandon C.Y. Yeung ,&nbsp;Oliver T. Schmidt ,&nbsp;Romit Maulik ,&nbsp;Lisandro Dalcin ,&nbsp;Matteo Parsani ,&nbsp;Gianmarco Mengaldo","doi":"10.1016/j.cpc.2024.109246","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109246","url":null,"abstract":"<div><p>We propose a parallel (distributed) version of the spectral proper orthogonal decomposition (SPOD) technique. The parallel SPOD algorithm distributes the spatial dimension of the dataset preserving time. This approach is adopted to preserve the non-distributed fast Fourier transform of the data in time, thereby avoiding the associated bottlenecks. The parallel SPOD algorithm is implemented in the <span>PySPOD</span><svg><path></path></svg> library and makes use of the standard message passing interface (MPI) library, implemented in Python via <span>mpi4py</span><svg><path></path></svg>. An extensive performance evaluation of the parallel package is provided, including strong and weak scalability analyses. The open-source library allows the analysis of large datasets of interest across the scientific community. Here, we present applications in fluid dynamics and geophysics, that are extremely difficult (if not impossible) to achieve without a parallel algorithm. This work opens the path toward modal analyses of big quasi-stationary data, helping to uncover new unexplored spatio-temporal patterns.</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> PySPOD</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/jf5bf26jcj.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/MathEXLab/PySPOD</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> MIT License</p><p><em>Programming language:</em> Python</p><p><em>Nature of problem:</em> Large spatio-temporal datasets may contain coherent patterns that can be leveraged to better understand, model, and possibly predict the behavior of complex dynamical systems. To this end, modal decomposition methods, such as the proper orthogonal decomposition (POD) and its spectral counterpart (SPOD), constitute powerful tools. The SPOD algorithm allows the systematic identification of space-time coherent patterns. This can be used to understand better the physics of the process of interest, and provide a path for mathematical modeling, including reduced order modeling. The SPOD algorithm has been successfully applied to fluid dynamics, geophysics and other domains. However, the existing open-source implementations are serial, and they prevent running on the increasingly large datasets that are becoming available, especially in computational physics. The inability to analyze via SPOD large dataset in turn prevents unlocking novel mechanisms and dynamical behaviors in complex systems.</p><p><em>Solution method:</em> We provide an open-source parallel (MPI distributed) code, namely PySPOD, that is able to run on large datasets (the ones considered in the present paper reach about 200 Terabytes). The code is built on the previous serial open-source code PySPOD that was published in <span>https://joss.theoj.org/papers/10.21105/joss.02862.pdf</span><svg><path></path></svg>. The new parallel implementation is able to s","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}