Computer Physics Communications最新文献

{"title":"Corrigendum to “SimpleBounce: A simple package for the false vacuum decay” [Computer Physics Communications 258 (2021) 107566]","authors":"Ryosuke Sato","doi":"10.1016/j.cpc.2025.110006","DOIUrl":"10.1016/j.cpc.2025.110006","url":null,"abstract":"","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110006"},"PeriodicalIF":3.4,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880065","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":"Semi-implicit scheme for multi-species collision operators in Tokamak Plasma Simulations","authors":"Dandan Liao ,&nbsp;Lei Ye ,&nbsp;Pengfei Zhao ,&nbsp;Qilong Ren ,&nbsp;Nong Xiang","doi":"10.1016/j.cpc.2025.110012","DOIUrl":"10.1016/j.cpc.2025.110012","url":null,"abstract":"<div><div>A second-order semi-implicit time integration method has been developed for solving the linearized collision operator in multi-species plasmas. A key feature of this method is that it treats the collision operator as a single entity, avoiding the operator splitting between its test particle and field particle components. This scheme employs an implicit trapezoidal time integration scheme for the isothermal test particle part (including pitch-angle scattering and energy diffusion) with a finite volume discretization in (<em>v</em>_∥, <em>μ</em>) velocity coordinates, while the non-isothermal model term and field particle part are treated explicitly. This approach avoids the species cross-coupling required by fully implicit schemes, enabling the collision term to be computed efficiently with a banded/sparse-matrix solver. The method has been implemented in the gyrokinetic semi-Lagrangian code NLT and verified through multi-species relaxation tests and neoclassical transport simulations. Numerical benchmarks against explicit methods confirm its robustness, achieving order-of-magnitude improvements in the allowable time-step size, particularly in simulations of electron-ion collisions. Furthermore, the numerical discretization rigorously preserves particle number, momentum, and energy conservation, maintains the self-adjoint property of the collision operator, and satisfies Boltzmann’s H-theorem.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110012"},"PeriodicalIF":3.4,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880486","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":"VacHopPy: A Python package for vacancy hopping analysis based on molecular dynamics simulations","authors":"Taeyoung Jeong ,&nbsp;Kun Hee Ye ,&nbsp;Seungjae Yoon ,&nbsp;Dohyun Kim ,&nbsp;Yunjae Kim ,&nbsp;Cheol Seong Hwang ,&nbsp;Jung-Hae Choi","doi":"10.1016/j.cpc.2025.110010","DOIUrl":"10.1016/j.cpc.2025.110010","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Multiscale modeling, which integrates material properties from &lt;em&gt;ab initio&lt;/em&gt; calculations into continuum-scale simulations, is a promising strategy for optimizing semiconductor devices. However, a key challenge remains: while &lt;em&gt;ab initio&lt;/em&gt; methods provide diffusion parameters specific to individual migration paths, continuum equations require a single effective set of parameters that captures the overall diffusion behavior. To address this issue, we present &lt;em&gt;VacHopPy&lt;/em&gt;, an open-source Python package for vacancy hopping analysis based on molecular dynamics (MD). &lt;em&gt;VacHopPy&lt;/em&gt; extracts an effective set of hopping parameters, including hopping distance, hopping barrier, number of effective paths, correlation factor, and attempt frequency, by statistically integrating energetic, kinetic, and geometric contributions across all paths. It also includes tools for tracking vacancy trajectories and for detecting phase transitions during MD simulations. The applicability of &lt;em&gt;VacHopPy&lt;/em&gt; is demonstrated in three representative materials: face-centered cubic Al, rutile TiO&lt;sub&gt;2&lt;/sub&gt;, and monoclinic HfO&lt;sub&gt;2&lt;/sub&gt;. The extracted effective parameters reproduce temperature-dependent diffusion behavior and are in good agreement with previous experimental data. Provided in a simplified form, these parameters are well suited for continuum-scale models and remain valid over a wide temperature range spanning several hundred kelvins. Furthermore, &lt;em&gt;VacHopPy&lt;/em&gt; inherently accounts for anisotropy in thermal vibrations, a factor often overlooked, making it suitable for simulating diffusion in complex crystals. Overall, &lt;em&gt;VacHopPy&lt;/em&gt; establishes a robust bridge between atomic- and continuum-scale models, enabling more reliable multiscale simulations.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Program Summary&lt;/strong&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;Program Title: VacHopPy&lt;/em&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/nfd44zrb24.1&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/TY-Jeong/VacHopPy&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; MIT License&lt;/div&gt;&lt;div&gt;&lt;em&gt;Programming language:&lt;/em&gt; Python&lt;/div&gt;&lt;div&gt;&lt;em&gt;Supplementary material:&lt;/em&gt; Supplementary Figures (S1–S11), Supplementary Tables (S1–S6), and Supplementary Notes (1–4) are provided in a separate PDF file.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Nature of problem:&lt;/em&gt; For modeling of vacancy-mediated diffusion, &lt;em&gt;ab initio&lt;/em&gt; calculations provide path-specific diffusion parameters that are not directly compatible with continuum-scale models, which typically require a single set of effective parameters. Such incompatibility poses a significant challenge in accurately integrating atomistic diffusion behavior into multiscale simulation frameworks, particularly when multiple hopping paths exist in a material system.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Solution method:&lt;/em&gt; Vacancy trajectories are identif","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110010"},"PeriodicalIF":3.4,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880079","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":"OpenSn: A massively parallel, open-source simulation environment for discrete ordinates radiation transport","authors":"David Andrs ,&nbsp;Zachary Hardy ,&nbsp;Daryl Hawkins ,&nbsp;Jim Morel ,&nbsp;Dinh Quoc Dang Nguyen ,&nbsp;Jean C. Ragusa","doi":"10.1016/j.cpc.2025.110001","DOIUrl":"10.1016/j.cpc.2025.110001","url":null,"abstract":"&lt;div&gt;&lt;div&gt;OpenSn is an open-source, massively parallel deterministic radiation transport code for solving the discrete-ordinates (S&lt;sub&gt;&lt;em&gt;N&lt;/em&gt;&lt;/sub&gt;) form of the Boltzmann transport equation on unstructured, arbitrary polyhedral meshes. It supports high-fidelity simulations involving steady-state, eigenvalue, and adjoint problems for neutral particles (e.g., neutrons, photons, multi-particles), using the multigroup approximation in energy.&lt;/div&gt;&lt;div&gt;OpenSn combines angular discretization via discrete ordinates with a discontinuous Galerkin finite element method (DGFEM) in space, enabling accurate resolution of transport physics on arbitrary polyhedral cells, included locally refined spatial grids. It includes multiple angular quadrature types, including locally refined angular quadratures.&lt;/div&gt;&lt;div&gt;Written in modern C++ with a Python API, OpenSn runs efficiently on platforms ranging from laptops to supercomputers. The transport sweep algorithm is implemented using a task-based, directed-acyclic-graph (DAG) approach for each angle and supports asynchronous parallelism across thousands of MPI ranks. Group-set aggregation improves compute intensity, and synthetic acceleration techniques (e.g., diffusion synthetic acceleration, second-moment method) enhance solver convergence.&lt;/div&gt;&lt;div&gt;OpenSn has been verified on reactor physics problems and demonstrated excellent weak and strong scaling performance on more than 32,768 processes, making it a versatile and robust platform for large-scale transport simulations in complex geometries.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;PROGRAM SUMMARY&lt;/strong&gt;&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Program Title:&lt;/strong&gt; OpenSn&lt;/div&gt;&lt;div&gt;&lt;strong&gt;CPC Library link to program files:&lt;/strong&gt; &lt;span&gt;&lt;span&gt;https://doi.org/10.17632/gvrs69dzcv.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;strong&gt;Developer’s repository link:&lt;/strong&gt; &lt;span&gt;&lt;span&gt;https://github.com/Open-Sn/OpenSn&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;strong&gt;Licensing provisions:&lt;/strong&gt; MIT license&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Programming language:&lt;/strong&gt; C++ (core), Python (API)&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Supplementary material:&lt;/strong&gt; User manual, theory documentation, and tutorial notebooks available at &lt;span&gt;&lt;span&gt;https://open-sn.github.io/opensn/&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;strong&gt;Nature of problem:&lt;/strong&gt;Radiation transport simulations are central to numerous applications in physics and engineering, including reactor analysis, shielding, radiography, and detector modeling. Solving the linear Boltzmann transport equation in its discrete-ordinates form (S&lt;sub&gt;&lt;em&gt;N&lt;/em&gt;&lt;/sub&gt;) on complex geometries requires robust numerical methods and scalable parallel algorithms. Many existing codes are closed-source, lack support for polyhedral meshes, or do not efficiently exploit modern HPC systems. A flexible, open-source tool is needed to address these challenges while supporting methodological innovation and large-scale computation.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Solution method:&lt;/strong&gt;","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110001"},"PeriodicalIF":3.4,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145920953","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":"QR2-code: An open-source program for double resonance Raman spectra","authors":"Jianqi Huang ,&nbsp;Renhui Liu ,&nbsp;Ye Zhang ,&nbsp;Nguyen Tuan Hung ,&nbsp;Huaihong Guo ,&nbsp;Riichiro Saito ,&nbsp;Teng Yang","doi":"10.1016/j.cpc.2025.110005","DOIUrl":"10.1016/j.cpc.2025.110005","url":null,"abstract":"<div><div>We present an open-source program <span>QR²-code</span> that computes double-resonance Raman (DRR) spectra using first-principles calculations. <span>QR²-code</span> can calculate not only two-phonon DRR spectra but also single-resonance Raman spectra and defect-induced DRR spectra. For defect-induced DRR spectra, we simply assume that the electron-defect matrix element of elastic scattering is a constant. Hands-on tutorials for graphene are given to show how to run <span>QR²-code</span> for single-resonance, double-resonance, and defect-induced Raman spectra. We also compare the single-resonance Raman spectra by <span>QR²-code</span> with that by <span>QERaman</span> code. In <span>QR²-code</span>, the Raman spectrum is calculated by the time-dependent perturbation theory, in which the energy dispersions of electron and phonon are taken from <span>Quantum ESPRESSO</span> (<span>QE</span>) code and the electron-phonon matrix element is obtained from the modified Electron-Phonon-Wannier (<span>EPW</span>) code. All codes, examples, and scripts are available on the GitHub repository.</div><div><strong>Program Summary</strong></div><div><em>Program Title:</em> <span>QR²-code</span></div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/vstc3hx5bs.1</span><svg><path></path></svg></span></div><div><em>Developer’s repository link:</em> <span><span>https://github.com/JoeyyHuang/QR2-code</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GNU General Public Licence 3.0</div><div><em>Programming language:</em> Fortran</div><div><em>External routines</em>: <span>Quantum ESPRESSO v7.3.1</span>, <span>EPW v5.8.1</span></div><div><em>Nature of problem:</em>Single-resonance, double-resonance, and defect-induced Raman spectra with first-principles calculations.</div><div><em>Solution method:</em>The Raman spectrum is calculated by the time-dependent perturbation theory, in which the energy dispersions of electron and phonon and electron-phonon matrix elements are obtained from the <span>Quantum ESPRESSO</span> and modified <span>EPW</span> codes. <em>Supplementary material:</em> <span><span>http://qr2-code.com</span><svg><path></path></svg></span></div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110005"},"PeriodicalIF":3.4,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880068","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":"2025-12-20","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":"Dofulator: A tool for calculating degrees of freedom of atoms in molecules with geometry constraints","authors":"Stephen Sanderson ,&nbsp;Sobin Alosious ,&nbsp;Debra J. Searles","doi":"10.1016/j.cpc.2025.110003","DOIUrl":"10.1016/j.cpc.2025.110003","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Recently, we proposed a method for calculating per-atom and per-direction degrees of freedom (DoF) in the presence of geometric constraints, enabling fine-grained local kinetic temperature calculations. Here, we discuss relevant implementation details for various constraint geometries, including those which feature kinematic loops (e.g. benzene with rigid bond lengths). Furthermore, by analyzing the effects of deformation of semi-rigid molecules on the DoF of each constituent atom, we gain insight into conditions under which atomic DoF may vary significantly during a simulation. This provides some guidance towards cases where local DoF should be calculated dynamically to obtain reliable local temperature measurements, and cases where using the atomic DoF of the equilibrium geometry as a constant throughout the simulation would be sufficient. We have implemented the presented algorithms in an open-source C library, &lt;span&gt;dofulator&lt;/span&gt;, which can be used on its own or through a Python interface that includes compatibility with the popular MDAnalysis package.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Program summary&lt;/strong&gt; &lt;em&gt;Program Title:&lt;/em&gt; &lt;span&gt;dofulator&lt;/span&gt; &lt;em&gt;CPC Library link to program files:&lt;/em&gt; (to be added by Technical Editor) &lt;em&gt;Developer’s repository link:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://github.com/CTCMS-UQ/dofulator&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; MPL-2.0 &lt;em&gt;Programming language:&lt;/em&gt; C, Python&lt;/div&gt;&lt;div&gt;&lt;em&gt;Nature of problem:&lt;/em&gt; In molecular simulations with geometry constraints, determining the degrees of freedom (DoF) associated with a local kinetic temperature measurement can become non-trivial when constraints include atoms both inside and outside the local subset of interest [1]. The (fractional) DoF of atoms in a rigid body depends on their masses and the molecular geometry. If constraints do not form a rigid body, but instead a semi-rigid fragment, then the partitioning of atomic DoF can vary as the fragment deforms. Furthermore, if directional kinetic temperatures are required, DoF along each direction must be determined, which additionally depend on the orientation of the rigid body or semi-rigid fragment.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Solution method:&lt;/em&gt; Atomic DoF can be calculated by the relative contribution of each atom to the inertia of each mode of motion [1]. This software allows rigid bodies and semi-rigid fragments to be defined, from which a plan is constructed for determining said modes and contributions. Once constructed, a plan can be applied repeatedly to calculate atomic DoF on required frames of a molecular dynamics trajectory.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Additional comments including restrictions and unusual features:&lt;/em&gt; The core &lt;span&gt;dofulator&lt;/span&gt; library is provided as a C API, depending only on a BLAS and LAPACK implementation and suitable for direct integration with a molecular dynamics engine (possibly with some modifications). For convenience, a thin Python wrapper is also provided, and this","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110003"},"PeriodicalIF":3.4,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836433","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":"Efficient algorithms for accurately simulating radiative transfer in binary stochastic mixtures in two dimensions","authors":"Cong-Zhang Gao ,&nbsp;Jian-Wei Yin ,&nbsp;Ying Cai ,&nbsp;Xu Liu ,&nbsp;Zheng-Feng Fan ,&nbsp;Pei Wang ,&nbsp;Shao-Ping Zhu","doi":"10.1016/j.cpc.2025.110007","DOIUrl":"10.1016/j.cpc.2025.110007","url":null,"abstract":"<div><div>In recent decades, radiative transfer through the binary stochastic mixtures (i.e., a fraction of particulate high-<em>Z</em> materials are randomly dispersed into the low-<em>Z</em> background material, where the label <em>Z</em> means the atomic number) has received great attention in many scientific and engineering disciplines, accurate and efficient simulations in multidimensions are much in demand. In this work, we primarily focus on the efficient algorithms for accurately simulating radiative transfer in binary stochastic mixtures in two dimensions. Our computational model is to solve the radiation-material coupled equations for an ensemble of binary stochastic mixtures. In this context, a subgrid-based nearest-neighbor searching (SNNS) algorithm is introduced to explicitly model the binary stochastic mixture, resulting in an <em>O</em>(<em>N</em>) scaling with the number of particles, which is more flexible than the fast random sequential addition (RSA) algorithm. In order to accurately determine the grid-based parameters, a particle-resolved algorithm is developed by dividing the relationship between the particle’s location and the grid into four categories, reproducing analytical results exactly and efficiently. A parallel algorithm using the spatial domain decomposition with directed acylic graph (DAG) techniques is proposed to efficiently solve the radiation-material coupled equations. These algorithms are combined to enable accurate and efficient simulations in two dimensions, which is validated by reported benchmark results. We find that convergent results require a sufficiently high resolution of the particle and a high-order quadrature. Although results based on one physical realization are somewhat representative, the ensemble-averaged results are more meaningful to avoid the statistical anomalies in some cases. Moreover, case studies on the influence of particle size distribution, the validation of the effective opacity models, and the particle size effect are presented and analyzed. Our work provides efficient algorithms for routinely simulating radiative transfer in binary stochastic mixtures in multidimensions, which can yield the benchmark results for analytical homogenized models of relevance.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110007"},"PeriodicalIF":3.4,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836435","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":"AFIS - A simulation framework for detection of aerosol fluorescence with integrating spheres","authors":"Julian Soltau ,&nbsp;Arne Walter ,&nbsp;Frank Duschek ,&nbsp;Thomas Dekorsy","doi":"10.1016/j.cpc.2025.110008","DOIUrl":"10.1016/j.cpc.2025.110008","url":null,"abstract":"<div><div>We present a new simulation framework for the detection of aerosol fluorescence with integration spheres. Utilizing a Monte Carlo based ray-tracing approach, aerosol fluorescence within integrating sphere setups is simulated from photon generation through laser excitation over interactions with the setup components to losses and finally detection. Through modular design, the position and number of openings, sensors, etc. can be freely configured. Therefore, potential experimental setups can be evaluated with regard to overall performance, bottlenecks can be identified and the impact of different component parameters determined.</div><div><strong>PROGRAM SUMMARY</strong></div><div><em>Program Title:</em> AFIS - <strong>A</strong>erosol <strong>F</strong>luorescence in <strong>I</strong>ntegrating <strong>S</strong>pheres</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/nj9dg3tr6d.1</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> BSD 3-clause</div><div><em>Programming language:</em> Python</div><div><em>Nature of problem:</em> Measuring (bio-)aerosol fluorescence is a complex task, especially for thin aerosols. In order to evaluate new experimental setups utilizing an integrating sphere, simulation data is essential to asses which system configurations yield promising results. Therefore, a simulation environment capable of calculating the different interactions within the setup is necessary, ideally providing a high level of customizability for the simulated setups.</div><div><em>Solution method:</em> The AFIS simulation framework utilizes a ray-tracing approach based on a classical Monte Carlo description of the involved processes. Through batch-wise processing and penalization the computational efficiency is increased.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"321 ","pages":"Article 110008"},"PeriodicalIF":3.4,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145974179","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":"OpenEdge: A collaborative, open-source, multi-purpose direct simulation Monte Carlo for plasma simulation in magnetic fusion environments","authors":"A. Diaw,&nbsp;C.A. Johnson,&nbsp;E.A. Unterberg,&nbsp;J. Nichols","doi":"10.1016/j.cpc.2025.109993","DOIUrl":"10.1016/j.cpc.2025.109993","url":null,"abstract":"<div><div>OpenEdge is a collaborative, open-source, object-oriented Direct Simulation Monte Carlo (DSMC) code, designed specifically for plasma simulations in magnetic fusion environments. The code features include advanced structures, robust capabilities, and an effective parallelization strategy, all of which significantly enhance performance. It includes specialized modules for managing complex particle interactions, including collisions, ionization/recombination, and reflection/sputtering. Benchmarks and performance analyses have confirmed its efficiency and scalability. Versatile and adaptable, OpenEdge is applied across a broad spectrum of plasma-material interaction studies and charged particle transport in various fusion research settings.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109993"},"PeriodicalIF":3.4,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836437","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}