We present a software package for the simulation and analysis of far-field diffraction patterns in transient grating (TG) spectroscopy. The code is designed to assist both experimental planning and post-processing interpretation by modeling the optical response of TG configurations across a wide range of conditions. It supports input through structured MATLAB variables or Excel-based spreadsheets and provides automated consistency checks and visual output generation. The implementation includes integration over detector pixels, enabling realistic simulations that account for spatial averaging and resolution effects. We demonstrate the software’s capabilities through representative use cases, including the influence of the grating-to-sample distance, the pump-to-probe intensity ratio, and the selection of the division parameter governing pixel integration accuracy. The code is freely available and modular, facilitating its adaptation to different experimental geometries and beam conditions. While full validation is provided elsewhere, this work establishes the core methodology and illustrates the practical value of the tool for TG spectroscopy research.
Program summary
Program title: TGCalc.
Licensing provisions: GNU GPLv3.
Programming language: MATLAB/GNU Octave.
Operating system: Linux and Windows.
Nature of problem: The code has been developed to compute diffraction patterns of light in a transient grating geometry scheme. The output intensity distribution is calculated based on the diffraction integral in the Fresnel and Fraunhofer regimes. Together with the diffraction pattern, the spatial harmonics are obtained using a post-processing script based on the input data filename.
Solution method: The diffraction image is calculated as the diffraction integral over the whole space of a Gaussian beam and normalized by its maximum value. For a Gaussian beam with a spherical approximation of the wavefront, an analytical expression of the electromagnetic field in the Fresnel and Fraunhofer regimes is developed, and a calculation code is implemented.
Additional comments: The TGCalc script has been tested with MATLAB versions R2021a, R2022b, and R2024b. The script also works under GNU Octave software (tested with version 4.0.0). However, under GNU Octave, the matrix data writing could give an error due to the file writeout permissions.
{"title":"Software for simulation and analysis of far-field diffraction patterns in transient grating spectroscopy","authors":"Andrii Goloborodko , Myhailo Kotov , Carles Serrat","doi":"10.1016/j.cpc.2025.109964","DOIUrl":"10.1016/j.cpc.2025.109964","url":null,"abstract":"<div><div>We present a software package for the simulation and analysis of far-field diffraction patterns in transient grating (TG) spectroscopy. The code is designed to assist both experimental planning and post-processing interpretation by modeling the optical response of TG configurations across a wide range of conditions. It supports input through structured MATLAB variables or Excel-based spreadsheets and provides automated consistency checks and visual output generation. The implementation includes integration over detector pixels, enabling realistic simulations that account for spatial averaging and resolution effects. We demonstrate the software’s capabilities through representative use cases, including the influence of the grating-to-sample distance, the pump-to-probe intensity ratio, and the selection of the division parameter governing pixel integration accuracy. The code is freely available and modular, facilitating its adaptation to different experimental geometries and beam conditions. While full validation is provided elsewhere, this work establishes the core methodology and illustrates the practical value of the tool for TG spectroscopy research.</div><div><strong>Program summary</strong></div><div><em>Program title</em>: TGCalc.</div><div><em>Licensing provisions</em>: GNU GPLv3.</div><div><em>Programming language</em>: MATLAB/GNU Octave.</div><div><em>Operating system</em>: Linux and Windows.</div><div><em>Nature of problem</em>: The code has been developed to compute diffraction patterns of light in a transient grating geometry scheme. The output intensity distribution is calculated based on the diffraction integral in the Fresnel and Fraunhofer regimes. Together with the diffraction pattern, the spatial harmonics are obtained using a post-processing script based on the input data filename.</div><div><em>Solution method</em>: The diffraction image is calculated as the diffraction integral over the whole space of a Gaussian beam and normalized by its maximum value. For a Gaussian beam with a spherical approximation of the wavefront, an analytical expression of the electromagnetic field in the Fresnel and Fraunhofer regimes is developed, and a calculation code is implemented.</div><div><em>Additional comments</em>: The <span>TGCalc</span> script has been tested with MATLAB versions R2021a, R2022b, and R2024b. The script also works under GNU Octave software (tested with version 4.0.0). However, under GNU Octave, the matrix data writing could give an error due to the file writeout permissions.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109964"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681709","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}
Pub Date : 2026-03-01Epub Date: 2025-12-11DOI: 10.1016/j.cpc.2025.109989
Luciano G. Silvestri, Zachary A. Johnson, Michael S. Murillo
We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar system. Our comprehensive evaluation of seven initialization approaches (uniform random, uniform random with rejection, Halton and Sobol sequences, perfect and perturbed lattices, and a Monte Carlo pair distribution method) demonstrates that initialization significantly impacts equilibration efficiency, with microfield distribution analysis providing diagnostic insights into thermal behaviors. Our results establish that initialization method selection is relatively inconsequential at low coupling strengths, while physics-informed methods demonstrate superior performance at high coupling strengths, reducing equilibration time. We establish direct relationships between temperature stability and uncertainties in transport properties (diffusion coefficient and viscosity), comparing thermostating protocols including ON-OFF versus OFF-ON duty cycles, Berendsen versus Langevin thermostats, and thermostat coupling strengths. Our findings demonstrate that weaker thermostat coupling generally requires fewer equilibration cycles, and OFF-ON thermostating sequences outperform ON-OFF approaches for most initialization methods. The methodology implements temperature forecasting as a quantitative metric for system thermalization, enabling users to determine equilibration adequacy based on specified uncertainty tolerances in desired output properties, thus transforming equilibration from a heuristic process to a rigorously quantifiable procedure with clear termination criteria.
{"title":"Adaptive equilibration of molecular dynamics simulations","authors":"Luciano G. Silvestri, Zachary A. Johnson, Michael S. Murillo","doi":"10.1016/j.cpc.2025.109989","DOIUrl":"10.1016/j.cpc.2025.109989","url":null,"abstract":"<div><div>We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar system. Our comprehensive evaluation of seven initialization approaches (uniform random, uniform random with rejection, Halton and Sobol sequences, perfect and perturbed lattices, and a Monte Carlo pair distribution method) demonstrates that initialization significantly impacts equilibration efficiency, with microfield distribution analysis providing diagnostic insights into thermal behaviors. Our results establish that initialization method selection is relatively inconsequential at low coupling strengths, while physics-informed methods demonstrate superior performance at high coupling strengths, reducing equilibration time. We establish direct relationships between temperature stability and uncertainties in transport properties (diffusion coefficient and viscosity), comparing thermostating protocols including ON-OFF versus OFF-ON duty cycles, Berendsen versus Langevin thermostats, and thermostat coupling strengths. Our findings demonstrate that weaker thermostat coupling generally requires fewer equilibration cycles, and OFF-ON thermostating sequences outperform ON-OFF approaches for most initialization methods. The methodology implements temperature forecasting as a quantitative metric for system thermalization, enabling users to determine equilibration adequacy based on specified uncertainty tolerances in desired output properties, thus transforming equilibration from a heuristic process to a rigorously quantifiable procedure with clear termination criteria.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109989"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880487","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}
<div><div>This paper presents GeoDualSPHysics, an open-source, graphics processing unit (GPU)-accelerated smoothed particle hydrodynamics (SPH) solver designed for simulating large-deformation geomaterial and their interactions with multi-body systems. Built upon the popular open-source SPH solver DualSPHysics, the solver leverages its highly parallelised SPH scheme empowered by the CUDA parallelisation while extending its capabilities to large-deformation geomechanics problems with particles up to the order of 10⁸ on a single GPU. The SPH geomechanics model is enhanced by a noise-free stress treatment technique that stabilizes and accurately resolves stress fields, as well as an extended modified Dynamic Boundary Condition (mDBC) ensuring first-order consistency in solid boundary modelling. Additionally, the coupling interface between DualSPHysics and the multi-body dynamics solver Project Chrono is adapted for simulating interactions between geomaterials and multiple interacting rigid bodies. Benchmark validations confirm the solver’s accuracy in resolving geotechnical failures, impact forces on solid boundaries, and geomaterial-multibody system interactions. GPU profiling of the newly implemented CUDA kernels demonstrates their performance metrics are similar to those of the original DualSPHysics solver. Performance evaluations demonstrate its saving in memory usage of 30-50% and improvements in computational efficiency over existing SPH geomechanics solvers, achieving practical simulation speeds for systems with tens of millions of particles and showing a speedup of up to 180x compared to the optimised multi-core CPU implementation. These advances position GeoDualSPHysics as a versatile, efficient tool for high-fidelity simulations of complex geotechnical systems.</div></div><div><h3>Program summary</h3><div>Program title: GeoDualSPHysics</div><div>CPC Library link to program files: <span><span>https://doi.org/10.17632/z4sh62y97g.1</span><svg><path></path></svg></span></div><div>Licensing provisions: GNU Lesser General Public License</div><div>Programming language: C++ and CUDA</div><div>Nature of problem: Simulating large deformations in geomaterials and their interactions with movable or fixed solid bodies is critical for addressing engineering challenges such as landslides, soil-machine interactions, and off-road vehicle mobility. While the Smoothed Particle Hydrodynamics (SPH) method is well-suited for modelling continuum-based geomaterial behaviour in these scenarios, critical computational barriers persist, including: (1) numerical instabilities and unphysical noise in large-deformation regimes, (2) inefficiency in scaling simulations to millions of particles for real-world systems, and (3) inadequate frameworks for robust, two-way coupling between deformable geomaterials and multi-body systems. Overcoming these limitations demands stabilized SPH formulations, high-performance computing architectures, and two-way coupling with multibody
{"title":"GeoDualSPHysics: a high-performance SPH solver for large deformation modelling of geomaterials with two-way coupling to multi-body systems","authors":"Ruofeng Feng , Jidong Zhao , Georgios Fourtakas , Benedict D Rogers","doi":"10.1016/j.cpc.2025.109965","DOIUrl":"10.1016/j.cpc.2025.109965","url":null,"abstract":"<div><div>This paper presents GeoDualSPHysics, an open-source, graphics processing unit (GPU)-accelerated smoothed particle hydrodynamics (SPH) solver designed for simulating large-deformation geomaterial and their interactions with multi-body systems. Built upon the popular open-source SPH solver DualSPHysics, the solver leverages its highly parallelised SPH scheme empowered by the CUDA parallelisation while extending its capabilities to large-deformation geomechanics problems with particles up to the order of 10⁸ on a single GPU. The SPH geomechanics model is enhanced by a noise-free stress treatment technique that stabilizes and accurately resolves stress fields, as well as an extended modified Dynamic Boundary Condition (mDBC) ensuring first-order consistency in solid boundary modelling. Additionally, the coupling interface between DualSPHysics and the multi-body dynamics solver Project Chrono is adapted for simulating interactions between geomaterials and multiple interacting rigid bodies. Benchmark validations confirm the solver’s accuracy in resolving geotechnical failures, impact forces on solid boundaries, and geomaterial-multibody system interactions. GPU profiling of the newly implemented CUDA kernels demonstrates their performance metrics are similar to those of the original DualSPHysics solver. Performance evaluations demonstrate its saving in memory usage of 30-50% and improvements in computational efficiency over existing SPH geomechanics solvers, achieving practical simulation speeds for systems with tens of millions of particles and showing a speedup of up to 180x compared to the optimised multi-core CPU implementation. These advances position GeoDualSPHysics as a versatile, efficient tool for high-fidelity simulations of complex geotechnical systems.</div></div><div><h3>Program summary</h3><div>Program title: GeoDualSPHysics</div><div>CPC Library link to program files: <span><span>https://doi.org/10.17632/z4sh62y97g.1</span><svg><path></path></svg></span></div><div>Licensing provisions: GNU Lesser General Public License</div><div>Programming language: C++ and CUDA</div><div>Nature of problem: Simulating large deformations in geomaterials and their interactions with movable or fixed solid bodies is critical for addressing engineering challenges such as landslides, soil-machine interactions, and off-road vehicle mobility. While the Smoothed Particle Hydrodynamics (SPH) method is well-suited for modelling continuum-based geomaterial behaviour in these scenarios, critical computational barriers persist, including: (1) numerical instabilities and unphysical noise in large-deformation regimes, (2) inefficiency in scaling simulations to millions of particles for real-world systems, and (3) inadequate frameworks for robust, two-way coupling between deformable geomaterials and multi-body systems. Overcoming these limitations demands stabilized SPH formulations, high-performance computing architectures, and two-way coupling with multibody","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109965"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733045","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}
Pub Date : 2026-03-01Epub Date: 2025-11-17DOI: 10.1016/j.cpc.2025.109949
Christoph Gorgulla , Alejandro J. Garza , Venkat Kapil , Konstantin Fackeldey
Quantum mechanical models of molecules theoretically offer unprecedented accuracy in predicting values associated with these systems, including the free energy of interaction between two molecules. However, high-accuracy quantum mechanical methods are computationally too expensive to be applied to larger systems, including most biomolecular systems such as proteins. To circumvent this challenge, the hybrid quantum mechanics/molecular mechanics (QM/MM) method was developed, allowing one to treat only the most important part of the system on the quantum mechanical level and the remaining part on the classical level. To date, QM/MM simulations for biomolecular systems have been carried out almost exclusively on the electronic structure level, neglecting nuclear quantum effects (NQEs). Yet NQEs can play a major role in biomolecular systems [1]. Here, we present i-QI, a QM/MM client for the path integral molecular dynamics (PIMD) software i-PI [2, 3, 4]. i-QI allows for carrying out QM/MM simulations simultaneously, allowing for the inclusion of electronic as well as NQEs. i-QI implements a new QM/MM scheme based on constraining potentials called QUASAR, which allows handling diffusive systems, such as biomolecules solvated in water solvent. The QUASAR method is suitable in particular when the properties of interest are equilibrium properties, such as the free energy of binding. i-QI is freely available and open source, and we demonstrate it on a test system.
{"title":"QUASAR: A flexible QM-MM method for biomolecular systems based on restraining spheres","authors":"Christoph Gorgulla , Alejandro J. Garza , Venkat Kapil , Konstantin Fackeldey","doi":"10.1016/j.cpc.2025.109949","DOIUrl":"10.1016/j.cpc.2025.109949","url":null,"abstract":"<div><div>Quantum mechanical models of molecules theoretically offer unprecedented accuracy in predicting values associated with these systems, including the free energy of interaction between two molecules. However, high-accuracy quantum mechanical methods are computationally too expensive to be applied to larger systems, including most biomolecular systems such as proteins. To circumvent this challenge, the hybrid quantum mechanics/molecular mechanics (QM/MM) method was developed, allowing one to treat only the most important part of the system on the quantum mechanical level and the remaining part on the classical level. To date, QM/MM simulations for biomolecular systems have been carried out almost exclusively on the electronic structure level, neglecting nuclear quantum effects (NQEs). Yet NQEs can play a major role in biomolecular systems [1]. Here, we present i-QI, a QM/MM client for the path integral molecular dynamics (PIMD) software i-PI [2, 3, 4]. i-QI allows for carrying out QM/MM simulations simultaneously, allowing for the inclusion of electronic as well as NQEs. i-QI implements a new QM/MM scheme based on constraining potentials called QUASAR, which allows handling diffusive systems, such as biomolecules solvated in water solvent. The QUASAR method is suitable in particular when the properties of interest are equilibrium properties, such as the free energy of binding. i-QI is freely available and open source, and we demonstrate it on a test system.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109949"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733046","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}
Pub Date : 2026-03-01Epub Date: 2025-12-21DOI: 10.1016/j.cpc.2025.110001
David Andrs , Zachary Hardy , Daryl Hawkins , Jim Morel , Dinh Quoc Dang Nguyen , Jean C. Ragusa
<div><div>OpenSn is an open-source, massively parallel deterministic radiation transport code for solving the discrete-ordinates (S<sub><em>N</em></sub>) 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.</div><div>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.</div><div>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.</div><div>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.</div><div><strong>PROGRAM SUMMARY</strong></div><div><strong>Program Title:</strong> OpenSn</div><div><strong>CPC Library link to program files:</strong> <span><span>https://doi.org/10.17632/gvrs69dzcv.1</span><svg><path></path></svg></span></div><div><strong>Developer’s repository link:</strong> <span><span>https://github.com/Open-Sn/OpenSn</span><svg><path></path></svg></span></div><div><strong>Licensing provisions:</strong> MIT license</div><div><strong>Programming language:</strong> C++ (core), Python (API)</div><div><strong>Supplementary material:</strong> User manual, theory documentation, and tutorial notebooks available at <span><span>https://open-sn.github.io/opensn/</span><svg><path></path></svg></span></div><div><strong>Nature of problem:</strong>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<sub><em>N</em></sub>) 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.</div><div><strong>Solution method:</strong>
OpenSn是一个开源的、大规模并行的确定性辐射输运代码，用于求解非结构化、任意多面体网格上玻尔兹曼输运方程的离散坐标（SN）形式。它支持高保真模拟涉及稳态，特征值，和伴随问题的中性粒子（例如，中子，光子，多粒子），使用多群近似的能量。OpenSn结合了离散坐标的角度离散化和空间中的不连续Galerkin有限元法（DGFEM），可以在任意多面体单元（包括局部细化的空间网格）上实现精确的传输物理分辨率。它包括多种角正交类型，包括局部精细角正交。OpenSn使用现代c++和Python API编写，可以在从笔记本电脑到超级计算机的各种平台上高效运行。传输扫描算法对每个角度使用基于任务的定向无循环图（DAG）方法实现，并支持跨数千个MPI等级的异步并行性。群集聚集提高了计算强度，合成加速技术（如扩散合成加速、二阶矩法）增强了求解器的收敛性。OpenSn已经在反应堆物理问题上进行了验证，并在超过32,768个过程中展示了出色的弱和强缩放性能，使其成为复杂几何结构中大规模传输模拟的通用和健壮的平台。项目简介项目名称：OpenSnCPC库链接到程序文件：https://doi.org/10.17632/gvrs69dzcv.1Developer的存储库链接：https://github.com/Open-Sn/OpenSnLicensing条款：MIT许可编程语言：c++（核心），Python （API）补充材料：用户手册，理论文档和教程笔记本可在https://open-sn.github.io/opensn/Nature的问题：辐射输运模拟是核心的许多应用在物理和工程，包括反应堆分析，屏蔽，射线照相，和探测器建模。求解复杂几何上离散坐标形式的线性玻尔兹曼输运方程需要鲁棒的数值方法和可扩展的并行算法。许多现有的代码是闭源的，缺乏对多面体网格的支持，或者不能有效地利用现代高性能计算系统。在支持方法创新和大规模计算的同时，需要一个灵活的开源工具来解决这些挑战。求解方法：OpenSn利用能量上的多群近似、空间上的不连续伽辽金有限元法（DGFEM）和角度上的配点法求解离散坐标玻尔兹曼输运方程[1]的稳态、特征值和伴随形式。它支持任意的非结构化多边形和多面体网格，以及角正交集。传输扫描使用基于有向无循环图（DAG）的任务执行模型实现，支持高度可扩展的基于mpi的并行性[2]。代码是用c++编写的，并提供了一个Python接口用于预处理和后处理。采用加速技术[3,4]，包括扩散合成加速（DSA）和基于第二矩的方法，以提高收敛性。OpenSn已经在数千个核心上进行了测试，并根据已知的基准进行了验证。其他评论包括限制和不寻常的功能：OpenSn被设计为一个研究级的，可扩展的高保真辐射传输模拟平台。它特别适合于对实验新的数值方法、网格类型和求解器加速策略感兴趣的用户。代码具有最小的外部依赖，使用CMake进行构建，并包含示例问题和教程。GPU加速正在开发中。对问题的大小没有特别的限制，但是大规模的模拟需要访问并行计算资源。李建军，李建军，李建军，中子输运的计算方法，原子物理学报，1993.2.J。I. C. Vermaak， J. C. Ragusa， M. L. Adams和J. E. Morel。，“基于循环依赖的网格的大规模并行传输扫描”，计算物理学报，42 (10):1098 - 992,2021.1 . m。L. Adams和E. W. Larsen，“离散坐标粒子输运计算的快速迭代方法”，硕士论文。诊断。能源学报，40(1):3-159,2002.4.B。李志刚，“二维任意多边形网格中SN输运的非连续扩散合成加速度，”计算物理学报，34(4):356-369,2014。
{"title":"OpenSn: A massively parallel, open-source simulation environment for discrete ordinates radiation transport","authors":"David Andrs , Zachary Hardy , Daryl Hawkins , Jim Morel , Dinh Quoc Dang Nguyen , Jean C. Ragusa","doi":"10.1016/j.cpc.2025.110001","DOIUrl":"10.1016/j.cpc.2025.110001","url":null,"abstract":"<div><div>OpenSn is an open-source, massively parallel deterministic radiation transport code for solving the discrete-ordinates (S<sub><em>N</em></sub>) 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.</div><div>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.</div><div>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.</div><div>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.</div><div><strong>PROGRAM SUMMARY</strong></div><div><strong>Program Title:</strong> OpenSn</div><div><strong>CPC Library link to program files:</strong> <span><span>https://doi.org/10.17632/gvrs69dzcv.1</span><svg><path></path></svg></span></div><div><strong>Developer’s repository link:</strong> <span><span>https://github.com/Open-Sn/OpenSn</span><svg><path></path></svg></span></div><div><strong>Licensing provisions:</strong> MIT license</div><div><strong>Programming language:</strong> C++ (core), Python (API)</div><div><strong>Supplementary material:</strong> User manual, theory documentation, and tutorial notebooks available at <span><span>https://open-sn.github.io/opensn/</span><svg><path></path></svg></span></div><div><strong>Nature of problem:</strong>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<sub><em>N</em></sub>) 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.</div><div><strong>Solution method:</strong>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110001"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","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}
Pub Date : 2026-03-01Epub Date: 2025-12-11DOI: 10.1016/j.cpc.2025.109987
Esteban Cisneros–Garibay , Henry Le Berre , Dimitrios Adam , Spencer H. Bryngelson , Jonathan B. Freund
The cost of combustion simulations is often dominated by the evaluation of net production rates of chemical species and mixture thermodynamics (thermochemistry). Execution on computing accelerators (XPUs) such as graphics processing units (GPUs) can greatly reduce this cost. Established thermochemistry software is not readily portable to such devices, as it sacrifices valuable analytical forms that enable differentiation, sensitivity analysis, and implicit time integration. Symbolic abstractions are developed with corresponding transformations that enable computation on accelerators and automatic differentiation by avoiding premature specification of detail. The software package Pyrometheus is introduced as an implementation of these abstractions and their transformations for combustion thermochemistry. The formulation facilitates code generation from the symbolic representation of a specific thermochemical mechanism in multiple target languages, including Python, C++, and Fortran. The generated code processes array-valued expressions, but does not specify their semantics. The semantics are provided by compatible array libraries, including NumPy, Pytato, and Google JAX. Thus, the generated code retains a symbolic representation of the thermochemistry, which enables computation on accelerators and CPUs and facilitates automatic differentiation. The design and operation of the symbolic abstractions and their companion tool, Pyrometheus, are discussed throughout. Roofline demonstrations show that the computation of chemical source terms within MFC, a Fortran-based flow solver we link to Pyrometheus, is performant.
{"title":"Pyrometheus: Symbolic abstractions for XPU and automatically differentiated computation of combustion kinetics and thermodynamics","authors":"Esteban Cisneros–Garibay , Henry Le Berre , Dimitrios Adam , Spencer H. Bryngelson , Jonathan B. Freund","doi":"10.1016/j.cpc.2025.109987","DOIUrl":"10.1016/j.cpc.2025.109987","url":null,"abstract":"<div><div>The cost of combustion simulations is often dominated by the evaluation of net production rates of chemical species and mixture thermodynamics (thermochemistry). Execution on computing accelerators (XPUs) such as graphics processing units (GPUs) can greatly reduce this cost. Established thermochemistry software is not readily portable to such devices, as it sacrifices valuable analytical forms that enable differentiation, sensitivity analysis, and implicit time integration. Symbolic abstractions are developed with corresponding transformations that enable computation on accelerators and automatic differentiation by avoiding premature specification of detail. The software package Pyrometheus is introduced as an implementation of these abstractions and their transformations for combustion thermochemistry. The formulation facilitates code generation from the symbolic representation of a specific thermochemical mechanism in multiple target languages, including Python, C<strong>++</strong>, and Fortran. The generated code processes array-valued expressions, but does not specify their semantics. The semantics are provided by compatible array libraries, including NumPy, Pytato, and Google JAX. Thus, the generated code retains a symbolic representation of the thermochemistry, which enables computation on accelerators and CPUs and facilitates automatic differentiation. The design and operation of the symbolic abstractions and their companion tool, Pyrometheus, are discussed throughout. Roofline demonstrations show that the computation of chemical source terms within MFC, a Fortran-based flow solver we link to Pyrometheus, is performant.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109987"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836438","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}
Pub Date : 2026-03-01Epub Date: 2025-12-19DOI: 10.1016/j.cpc.2025.110003
Stephen Sanderson , Sobin Alosious , Debra J. Searles
<div><div>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, <span>dofulator</span>, which can be used on its own or through a Python interface that includes compatibility with the popular MDAnalysis package.</div><div><strong>Program summary</strong> <em>Program Title:</em> <span>dofulator</span> <em>CPC Library link to program files:</em> (to be added by Technical Editor) <em>Developer’s repository link:</em> <span><span>https://github.com/CTCMS-UQ/dofulator</span><svg><path></path></svg></span> <em>Licensing provisions:</em> MPL-2.0 <em>Programming language:</em> C, Python</div><div><em>Nature of problem:</em> 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.</div><div><em>Solution method:</em> 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.</div><div><em>Additional comments including restrictions and unusual features:</em> The core <span>dofulator</span> 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
最近，我们提出了一种在几何约束下计算单原子和单方向自由度（DoF）的方法，从而实现了细粒度的局部动力学温度计算。在这里，我们讨论了各种约束几何的相关实现细节，包括那些具有运动环的几何（例如具有刚性键长的苯）。此外，通过分析半刚性分子的变形对各组成原子的自由度的影响，我们深入了解了在模拟过程中原子自由度可能发生显著变化的条件。这为局部DoF应该动态计算以获得可靠的局部温度测量以及在整个模拟过程中使用平衡几何的原子DoF作为常数就足够的情况下提供了一些指导。我们已经在一个开源的C库dofulator中实现了所介绍的算法，dofulator可以单独使用，也可以通过Python接口使用，该接口包括与流行的MDAnalysis包的兼容性。程序摘要程序名称：dofulator CPC库链接到程序文件：（由技术编辑添加）开发人员存储库链接：https://github.com/CTCMS-UQ/dofulator许可条款：mpls -2.0编程语言：C， python问题性质：在具有几何约束的分子模拟中，当约束包括感兴趣的局部子集[1]内外的原子时，确定与局部动力学温度测量相关的自由度（DoF）可能变得非常重要。刚体中原子的（分数）自由度取决于它们的质量和分子几何形状。如果约束不形成刚体，而是半刚性碎片，那么原子自由度的划分可能随着碎片的变形而变化。此外，如果需要定向动力学温度，则必须确定沿每个方向的自由度，这还取决于刚体或半刚性碎片的方向。求解方法：原子自由度可以通过每个原子对每种运动模式惯性的相对贡献[1]来计算。该软件允许定义刚体和半刚体碎片，从中构建用于确定所述模式和贡献的计划。一旦建立，一个计划可以重复应用，以计算所需的框架的分子动力学轨迹的原子自由度。附加注释，包括限制和不寻常的功能：核心dofulator库作为C API提供，仅依赖于BLAS和LAPACK实现，适合与分子动力学引擎直接集成（可能需要进行一些修改）。为了方便起见，还提供了一个薄薄的Python包装器，它用于提供MDAnalysis的插件[2,3]，它提供了一种简单的方法来读取分子动力学轨迹并定义局部原子选择以进行局部DoF和温度的后处理。利益声明作者声明，他们没有已知的竞争经济利益或个人关系，可能会影响本文所报道的工作。引用文献[10]孙建军，李建军，李建军，基于分子动力学的局部温度测量方法，化学学报，20(23)(2024):1015 - 1024。doi: 10.1021 / acs.jctc。[c00957] m . michaod - agrawal， E. J. Denning， T. B. Woolf， O. Beckstein, m . analysis：一个分析分子动力学模拟的工具箱，计算化学32(10)(2011)2319-2327。doi: 10.1002 / jcc。[1787] R. Gowers， M. Linke， J. Barnoud， T. Reddy， M. Melo， S. Seyler， J. Domański， D. Dotson， S. Buchoux， I. Kenney， O. Beckstein， MDAnalysis：一个快速分析分子动力学模拟的Python包，第15届Python科学会议论文集，SciPy, 2016。doi: 10.25080 /改称- 629 - e541a - 00 - e。
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Pub Date : 2026-03-01Epub Date: 2025-11-02DOI: 10.1016/j.cpc.2025.109919
Laura A. Völker , John M. Abendroth , Christian L. Degen , Konstantin Herb
We present an open-source simulation framework for optically detected magnetic resonance, developed in Python. The framework is designed to simulate multipartite quantum systems composed of spins and electronic levels, enabling the study of systems such as nitrogen-vacancy centers in diamond and photo-generated spin-correlated radical pairs. Our library provides system-specific sub-modules for these and related problems. It supports efficient time-evolution in Lindblad form, along with tools for simulating spatial and generalized stochastic dynamics. Symbolic operator construction and propagation are also supported for simple model systems, making the framework well-suited for classroom instruction in magnetic resonance. Designed to be backend-agnostic, the library interfaces with existing Python packages as computational backends. We introduce the core functionality and illustrate the syntax through a series of representative examples.
{"title":"SimOS: A Python framework for simulations of optically addressable spins","authors":"Laura A. Völker , John M. Abendroth , Christian L. Degen , Konstantin Herb","doi":"10.1016/j.cpc.2025.109919","DOIUrl":"10.1016/j.cpc.2025.109919","url":null,"abstract":"<div><div>We present an open-source simulation framework for optically detected magnetic resonance, developed in Python. The framework is designed to simulate multipartite quantum systems composed of spins and electronic levels, enabling the study of systems such as nitrogen-vacancy centers in diamond and photo-generated spin-correlated radical pairs. Our library provides system-specific sub-modules for these and related problems. It supports efficient time-evolution in Lindblad form, along with tools for simulating spatial and generalized stochastic dynamics. Symbolic operator construction and propagation are also supported for simple model systems, making the framework well-suited for classroom instruction in magnetic resonance. Designed to be backend-agnostic, the library interfaces with existing Python packages as computational backends. We introduce the core functionality and illustrate the syntax through a series of representative examples.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109919"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681669","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}
Pub Date : 2026-03-01Epub Date: 2025-12-16DOI: 10.1016/j.cpc.2025.109991
Haritz Garai-Marin , María Blanco-Rey , Idoia G. Gurtubay , Jon Lafuente-Bartolome , Asier Eiguren
<div><div>We present <span>INTW</span>, a modular software environment designed for advanced electronic structure calculations. Developed in Fortran95, <span>INTW</span> is capable of reading self-consistent field (SCF) results, such as electron energies, wave functions, and potentials, generated by the <span>Quantum ESPRESSO</span> and <span>SIESTA</span> codes. Using these SCF results as input, <span>INTW</span> provides a suite of specialized subroutines and functions for the computation of various electron- and phonon-related physical properties, facilitating detailed analysis of material properties at the quantum level. <span>INTW</span> particularly stands out in its treatment of symmetry, fully exploiting it even when dealing with electron spinor wave functions. Furthermore, it can efficiently work with both localized basis set codes, such as <span>SIESTA</span>, and plane-wave codes like <span>Quantum ESPRESSO</span>. These capabilities make <span>INTW</span> unique, offering a versatile approach that effectively combines the use of symmetry with both localized basis sets and plane-wave methods.</div><div><strong>Program summary</strong></div><div><em>Program Title:</em> <span>INTW</span></div><div><em>CPC Library link to program files:</em> (to be added by Technical Editor)</div><div><em>Developer’s repository link:</em> <span><span>https://github.com/eiguren/intw</span><svg><path></path></svg></span></div><div><em>Code Ocean capsule:</em> (to be added by Technical Editor)</div><div><em>Licensing provisions:</em> GPL-3.0-or-later</div><div><em>Programming language:</em> Fortran95</div><div><em>Nature of problem:</em></div><div>Accessing advanced electronic structure problems, such as the anisotropic electron-phonon interaction on the Fermi surface, requires efficient treatment of the data generated by general-purpose codes such as <span>Quantum ESPRESSO</span> and <span>SIESTA</span>. Moreover, fully exploiting symmetry operations is challenging but offers significant efficiency gains and qualitative benefits. The problem is to provide a modular framework that enables such calculations in a flexible, symmetry-aware, and computationally efficient environment set of tools.</div><div><em>Solution method:</em></div><div>Electron and phonon states are calculated only in the irreducible Brillouin zone provided by <span>Quantum ESPRESSO</span> and <span>SIESTA</span>. <span>INTW</span> interfaces with these codes to generate electron (spinor) states and phonon induced (spinor) potentials at arbitrary momenta using symmetry operations. <span>INTW</span> efficiently calculates the nearest-neighbor overlap matrices for Wannier functions by exploiting symmetry. In <span>SIESTA</span>, phonons are calculated using the supercell method, although <span>INTW</span> computes only the irreducible atomic displacements needed to construct the force-constant matrix. The electron-phonon matrix elements are computed either (1) by Fourier interpolation of the
{"title":"INTW: A versatile modular environment for advanced treatment of electronic structure and electron-phonon related properties","authors":"Haritz Garai-Marin , María Blanco-Rey , Idoia G. Gurtubay , Jon Lafuente-Bartolome , Asier Eiguren","doi":"10.1016/j.cpc.2025.109991","DOIUrl":"10.1016/j.cpc.2025.109991","url":null,"abstract":"<div><div>We present <span>INTW</span>, a modular software environment designed for advanced electronic structure calculations. Developed in Fortran95, <span>INTW</span> is capable of reading self-consistent field (SCF) results, such as electron energies, wave functions, and potentials, generated by the <span>Quantum ESPRESSO</span> and <span>SIESTA</span> codes. Using these SCF results as input, <span>INTW</span> provides a suite of specialized subroutines and functions for the computation of various electron- and phonon-related physical properties, facilitating detailed analysis of material properties at the quantum level. <span>INTW</span> particularly stands out in its treatment of symmetry, fully exploiting it even when dealing with electron spinor wave functions. Furthermore, it can efficiently work with both localized basis set codes, such as <span>SIESTA</span>, and plane-wave codes like <span>Quantum ESPRESSO</span>. These capabilities make <span>INTW</span> unique, offering a versatile approach that effectively combines the use of symmetry with both localized basis sets and plane-wave methods.</div><div><strong>Program summary</strong></div><div><em>Program Title:</em> <span>INTW</span></div><div><em>CPC Library link to program files:</em> (to be added by Technical Editor)</div><div><em>Developer’s repository link:</em> <span><span>https://github.com/eiguren/intw</span><svg><path></path></svg></span></div><div><em>Code Ocean capsule:</em> (to be added by Technical Editor)</div><div><em>Licensing provisions:</em> GPL-3.0-or-later</div><div><em>Programming language:</em> Fortran95</div><div><em>Nature of problem:</em></div><div>Accessing advanced electronic structure problems, such as the anisotropic electron-phonon interaction on the Fermi surface, requires efficient treatment of the data generated by general-purpose codes such as <span>Quantum ESPRESSO</span> and <span>SIESTA</span>. Moreover, fully exploiting symmetry operations is challenging but offers significant efficiency gains and qualitative benefits. The problem is to provide a modular framework that enables such calculations in a flexible, symmetry-aware, and computationally efficient environment set of tools.</div><div><em>Solution method:</em></div><div>Electron and phonon states are calculated only in the irreducible Brillouin zone provided by <span>Quantum ESPRESSO</span> and <span>SIESTA</span>. <span>INTW</span> interfaces with these codes to generate electron (spinor) states and phonon induced (spinor) potentials at arbitrary momenta using symmetry operations. <span>INTW</span> efficiently calculates the nearest-neighbor overlap matrices for Wannier functions by exploiting symmetry. In <span>SIESTA</span>, phonons are calculated using the supercell method, although <span>INTW</span> computes only the irreducible atomic displacements needed to construct the force-constant matrix. The electron-phonon matrix elements are computed either (1) by Fourier interpolation of the ","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109991"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880066","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}
Pub Date : 2026-03-01Epub Date: 2025-12-06DOI: 10.1016/j.cpc.2025.109983
Janghoon Seo , Gahyung Jo , Jae-Min Kwon , Eisung Yoon
We present a computationally efficient implementation of the nonlinear Rosenbluth-Fokker-Planck (RFP) collision operator for multi-species kinetic simulations within the discontinuous Galerkin (DG) framework. Inter-species collisions with significant mass disparities require high-order Gaussian quadrature integration to accurately resolve the steep gradients in the Rosenbluth potentials of slower species. To mitigate the computational overhead associated with numerous quadrature points, we employ precomputed integration matrices. Since the conventional upwind scheme for the DG method is not compatible with precomputed matrices, we implement the Harten, Lax and van Leer (HLL) flux formulation for advective flow calculations at cell boundaries. Conservation of momentum and energy is ensured through an additional advective-diffusive operator, utilizing the slow-to-fast species collision as a reference state. We address the numerical challenge of artificial non-vanishing collisional effects at equilibrium through compensatory terms, thereby achieving stable collisional equilibrium states. Comprehensive numerical benchmarks validate both the efficiency and accuracy of our proposed scheme. In particular, our model achieves robust interspecies collisional equilibrium even under conditions of extreme mass disparity and relatively low velocity resolution.
{"title":"Multi-species Rosenbluth Fokker-Planck collision operator for discontinuous Galerkin method","authors":"Janghoon Seo , Gahyung Jo , Jae-Min Kwon , Eisung Yoon","doi":"10.1016/j.cpc.2025.109983","DOIUrl":"10.1016/j.cpc.2025.109983","url":null,"abstract":"<div><div>We present a computationally efficient implementation of the nonlinear Rosenbluth-Fokker-Planck (RFP) collision operator for multi-species kinetic simulations within the discontinuous Galerkin (DG) framework. Inter-species collisions with significant mass disparities require high-order Gaussian quadrature integration to accurately resolve the steep gradients in the Rosenbluth potentials of slower species. To mitigate the computational overhead associated with numerous quadrature points, we employ precomputed integration matrices. Since the conventional upwind scheme for the DG method is not compatible with precomputed matrices, we implement the Harten, Lax and van Leer (HLL) flux formulation for advective flow calculations at cell boundaries. Conservation of momentum and energy is ensured through an additional advective-diffusive operator, utilizing the slow-to-fast species collision as a reference state. We address the numerical challenge of artificial non-vanishing collisional effects at equilibrium through compensatory terms, thereby achieving stable collisional equilibrium states. Comprehensive numerical benchmarks validate both the efficiency and accuracy of our proposed scheme. In particular, our model achieves robust interspecies collisional equilibrium even under conditions of extreme mass disparity and relatively low velocity resolution.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109983"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733049","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}
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