Computer Physics Communications最新文献

{"title":"PyFR v2.0.3: Towards industrial adoption of scale-resolving simulations","authors":"Freddie D. Witherden ,&nbsp;Peter E. Vincent ,&nbsp;Will Trojak ,&nbsp;Yoshiaki Abe ,&nbsp;Amir Akbarzadeh ,&nbsp;Semih Akkurt ,&nbsp;Mohammad Alhawwary ,&nbsp;Lidia Caros ,&nbsp;Tarik Dzanic ,&nbsp;Giorgio Giangaspero ,&nbsp;Arvind S. Iyer ,&nbsp;Antony Jameson ,&nbsp;Marius Koch ,&nbsp;Niki Loppi ,&nbsp;Sambit Mishra ,&nbsp;Rishit Modi ,&nbsp;Gonzalo Sáez-Mischlich ,&nbsp;Jin Seok Park ,&nbsp;Brian C. Vermeire ,&nbsp;Lai Wang","doi":"10.1016/j.cpc.2025.109567","DOIUrl":"10.1016/j.cpc.2025.109567","url":null,"abstract":"<div><div>PyFR is an open-source cross-platform computational fluid dynamics framework based on the high-order Flux Reconstruction approach, specifically designed for undertaking high-accuracy scale-resolving simulations in the vicinity of complex engineering geometries. Since the initial release of PyFR v0.1.0 in 2013, a range of new capabilities have been added to the framework, with a view to enabling industrial adoption. In this work, we provide details of these enhancements as released in PyFR v2.0.3, including improvements to cross-platform performance (new backends, extensions of the DSL, new matrix multiplication providers, improvements to the data layout, use of task graphs) and improvements to numerical stability (modal filtering, anti-aliasing, artificial viscosity, entropy filtering), as well as the addition of prismatic, tetrahedral and pyramid shaped elements, improved domain decomposition support for mixed element grids, improved handling of curved element meshes, the addition of an adaptive time-stepping capability, the addition of incompressible Euler and Navier-Stokes solvers, improvements to file formats and the development of a plugin architecture. We also explain efforts to grow an engaged developer and user community and provided a range of examples that show how our user base is applying PyFR to solve a wide range of fundamental, applied and industrial flow problems. Finally, we demonstrate the accuracy of PyFR v2.0.3 for a supersonic Taylor-Green vortex case, with shocks and turbulence, and provided latest performance and scaling results on up to 1024 AMD Instinct MI250X accelerators of Frontier at ORNL (each with two GCDs) and up to 2048 Nvidia GH200 GPUs of Alps at CSCS. We note that absolute performance of PyFR accounting for the totality of both hardware and software improvements has, conservatively, increased by almost 50× over the last decade.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> PyFR</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/vmgh4kfjk6.1</span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span>https://github.com/PyFR/PyFR</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> BSD 3-clause</div><div><em>Programming language:</em> Python (generating C/OpenMP, CUDA, OpenCL, HIP, Metal)</div><div><em>Nature of problem:</em> Accurate and efficient scale-resolving simulation of industrial flows.</div><div><em>Solution method:</em> Massively parallel cross-platform implementation of high-order accurate Flux Reconstruction schemes.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109567"},"PeriodicalIF":7.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143529229","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":"Energy network for state estimation with random sensors and sparse labels","authors":"Yash Kumar ,&nbsp;Tushar ,&nbsp;Souvik Chakraborty","doi":"10.1016/j.cpc.2025.109566","DOIUrl":"10.1016/j.cpc.2025.109566","url":null,"abstract":"<div><div>State estimation is imperative while dealing with high-dimensional dynamical systems due to the unavailability of complete measurements. It plays a pivotal role in gaining insights, executing control, or optimizing design tasks. However, many deep learning approaches are constrained by the requirement for high-resolution labels and fixed sensor locations, limiting their practical applicability. To address these limitations, we propose a novel approach featuring an implicit optimization layer and a physics-based loss function capable of learning from sparse labels. This approach operates by minimizing the energy of neural network predictions, thereby accommodating varying sensor counts and locations. Our methodology is validated through the application of these models to two high-dimensional fluid problems: Burgers' equation and Flow Past Cylinder. Notably, our model exhibits robustness against noise in measurements, underscoring its effectiveness in practical scenarios.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109566"},"PeriodicalIF":7.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143552984","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":"New version of ZKCM, a C++ multiprecision matrix library usable for numerical studies of quantum information","authors":"Akira SaiToh","doi":"10.1016/j.cpc.2025.109564","DOIUrl":"10.1016/j.cpc.2025.109564","url":null,"abstract":"<div><div>Recent improvements in the ZKCM and ZKCM_QC libraries are presented in this announcement. ZKCM was released as a C++ library for multiprecision matrix computation and ZKCM_QC was developed as its extension for matrix-product-state (MPS) simulation of quantum circuits. Their parallel processing extensions using OpenMP and CUDA were briefly reported in a previous contribution [A. SaiToh, to appear in Proc. CCP2023]. Here, their most recent developments are reported, which include the employments of advanced FFT and Moore-Penrose inverse routines.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109564"},"PeriodicalIF":7.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143508993","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":"Adaptive mesh refinement algorithm for CESE schemes on unstructured quadrilateral meshes","authors":"Lisong Shi ,&nbsp;Chaoxiong Zhang ,&nbsp;Chih-Yung Wen","doi":"10.1016/j.cpc.2025.109565","DOIUrl":"10.1016/j.cpc.2025.109565","url":null,"abstract":"<div><div>This study introduces the development of space-time Conservation Element and Solution Element (CESE) methods tailored for adaptive unstructured quadrilateral meshes. An efficient algorithm is then proposed to manage the mesh adaptation process for these staggered schemes, utilizing a unique cell-tree-vertex data structure. This structure accelerates the construction of conservation elements and simplifies the interconnection of computational cells, enabling a flexible approach for handling adaptive mesh refinement in complex computational domains. The integration of second-order <em>a</em>-<em>α</em>, Courant number-insensitive, and upwind CESE schemes with this adaptation algorithm is demonstrated. Numerical simulations of compressible inviscid flows are conducted to validate the global conservation property, ensure second-order accuracy across interfaces at different refinement levels, and evaluate the effectiveness of the extended schemes and adaptation algorithm.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109565"},"PeriodicalIF":7.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143511373","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":"Modeling of heterogeneous catalytic reactions with the simulation tool PICLas","authors":"S. Lauterbach,&nbsp;S. Fasoulas,&nbsp;M. Pfeiffer","doi":"10.1016/j.cpc.2025.109560","DOIUrl":"10.1016/j.cpc.2025.109560","url":null,"abstract":"<div><div>The gas-surface interaction model of the open-source gas and plasma simulation tool PICLas has been extended for the simulation of catalytic reactions. A variety of reaction mechanisms have been implemented, including multiple adsorption models, desorption, the Eley-Rideal and the Langmuir-Hinshelwood mechanism. Modeling is based upon macroscopic reaction data and parameters derived from experiments or ab-initio quantum calculations. The implementation has been validated through a comparison to analytical reaction rates. Simulations of the carbon monoxide and oxygen reaction network on a Pd(111) surface are performed and compared to experimental data obtained by temperature-programmed desorption spectra and molecular beam measurements. The results show good agreement with the measurement data.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109560"},"PeriodicalIF":7.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143511374","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":"Functional analytic derivation and CP2K implementation of the SCCS model based on the solvent-aware interface","authors":"Ziwei Chai,&nbsp;Sandra Luber","doi":"10.1016/j.cpc.2025.109563","DOIUrl":"10.1016/j.cpc.2025.109563","url":null,"abstract":"<div><div>In the self-consistent continuum solvation (SCCS) approach (<em>J. Chem. Phys.</em> 136, 064102 (2012)), the analytical expressions of the local solute-solvent interface functions determine the interface function and dielectric function values at a given real space position based solely on the electron density at that position, completely disregarding the surrounding electron density distribution. Therefore, the low electron density areas inside the solute will be identified by the algorithm as regions where implicit solvent exists, resulting in the emergence of non-physical implicit solvent regions within the solute and even potentially leading to the divergence catastrophe of Kohn-Sham SCF calculations. We present a new and efficient SCCS implementation based on the solvent-aware interface (<em>J. Chem. Theory Comput.</em> 15, 3, 1996–2009 (2019)) which addresses this issue by utilizing a solute-solvent interface function based on convolution of electron density in the CP2K software package, which is based on the mixed Gaussian and plane waves (GPW) approach. Starting with the foundational formulas of SCCS, we have rigorously derived the contributions of the newly defined electrostatic energy to the Kohn-Sham potential and the analytical forces. This comprehensive derivation, which to the best of our knowledge is not available in the current literature, utilizes the updated versions of the solute-solvent interface function and the dielectric function, tailored to align with the specifics of the GPW implementation. Our implementation has been tested to successfully eliminate non-physical implicit solvent regions within the solute and achieve good SCF convergence, as demonstrated by test results for both bulk and surface models, namely liquid H₂O, titanium dioxide, and platinum.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109563"},"PeriodicalIF":7.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143508991","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":"Kernel methods for evolution of generalized parton distributions","authors":"A. Freese ,&nbsp;D. Adamiak ,&nbsp;I. Cloët ,&nbsp;W. Melnitchouk ,&nbsp;J.-W. Qiu ,&nbsp;N. Sato ,&nbsp;M. Zaccheddu","doi":"10.1016/j.cpc.2025.109552","DOIUrl":"10.1016/j.cpc.2025.109552","url":null,"abstract":"<div><div>Generalized parton distributions (GPDs) characterize the 3-dimensional structure of hadrons, combining information about their internal quark and gluon longitudinal momentum distributions and transverse position within the hadron. The dependence of GPDs on the factorization scale <span><math><msup><mrow><mi>Q</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> allows one to connect hard exclusive processes involving GPDs at disparate energy and momentum scales, which is needed in global analyses of experimental data. In this work we explore how finite element methods can be used to construct fast and differentiable <span><math><msup><mrow><mi>Q</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> evolution codes for GPDs in momentum space, which can be used in a machine learning framework. We show numerical benchmarks of the methods' accuracy, including a comparison to an existing evolution code from PARTONS/APFEL++, and provide a repository where the code can be accessed.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109552"},"PeriodicalIF":7.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509004","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":"A data-driven multi-physics coupling analysis method for multi-objective optimization design of an innovative heat pipe reactor core","authors":"Zhenlan Wang,&nbsp;Junli Gou,&nbsp;Dingyu Jiang,&nbsp;Di Yun","doi":"10.1016/j.cpc.2025.109551","DOIUrl":"10.1016/j.cpc.2025.109551","url":null,"abstract":"<div><div>Heat pipe cooled reactors have been developed more than 60 years, primarily utilizing ceramic fuels such as UO₂ and UN. However, the inherent characteristics of ceramic fuels impose limitations on the power density improvement of the heat pipe reactor core. In response to this challenge, an innovative conceptual design of a heat pipe reactor core with U-50Zr metallic fuel is proposed in this study. When addressing the multi-objective, multi-parameter and multi-physics coupling design challenges of heat pipe reactor cores, it is essential to introduce an efficient design and optimization method based on data-driven multi-physics coupling and multi-objective optimization analysis. Therefore, a three-dimensional multi-physics coupling analysis code is developed employing Matlab, OpenMC, and COMSOL. To enhance computational efficiency, the neural network surrogate models are established to replace the original code. Additionally, NSGA-II is utilized to obtain the optimal core design schemes, focusing on the objectives of higher power density of the core and lower fuel enrichment. Finally, in the results of the Pareto front, the detailed multi-physics coupling analyses are studied on two different core design schemes characterized by lower fuel enrichment and higher power density of the core, respectively. The design scheme with high power density features lower peak temperatures and lower peak stresses. In contrast, the design scheme with low enrichment provides a more uniform power distribution and greater backup reactivity. Both design schemes satisfy the operational requirements for a ten-year lifecycle, with temperatures and stresses remaining within the safety limits. This demonstrates the effectiveness of the proposed design approach and the analytical code. This study provides a reference for the design and multi-objective optimization of the heat pipe reactor core with U-50Zr metallic fuel and establishes a foundation for future transient optimization efforts.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109551"},"PeriodicalIF":7.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143474532","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":"The qspec Python package: A physics toolbox for laser spectroscopy","authors":"P. Müller ,&nbsp;W. Nörtershäuser","doi":"10.1016/j.cpc.2025.109550","DOIUrl":"10.1016/j.cpc.2025.109550","url":null,"abstract":"<div><div>The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The <span>qspec</span> Python package was developed to provide functions for physical formulas, simulations and data analysis routines widely used in laser spectroscopy and related fields. Most functions are compatible with <span>numpy</span> arrays, enabling fast calculations with large samples of data. A multidimensional linear regression algorithm enables a King plot analyses over multiple atomic transitions. A modular framework for constructing lineshape models can be used to fit large sets of spectroscopy data. A simulation module within the package provides user-friendly methods to simulate the coherent time-evolution of atoms in electromagnetic fields without the need to explicitly derive a Hamiltonian.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109550"},"PeriodicalIF":7.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143529302","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":"eTraj.jl: Trajectory-based simulation for strong-field ionization","authors":"Mingyu Zhu ,&nbsp;Hongcheng Ni ,&nbsp;Jian Wu","doi":"10.1016/j.cpc.2025.109549","DOIUrl":"10.1016/j.cpc.2025.109549","url":null,"abstract":"&lt;div&gt;&lt;div&gt;The dynamics of light-matter interactions in the realm of strong-field ionization has been a focal point and has attracted widespread interest. We present the &lt;span&gt;eTraj.jl&lt;/span&gt; program package, designed to implement established classical/semiclassical trajectory-based methods to determine the photoelectron momentum distribution resulting from strong-field ionization of both atoms and molecules. The program operates within a unified theoretical framework that separates the trajectory-based computation into two stages: initial-condition preparation and trajectory evolution. For initial-condition preparation, we provide several methods, including the Strong-Field Approximation with Saddle-Point Approximation (SFA-SPA), SFA-SPA with Non-adiabatic Expansion (SFA-SPANE), and the Ammosov-Delone-Krainov theory (ADK), with atomic and molecular variants, as well as the Weak-Field Asymptotic Theory (WFAT) for molecules. For trajectory evolution, available options are Classical Trajectory Monte-Carlo (CTMC), which employs purely classical electron trajectories, and the Quantum Trajectory Monte-Carlo (QTMC) and Semi-Classical Two-Step model (SCTS), which include the quantum phase during trajectory evolution. The program is a versatile, efficient, flexible, and out-of-the-box solution for trajectory-based simulations for strong-field ionization. It is designed with user-friendliness in mind and is expected to serve as a valuable and powerful tool for the community of strong-field physics.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Program summary&lt;/h3&gt;&lt;div&gt;&lt;em&gt;Program title:&lt;/em&gt; &lt;span&gt;eTraj.jl&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;CPC Library link to program files:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://doi.org/10.17632/33fm297cz4.1&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;Developer's repository link:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://github.com/TheStarAlight/eTraj.jl&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;Licensing provisions:&lt;/em&gt; Apache-2.0&lt;/div&gt;&lt;div&gt;&lt;em&gt;Programming language:&lt;/em&gt; Julia&lt;/div&gt;&lt;div&gt;&lt;em&gt;Nature of problem:&lt;/em&gt; Atoms and molecules exposed in an intense laser field go through complex processes of ionization through mechanisms such as multi-photon ionization and tunneling ionization. The trajectory-based methods are powerful tools for simulating these processes, and have considerable advantages over the time-dependent Schrödinger equation (TDSE) and the strong-field approximation (SFA). However, the community lacks a unified theoretical framework for trajectory-based methods, and there are no public-available code that implements the schemes.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Solution method:&lt;/em&gt; We developed a general, efficient, flexible, and out-of-the-box solution for trajectory-based simulation program named after &lt;span&gt;eTraj.jl&lt;/span&gt; using the Julia programming language. This program conducts trajectory-based classical/semiclassical simulations of photoelectron dynamics under the single-active-electron approximation and the Born-Oppenheimer approximation. It supports multiple method","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"311 ","pages":"Article 109549"},"PeriodicalIF":7.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143508992","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}