Computer Physics Communications最新文献

{"title":"First-principles calculation of higher-order elastic constants from divided differences","authors":"Ruvini Attanayake ,&nbsp;Umesh C. Roy ,&nbsp;Abhiyan Pandit ,&nbsp;Angelo Bongiorno","doi":"10.1016/j.cpc.2025.109877","DOIUrl":"10.1016/j.cpc.2025.109877","url":null,"abstract":"<div><div>A method is presented to calculate from first principles the higher-order elastic constants of a solid material. The method relies on finite strain deformations, a density functional theory approach to calculate the Cauchy stress tensor, and a recursive numerical differentiation technique homologous to the divided differences polynomial interpolation algorithm. The method is applicable as is to any material, regardless its symmetry, to calculate elastic constants of, in principle, any order. Here, we introduce conceptual framework and technical details of our method, we discuss sources of errors, we assess convergence trends, and we present selected applications. In particular, our method is used to calculate elastic constants up to the 6<span><math><msup><mrow></mrow><mrow><mi>t</mi><mi>h</mi></mrow></msup></math></span> order of two crystalline materials with the cubic symmetry, silicon and gold. To demonstrate general applicability, our method is also used to calculate the elastic constants up to the 5<span><math><msup><mrow></mrow><mrow><mi>t</mi><mi>h</mi></mrow></msup></math></span> order of <em>α</em>-quartz, a crystalline material belonging to the trigonal crystal system, and the second- and third-order elastic constants of kevlar, a material with an anisotropic bonding network. Higher order elastic constants computed with our method are validated against density functional theory calculations by comparing stress responses to large deformations derived within the continuum approximation.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109877"},"PeriodicalIF":3.4,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145156860","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":"Modeling and verification of dynamic field ionization for laser-target interactions","authors":"Brandon M. Medina,&nbsp;Scott V. Luedtke,&nbsp;Lin Yin,&nbsp;Brian J. Albright","doi":"10.1016/j.cpc.2025.109875","DOIUrl":"10.1016/j.cpc.2025.109875","url":null,"abstract":"<div><div>Integrating field ionization models into kinetic plasma simulations is required for a variety of applications, especially when field strengths vary from low to high regimes, such as in laser-target interactions. The introduction of new physics models into kinetic codes requires a rigorous verification of their accuracy through well-defined verification problems. In this work, the field ionization model that has been included in the kinetic plasma code VPIC is presented, along with the detailed approach adopted for its integration. This model includes a comprehensive range of field ionization mechanisms: multiphoton ionization, tunneling ionization, and barrier suppression ionization. New verification problems employed to evaluate the ionization model's fidelity are outlined, and the simulation parameters that affect the accuracy of simulation results are explored. Additionally, this work addresses the impact of field ionization on computational performance.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109875"},"PeriodicalIF":3.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145156859","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":"GRILLIX as unified fluid turbulence code for tokamaks and stellarators","authors":"Andreas Stegmeir ,&nbsp;Marion E. Finkbeiner ,&nbsp;Christoph Pitzal ,&nbsp;Joachim Geiger ,&nbsp;Frank Jenko","doi":"10.1016/j.cpc.2025.109874","DOIUrl":"10.1016/j.cpc.2025.109874","url":null,"abstract":"<div><div>The Flux-Coordinate Independent (FCI) approach in the edge fluid turbulence code <span>GRILLIX</span> has proven very successful for tokamaks in handling anisotropic turbulent structures in complex diverted geometries. We extend GRILLIX to non-axisymmetric geometries, maintaining a single, unified codebase for both tokamaks and stellarators. For this proof of principle, the 3D magnetic configurations are based on analytical expressions, that can be adjusted to experimental scenarios, and we demonstrate the code's ability to resolve stellarator geometries correctly via various numerical tests and verifications. We apply the global electromagnetic drift-reduced Braginskii fluid model with trans-collisional extensions and a three-moment fluid neutrals model to two distinct cases. In the first case, we simulate a configuration with imposed magnetic islands and observe profile flattening across the island on time scales consistent with analytic theory. In the second case, we perform a comprehensive turbulence simulation of the Wendelstein 7-AS (W7-AS) stellarator at realistic parameters, including segmented target plates modeled via the immersed boundary approach. Following an initial transient phase, the plasma settles into a self-consistent equilibrium state with Shafranov shift. We then observe small-scale turbulence, characterized by strong elongation along magnetic field lines, which drives turbulent cross-field transport of particles and heat, ultimately directed to target plates in the open field line region. Notably, a parallel mode reflecting the discrete toroidal symmetry of W7-AS is also present. Furthermore, we introduce a novel approach for visualizing data from locally aligned numerical frameworks.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109874"},"PeriodicalIF":3.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145156857","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 efficient GPU-accelerated adaptive mesh refinement framework for high-fidelity compressible reactive flows modeling","authors":"Yuqi Wang ,&nbsp;Yadong Zeng ,&nbsp;Ralf Deiterding ,&nbsp;Jianhan Liang","doi":"10.1016/j.cpc.2025.109870","DOIUrl":"10.1016/j.cpc.2025.109870","url":null,"abstract":"<div><div>This paper presents a heterogeneous adaptive mesh refinement (AMR) framework for exascale simulations of non-stiff/moderately stiff chemical kinetics. The framework features an efficient time-subcycling stepping algorithm along with a specialized refluxing method, all unified in a highly parallel, scalable codebase. In addition, we develope a GPU-optimized low-storage explicit Runge–Kutta chemical integrator designed to minimize register usage, achieving higher efficiency than its implicit counterparts for detailed chemical kinetics with small mechanism size in high-speed combustion problems. A suite of benchmarks demonstrates the framework's high fidelity for both non-reactive and reactive simulations on both uniform and adaptively refined grids. By leveraging our parallelization strategy developed on top of AMReX, we demonstrate significant speedups on various problems using an NVIDIA V100 GPU compared to an Intel i9 CPU within the same codebase. In particular, for problems with complex physics and spatiotemporally distributed stiffness, such as hydrogen detonation propagation, we achieve an overall speedup of 6.49× with substantial computational throughput. Finally, this AMR framework is applied to a large-scale three-dimensional direct numerical simulation. Compared to prior CPU computations on a uniform grid, it yields a substantial reduction in total degrees of freedom involved in the calculation without compromising accuracy.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109870"},"PeriodicalIF":3.4,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145120734","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":"JAX-WSPM: A GPU-accelerated parallel framework based on the JAX library for modeling water flow and solute transport in unsaturated porous media using an implicit finite element method","authors":"Nour-Eddine Toutlini ,&nbsp;Azzeddine Soulaïmani ,&nbsp;Abdelaziz Beljadid","doi":"10.1016/j.cpc.2025.109866","DOIUrl":"10.1016/j.cpc.2025.109866","url":null,"abstract":"<div><div>Accurate simulation of water flow and solute transport in unsaturated porous media requires solving complex, nonlinear partial differential equations. Traditionally, implicit finite element methods have been used due to their robustness and stability. However, they are well known for their computational expense when addressing coupled dynamics. In this study, we present JAX-WSPM, a GPU-accelerated framework built with the JAX library that leverages just-in-time (JIT) compilation and automatic differentiation (AD) to reduce computational cost and improve scalability for coupled water flow and solute transport systems in porous media. We use an implicit finite element method to solve the Richards equation, which models water flow in unsaturated media, and the transport equation. JAX-WSPM implements two complementary strategies for computing water fluxes that are critical for the solute transport equation: one based on conventional finite element formulations and another that supports automatic differentiation. In addition, an adaptive time-stepping strategy is employed to optimize performance.</div><div>Benchmark tests are conducted to examine the accuracy, efficiency, and scalability of JAX-WSPM in solving the Richards equation and the coupled flow-solute transport system. The results confirm the accuracy and efficiency of the framework and demonstrate significant speedups when comparing the GPU-accelerated JAX-WSPM implementation to both the CPU-based JAX-WSPM and serial Python implementations. For example, when performing simulations on a mesh with 1.03 million degrees of freedom, the GPU-accelerated solver achieved a speedup of approximately 107× relative to the serial Python implementation running on a single CPU. JAX-WSPM is available at <span><span>https://github.com/NourEddine-Toutlini/JAX-WSPM</span><svg><path></path></svg></span>, offering a flexible, user-friendly, and high-performance tool for simulations in porous media.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109866"},"PeriodicalIF":3.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145156845","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":"BESLE: Boundary element software for 3D linear elasticity. Version 2.0","authors":"Andres F. Galvis ,&nbsp;Rahim Si Hadj Mohand","doi":"10.1016/j.cpc.2025.109871","DOIUrl":"10.1016/j.cpc.2025.109871","url":null,"abstract":"<div><div>The version 2.0 of the <strong>B</strong>oundary <strong>E</strong>lement <strong>S</strong>oftware for 3D <strong>L</strong>inear <strong>E</strong>lasticity (<span>BESLE</span>) is presented. <span>BESLE</span> is an open-source Fortran 90 code for the simulation of isotropic and anisotropic solids under quasi-static, dynamic, and high-rate boundary conditions using elastostatic and elastodynamic boundary element formulations. Compared to the initial release, this new version introduces a substantially simplified installation procedure. <span>BESLE</span> v1.0 required users to manually download, configure, and integrate external libraries such as MUMPS, SCOTCH, and ScaLAPACK, which often represented a barrier for new users. In contrast, version 2.0 provides an online installer, which automatically downloads, prepares, and installs the required libraries from public repositories. This new approach makes the deployment of <span>BESLE</span> straightforward, reducing installation time and minimising potential user errors. No changes have been made to the core numerical methods, input structure, or supported physics. <span>BESLE</span> v2.0 therefore retains full compatibility with existing simulations and examples, while significantly improving ease of installation, accessibility, and reproducibility.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109871"},"PeriodicalIF":3.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145109930","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":"Secure numerical simulations using fully homomorphic encryption","authors":"Arseniy Kholod ,&nbsp;Yuriy Polyakov ,&nbsp;Michael Schlottke-Lakemper","doi":"10.1016/j.cpc.2025.109868","DOIUrl":"10.1016/j.cpc.2025.109868","url":null,"abstract":"<div><div>Data privacy is a significant concern when using numerical simulations for sensitive information such as medical, financial, or engineering data—especially in untrusted environments like public cloud infrastructures. Fully homomorphic encryption (FHE) offers a promising solution for achieving data privacy by enabling secure computations directly on encrypted data. Aimed at computational scientists, this work explores the viability of FHE-based, privacy-preserving numerical simulations of partial differential equations. The presented approach utilizes the Cheon-Kim-Kim-Song (CKKS) scheme, a widely used FHE method for approximate arithmetic on real numbers. Two Julia packages are introduced, OpenFHE.jl and SecureArithmetic.jl, which wrap the OpenFHE C++ library to provide a convenient interface for secure arithmetic operations. With these tools, the accuracy and performance of key FHE operations in OpenFHE are evaluated, and implementations of finite difference schemes for solving the linear advection equation with encrypted data are demonstrated. The results show that cryptographically secure numerical simulations are possible, but that careful consideration must be given to the computational overhead and the numerical errors introduced by using FHE. An analysis of the algorithmic restrictions imposed by FHE highlights potential challenges and solutions for extending the approach to other models and methods. While it remains uncertain how broadly the approach can be generalized to more complex algorithms due to CKKS limitations, these findings lay the groundwork for further research on privacy-preserving scientific computing.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109868"},"PeriodicalIF":3.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145120735","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 efficient second-order scalar auxiliary variable approach for unsteady non-Newtonian incompressible fluids","authors":"Mofdi El-Amrani ,&nbsp;Anouar Obbadi ,&nbsp;Mohammed Seaid ,&nbsp;Driss Yakoubi","doi":"10.1016/j.cpc.2025.109865","DOIUrl":"10.1016/j.cpc.2025.109865","url":null,"abstract":"<div><div>A novel second-order time-splitting method is proposed for the numerical solution of non-Newtonian fluid flows governed by the incompressible Navier-Stokes equations with a shear-rate dependent viscosity. In many applications, this class of fluid flows is challenging to numerically solve using the conventional monolithic methods. The proposed approach belongs to a family of viscosity-splitting methods and it separates the convection term from the incompressibility constraint into two steps using the second-order implicit backward differentiation formula for the time integration. To ensure the stability of this method, we introduce a numerical scheme based on the scalar auxiliary variable approach an efficient pressure incrementation is introduced using the scalar auxiliary variable approach. Unlike most projection methods for solving incompressible Navier-Stokes equations, the proposed method is free of any numerical inconsistencies generated by the treatment of boundary conditions in the pressure solution. A rigorous stability analysis is also carried out in this study and the proposed method is demonstrated to be consistent and stable with no restrictions on the time step. Numerical results are presented for three flow problems to validate the second-order convergence rates and to illustrate the performance of the proposed time-splitting scheme for unsteady non-Newtonian incompressible fluids.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"317 ","pages":"Article 109865"},"PeriodicalIF":3.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145109514","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":"TensorSymmetry: a package to get symmetry-adapted tensors disentangling spin-orbit coupling effect and establishing analytical relationship with magnetic order","authors":"Rui-Chun Xiao ,&nbsp;Yuanjun Jin ,&nbsp;Zhi-Fan Zhang ,&nbsp;Zi-Hao Feng ,&nbsp;Ding-Fu Shao ,&nbsp;Mingliang Tian","doi":"10.1016/j.cpc.2025.109872","DOIUrl":"10.1016/j.cpc.2025.109872","url":null,"abstract":"<div><div>The symmetry-constrained response tensors on transport, optical, and electromagnetic effects are of central importance in condensed matter physics because they can guide experimental detections and verify theoretical calculations. These tensors encompass various forms, including polar, axial, <em>i</em>-type (time-reversal even), and <em>c</em>-type (time-reversal odd) matrixes. The commonly used magnetic groups, however, fail to describe the phenomena without the spin-orbit coupling (SOC) effect and cannot build the analytical relationship between magnetic orders with response tensors in magnetic materials. Developing approaches on these two aspects is quite demanding for theory and experiment. In this paper, we use the magnetic group, spin group, and extrinsic parameter method comprehensively to investigate the symmetry-constrained response tensors, then implement the above method in a platform called \"TensorSymmetry\". With the package, we can get the response tensors disentangling the effect free of SOC and establish the analytical relationship with magnetic order, which provides useful guidance for theoretical and experimental investigation for magnetic materials.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"318 ","pages":"Article 109872"},"PeriodicalIF":3.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145156855","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":"chebgreen: Learning and interpolating continuous Empirical Green's Functions from data","authors":"Harshwardhan Praveen ,&nbsp;Jacob Brown ,&nbsp;Christopher Earls","doi":"10.1016/j.cpc.2025.109867","DOIUrl":"10.1016/j.cpc.2025.109867","url":null,"abstract":"<div><div>In this work, we present a mesh-independent, data-driven library, <span>chebgreen</span>, to mathematically model one-dimensional systems, possessing an associated control parameter, and whose governing partial differential equation is <em>unknown</em>. The proposed method learns an Empirical Green's Function for the associated, but hidden, boundary value problem, in the form of a Rational Neural Network from which we subsequently construct a bivariate representation in a Chebyshev basis. We uncover the Green's function, at an unseen control parameter value, by interpolating the left and right singular functions within a suitable library, expressed as points on a manifold of Quasimatrices, while the associated singular values are interpolated with Lagrange polynomials. This work improves upon prior work by extending the scope of applicability to non-self-adjoint operators and improves data efficiency.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"317 ","pages":"Article 109867"},"PeriodicalIF":3.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145109515","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}