Computer Physics Communications最新文献

{"title":"A projection method for particle resampling","authors":"Mark F. Adams ,&nbsp;Daniel S. Finn ,&nbsp;Matthew G. Knepley ,&nbsp;Joseph V. Pusztay","doi":"10.1016/j.cpc.2026.110024","DOIUrl":"10.1016/j.cpc.2026.110024","url":null,"abstract":"<div><div>Particle discretizations of partial differential equations are advantageous for high-dimensional kinetic models in phase-space due to their better scalability than continuum approaches with respect to dimension. Complex processes collectively referred to as <em>particle noise</em> hamper long time simulations with particle methods. One approach to address this problem is particle mesh adaptivity, or remapping, known as <em>particle resampling</em> and <em>remeshing</em>. This work introduces a resampling method that projects particles to and from a (finite element) function space. The method is simple, using standard sparse linear algebra and finite element techniques, and it preserves all moments up to the order of a polynomial represented exactly by the continuum function space. It is distinguished from most other mesh-based methods in that new particle positions and number are decoupled from the mesh, allowing particle and continuum meshes to be adapted relatively independently. While this work is developed with structured particle and continuum phase-space grids on 1<em>X</em> + 1<em>V</em> Vlasov-Poisson models of Landau damping and two-stream instability, the method is well-suited to unstructured grids. Stable long time dynamics are demonstrated up to time <span><math><mrow><mi>T</mi><mo>=</mo><mn>500</mn></mrow></math></span>. Reproducibility artifacts and data are publicly available.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110024"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034992","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":"Fast and memory-efficient strong simulation of noisy adaptive linear optical circuits","authors":"Timothée Goubault De Brugière ,&nbsp;Nicolas Heurtel","doi":"10.1016/j.cpc.2025.110016","DOIUrl":"10.1016/j.cpc.2025.110016","url":null,"abstract":"<div><div>Exactly computing the full output distribution of linear optical circuits remains a challenge, as existing methods are either time-efficient but memory-intensive or memory-efficient but slow. Moreover, any realistic simulation must account for noise, such as photon loss, and any viable quantum computing scheme based on linear optics requires feedforward. This adds additional layers of complexity in the classical simulation as one needs to deal with extra combinatorics due to, e.g, the measurement or loss scenarios. In this paper, we propose an algorithm that models the output amplitudes as partial derivatives of a multivariate polynomial. The algorithm explores the lattice of all intermediate partial derivatives, where each derivative is used to compute more efficiently ones with higher degree. In terms of memory, storing one path from the root to the leaves is sufficient to iterate over all amplitudes and requires only 2^<em>n</em> elements, as opposed to <span><math><mrow><mo>(</mo><mfrac><mrow><mi>n</mi><mo>+</mo><mi>m</mi><mo>−</mo><mn>1</mn></mrow><mi>n</mi></mfrac><mo>)</mo></mrow></math></span> for the fastest state of the art method. This approach effectively balances the time-memory trade-off while extending to both noisy and feedforward scenarios with negligible cost. To the best of our knowledge, this is the first approach in the literature to meet all these requirements. We demonstrate how this method enables the simulation of systems that were previously out of reach, while providing a concrete implementation and complexity analysis.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110016"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034919","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":"Numerical stability of force-gradient integrators and their Hessian-free variants in lattice QCD simulations","authors":"Kevin Schäfers ,&nbsp;Jacob Finkenrath ,&nbsp;Michael Günther ,&nbsp;Francesco Knechtli","doi":"10.1016/j.cpc.2026.110034","DOIUrl":"10.1016/j.cpc.2026.110034","url":null,"abstract":"<div><div>A comprehensive linear stability analysis of force-gradient integrators and their Hessian-free variants is carried out by investigating the harmonic oscillator as a test equation. The analysis reveals that the linear stability of conventional force-gradient integrators and their Hessian-free counterparts coincides. By performing detailed linear stability investigations for the entire family of self-adjoint integrators with up to eleven exponentials per time step, we detect promising integrator variants that are providing a good trade-off between accuracy and numerical stability. Special attention is given to the application of these promising integrator variants within the Hamiltonian Monte Carlo algorithm, particularly in the context of interacting field theories. Simulations for the two-dimensional Schwinger model are conducted to demonstrate that there are no significant differences in the stability domain of a force-gradient integrator and its Hessian-free counterpart. Lattice QCD simulations with two heavy Wilson fermions emphasize that Hessian-free force-gradient integrators with a larger stability threshold allow for a more efficient computational process compared to conventional splitting methods. Furthermore, detailed investigations of the stability threshold are performed by investigating <span><math><mrow><msub><mi>N</mi><mi>f</mi></msub><mo>=</mo><mn>2</mn></mrow></math></span> twisted-mass fermions and nested integrators, highlighting the reliability of the linear stability threshold for lattice QCD simulations.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110034"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034920","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":"Benchmarking Monte Carlo codes for the modelling of low-energy neutron production target reactions","authors":"Sherryn MacLeod ,&nbsp;Klaudiusz Jakubowski ,&nbsp;James Vohradsky ,&nbsp;Daniel R. Franklin ,&nbsp;Toshiro Sakabe ,&nbsp;Akram Hamato ,&nbsp;Masahiro Okamura ,&nbsp;Susanna Guatelli ,&nbsp;Mitra Safavi-Naeini","doi":"10.1016/j.cpc.2025.109998","DOIUrl":"10.1016/j.cpc.2025.109998","url":null,"abstract":"<div><div>The increasing adoption of accelerator-based neutron sources (ABNS) for applications including neutron capture therapy (NCT) research has highlighted the need for accurate simulation tools. Precise modelling of the neutron production target is crucial to ensure that simulated predictions of neutron beam characteristics used for subsequent beam shaping assembly design are reliable. This work presents a comprehensive benchmarking of four widely-used Monte Carlo codes - Geant4, PHITS, FLUKA (CERN), and MCNP - for modelling low-energy neutron production target reactions. Using their recommended physics models and cross-section libraries, we evaluate each code’s performance in simulating four beam-target reactions: ⁷Li(p,n)⁷Be, ⁹Be(p,n)⁹B, ⁹Be(d,n)¹⁰B, and C(d,n)N. Predictions of neutron yield, angular distributions, and energy spectra are compared against available thick target experimental data. Results show varying levels of agreement between the codes depending on the reaction type, energy range, and beam characteristics. Geant4, MCNP and PHITS are the overall best performing codes for the simulation of total neutron yield and yield in the forward direction across most reactions. Across energies where experimental benchmarks exist, inter-code discrepancies in total and forward-directed yield are typically 10 to 30%, with larger deviations at near-threshold incident ion energies. PHITS provides the best overall reproduction of experimental spectra, particularly for the ⁹Be(p,n)⁹B reaction. Additionally, PHITS demonstrates superior computational performance for most reactions. These findings provide valuable guidance for ABNS design, highlighting the strengths and limitations of each code for the simulation of low-energy neutron production reactions.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 109998"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145923459","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":"Chromo: A high-performance python interface to hadronic event generators for collider and cosmic-ray simulations","authors":"Anatoli Fedynitch ,&nbsp;Hans Dembinski ,&nbsp;Anton Prosekin","doi":"10.1016/j.cpc.2026.110031","DOIUrl":"10.1016/j.cpc.2026.110031","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Simulations of hadronic and nuclear interactions are essential in both collider and astroparticle physics. The Chromo package provides a unified Python interface to multiple widely used hadronic event generators, including EPOS, DPMJet, Sibyll, QGSJet, and Pythia. Built on top of their original Fortran and C&lt;span&gt;++&lt;/span&gt; implementations, Chromo offers a zero-overhead abstraction layer suitable for use in Python scripts, Jupyter notebooks, or from the command line, while preserving the performance of direct calls to the generators. It is easy to install via precompiled binary wheels distributed through PyPI, and it integrates well with the Scientific Python ecosystem. Chromo supports event export in HepMC, ROOT, and SVG formats and provides a consistent interface for inspecting, filtering, and modifying particle collision events. This paper describes the architecture, typical use cases, and performance characteristics of Chromo and its role in contemporary astroparticle simulations, such as in the MCEq cascade solver.&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; Chromo &lt;em&gt;CPC Library link to program files:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://doi.org/10.17632/wdf9bvwhns.1&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt; &lt;em&gt;Developer’s repository link:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://github.com/impy-project/chromo&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt; &lt;em&gt;Licensing provisions:&lt;/em&gt; BSD 3-clause &lt;em&gt;Programming language:&lt;/em&gt; Python, Fortran, C&lt;span&gt;++&lt;/span&gt; &lt;em&gt;Nature of problem:&lt;/em&gt;Simulating hadronic and nuclear interactions currently requires users to learn multiple generator APIs (Fortran or C&lt;span&gt;++&lt;/span&gt;), handle different build systems, and write glue code to translate between event formats. This complexity hinders rapid prototyping in Python, makes batch scripting cumbersome, and prevents seamless integration with the broader Scientific Python ecosystem (NumPy, SciPy, Matplotlib, etc.). A unified, zero-overhead interface is needed to streamline generator access, enforce consistent event I/O, and reduce boilerplate for both collider and astroparticle physics applications. &lt;em&gt;Solution method:&lt;/em&gt;Chromo provides lightweight Python bindings for supported generators. Fortran-based generators are wrapped using NumPy’s f2py, and the C&lt;span&gt;++&lt;/span&gt;-based Pythia8 is exposed via pybind11. Prebuilt wheels on PyPI simplify installation across platforms. After installation, Chromo offers a consistent Python API for generating, filtering, and editing events, and for exporting results to HepMC, ROOT, or SVG formats. It can be used interactively in Python scripts or Jupyter notebooks, or as a command-line tool for drop-in substitution of CRMC in shell workflows. Chromo is also suitable for integration into complex pipelines and batch systems. &lt;em&gt;Additional comments including restrictions and unusual features:&lt;/em&gt;Chromo officially supports Linux and macOS by providing prebuilt wheels for Python 3.9-3.13. While most functionality may work o","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110031"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073660","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 soft particle dynamics method based on shape degrees of freedom for core-shell particles","authors":"Yohann Trivino ,&nbsp;Vincent Richefeu ,&nbsp;Farhang Radjai ,&nbsp;Komlanvi Lampoh ,&nbsp;Jean-Yves Delenne","doi":"10.1016/j.cpc.2026.110030","DOIUrl":"10.1016/j.cpc.2026.110030","url":null,"abstract":"<div><div>In this paper, we present a 2D numerical model developed to simulate the dynamics of soft core-shell particles. To accommodate large particle deformations, the particle surface is represented as a thin shell composed of mass points that interact through elasto-plastic force laws governing their linear and angular relative displacements. Particle shape changes are controlled by these interactions, in conjunction with a uniform particle core stiffness. This model can be applied to simulate flexible beams and core-shell particles of arbitrary shape. We calibrate and verify this model by comparing the deformation of constrained beams under load with theoretical predictions. Subsequently, we explore the diametral compression of a single particle between two walls, focusing on the influence of the particle core stiffness and shell plasticity. Our findings indicate that increased core stiffness reduces particle volume change and promotes the development of flat contact areas with the walls. To further illustrate the model capabilities, we apply it to the uniaxial compaction of a granular material composed of core-shell particles. We show that, depending on the core stiffness and shell plastic threshold, the compaction leads to either a significant reduction of particle volumes or an improved pore filling due to particle shape changes. At high compaction, particle shapes vary such that elastic particles without core stiffness become mostly elongated, elastic particles with core stiffness form polygonal shapes, while plastic particles develop elliptical or highly irregular forms. Finally, we simulate the tensile fracture of a tissue composed of elastic or plastic cells, illustrating the model’s potential applicability to soft tissues that undergo both large cell deformations and fracture.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110030"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034996","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 machine learning based approach to online electron reconstruction at CLAS12","authors":"R. Tyson,&nbsp;G. Gavalian","doi":"10.1016/j.cpc.2026.110032","DOIUrl":"10.1016/j.cpc.2026.110032","url":null,"abstract":"<div><div>Online reconstruction is key for monitoring purposes and real time analysis in High Energy and Nuclear Physics experiments. A necessary component of reconstruction algorithms is particle identification that combines information left by a particle passing through several detector components to identify the particle’s type. Of particular interest to electro-production Nuclear Physics experiments such as CLAS12 is electron identification which is used to trigger data recording. A machine learning approach was developed for CLAS12 to reconstruct and identify electrons by combining raw signals at the data acquisition level from several detector components. This approach achieves an electron identification purity above 75% whilst retaining an efficiency close to 100%. The machine learning tools are capable of running at high rates exceeding the data acquisition rates and will allow electron reconstruction in real-time. This work enhances online analyses and monitoring and can contribute to improved triggering at CLAS12. This machine learning driven approach will also be crucial for experiments aiming to transition to streaming readout operations where online reconstruction will be a key component of the data taking paradigm.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110032"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034994","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 three-dimensional multi-phase-field vesicles model and its practical finite difference solver","authors":"Yutong Wu,&nbsp;Zecheng Qiu,&nbsp;Junxiang Yang","doi":"10.1016/j.cpc.2026.110053","DOIUrl":"10.1016/j.cpc.2026.110053","url":null,"abstract":"<div><div>This paper presents a numerical model for simulating the dynamics of multiple interacting vesicles using a multi-phase-field framework. We use <em>N</em> phase-field variables, each possibly containing multiple disconnected vesicles, and enforce volume and surface-area constraint per variable. Their evolution is governed by the variational derivatives of a total energy functional encompassing bending elasticity, surface area and volume conservation, and inter-vesicle repulsion. A semi-implicit finite difference scheme is developed to discretize the system, achieving numerical stability and efficiency. Extensive three-dimensional simulations demonstrate the method’s capability to maintain physical constraints and accurately capture complex vesicle deformations and interactions across various configurations. The simulation code corresponding to Sections 4.3.4 and 4.3.5 (Figs. 10 &amp; 11) in this paper can be accessed at <span><span>https://github.com/aaron-z-chiu/multiple-vesicles</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110053"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073661","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":"Full EPIC-GOD: An energy-conserving full particle-in-cell code for GPU acceleration using OpenACC","authors":"Sunjung Kim ,&nbsp;G.S. Choe ,&nbsp;Dongsu Ryu ,&nbsp;Sibaek Yi","doi":"10.1016/j.cpc.2026.110021","DOIUrl":"10.1016/j.cpc.2026.110021","url":null,"abstract":"<div><div>We present Full EPIC-GOD, a fully implicit, energy- and charge-conserving electromagnetic particle-in-cell (PIC) code. Unlike conventional full-PIC approaches that often suffer from numerical violations of conservation laws, Full EPIC-GOD tightly couples particle dynamics with Maxwell’s equations via an iterative predictor-corrector scheme. Charge conservation is rigorously enforced through Esirkepov’s method, while total energy conservation is achieved using consistent field interpolation and residual-based iterative convergence.</div><div>The algorithm employs second-order accurate discretization in both space and time and supports adaptive time stepping to enhance numerical stability and efficiency. The code is parallelized with OpenACC and demonstrates strong scaling on multi-GPU systems, enabling large-scale kinetic simulations.</div><div>We validate the code using standard benchmarks involving kinetic waves, electromagnetic instabilities, and magnetic reconnection. The results show excellent agreement with theory and prior simulations, confirming the method’s accuracy, stability, and conservation properties. Designed for fully kinetic plasma simulations, Full EPIC-GOD enables high-fidelity modeling of collisionless plasma dynamics across microscopic to relativistic regimes in space and astrophysical environments.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110021"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034993","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":"Advanced measurement techniques in quantum Monte Carlo: The permutation matrix representation approach","authors":"Nic Ezzell ,&nbsp;Itay Hen","doi":"10.1016/j.cpc.2026.110019","DOIUrl":"10.1016/j.cpc.2026.110019","url":null,"abstract":"<div><div>In a typical finite temperature quantum Monte Carlo (QMC) simulation, estimators for simple static observables such as specific heat and magnetization are known. With a great deal of system-specific manual labor, one can sometimes also derive more complicated non-local or even dynamic observable estimators. In contrast, we show that arbitrary static observables can be estimated within the permutation matrix representation (PMR) flavor for any Hamiltonian. We then generalize these results to general imaginary-time correlation functions and non-trivial integrated susceptibilities thereof. We demonstrate the practical versatility of our method by estimating various non-local, random observables for the transverse-field Ising model on a square lattice and a toy random model.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110019"},"PeriodicalIF":3.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034995","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}