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A Memory Reduction Compact Gas Kinetic Scheme on 3D Unstructured Meshes 三维非结构化网格上的内存缩减紧凑气体动力学方案
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-09 DOI: 10.1016/j.cpc.2025.109981
Hongyu Liu , Xing Ji , Yunpeng Mao , Zhe Qian , Kun Xu
This paper presents a memory-reduction third-order compact gas-kinetic scheme (CGKS) designed to solve compressible Euler and Navier-Stokes equations on 3D unstructured meshes. Utilizing the time-accurate gas distribution function, the gas kinetic solver provides a time-evolution solution at the cell interface, distinguishable from the Riemann solver with a constant solution. With the time evolution solution at the cell interface, evolving both the cell-averaged flow variables and the cell-averaged slopes of flow variables becomes feasible. Therefore, with the cell-averaged flow variables and their slopes inside each cell, the Hermite WENO (HWENO) techniques can be naturally implemented for the compact high-order reconstruction at the beginning of the next time step. However, the HWENO reconstruction method requires the storage of a reconstruction-coefficients matrix for the quadratic polynomial to achieve third-order accuracy, leading to substantial memory consumption. This memory overhead limits both computational efficiency and the scale of simulations.
A novel reconstruction method, built upon HWENO reconstruction, has been designed to enhance computational efficiency and reduce memory usage compared to the original CGKS. The simple idea is that the first-order and second-order terms of the quadratic polynomials are determined in a two-step way. In the first step, the second-order terms are obtained from the reconstruction of a linear polynomial of the first-order derivatives by only using the cell-averaged slopes, since the second-order derivatives are nothing but the ”derivatives of derivatives”. Subsequently, the first-order terms left can be determined by the linear reconstruction only using cell-averaged values. Thus, we successfully split one quadratic least-square regression into several linear least-square regressions, which are commonly used in a second-order finite volume code. Since only a 3 × 3 matrix inversion is needed in a 3-D linear least-square regression, the computational cost for the new reconstruction is dramatically reduced and the storage of the reconstruction-coefficient matrix is no longer necessary. The proposed memory reduction CGKS is tested for both inviscid and viscous flow at low and high speeds on hybrid unstructured meshes. The proposed new reconstruction technique can reduce the overall computational cost by about 20% to 30%. In the meantime, it also simplifies the algorithm. The challenging large-scale unsteady numerical simulation is performed, which demonstrates that the current improvement brings the CGKS to a new level for industrial applications.
针对三维非结构化网格上的可压缩欧拉方程和纳维-斯托克斯方程,提出了一种内存缩减型三阶紧凑气体动力学格式。利用时间精确的气体分布函数,气体动力学求解器提供了细胞界面的时间演化解,区别于具有常数解的黎曼求解器。有了单元界面处的时间演化解,单元平均流动变量和单元平均流动变量斜率的演化都变得可行。因此,有了单元平均流量变量及其在每个单元内的斜率,Hermite WENO (HWENO)技术可以在下一个时间步开始时自然地实现紧凑的高阶重建。然而,HWENO重建方法需要存储二次多项式的重建系数矩阵以达到三阶精度,导致大量内存消耗。这种内存开销限制了计算效率和模拟的规模。在HWENO重建的基础上,设计了一种新的重建方法,与原始CGKS相比,提高了计算效率并减少了内存使用。简单的想法是,二次多项式的一阶和二阶项是用两步的方式确定的。在第一步中,二阶项是通过仅使用单元平均斜率从一阶导数的线性多项式的重建中获得的,因为二阶导数只不过是“导数的导数”。随后,仅使用单元平均值进行线性重建即可确定剩余的一阶项。因此,我们成功地将一个二次最小二乘回归分解为几个线性最小二乘回归,这些回归通常用于二阶有限体积代码。由于在三维线性最小二乘回归中只需要3 × 3矩阵的反演,因此大大减少了新重构的计算成本,并且不再需要存储重构系数矩阵。在混合非结构化网格上,对所提出的内存减少CGKS进行了低速和高速无粘流和粘性流的测试。所提出的新重建技术可将总体计算成本降低约20% ~ 30%。同时,也简化了算法。进行了具有挑战性的大尺度非定常数值模拟,结果表明,目前的改进使CGKS达到了工业应用的新水平。
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引用次数: 0
Tessellation-based grain boundary determination for X-ray orientation microscopies 基于镶嵌的x射线取向显微镜晶界测定
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-07 DOI: 10.1016/j.cpc.2025.109988
Jaemyung Kim , Yujiro Hayashi , Sung Soo Ha , Makina Yabashi
In X-ray diffraction-based orientation microscopy, reconstructed grain structures can exhibit unrealistic or erroneous features due to the broadening and overlapping of diffraction peaks. Accurate grain boundary determination based on physical models remains a critical challenge for reliable microstructural characterization. While Voronoi tessellation is widely used to represent microstructures, its accuracy is often limited by the lack of weighting factors, leading to biased results. To address this, we developed a grain extraction algorithm combining a variation of the label-equivalent connected components labeling method with the marching squares algorithm for precise grain boundary detection. Using the extracted grain shapes, additively weighted Voronoi tessellation (AWVT) was applied, with each grain’s center of mass (COM) and equivalent radius serving as weighting factors. The AWVT boundaries showed strong agreement with experimental data, outperforming conventional Voronoi and Laguerre tessellations. Furthermore, the relationship between AWVT and curvature-driven grain growth models is discussed, demonstrating the method’s potential for improved microstructure characterization and grain growth analysis.
在基于x射线衍射的取向显微镜中,由于衍射峰的展宽和重叠,重建的晶粒结构可能表现出不真实或错误的特征。基于物理模型的精确晶界确定仍然是可靠的微观结构表征的关键挑战。虽然Voronoi镶嵌被广泛用于表示微观结构,但其准确性往往受到缺乏加权因子的限制,导致结果有偏差。为了解决这个问题,我们开发了一种谷物提取算法,该算法将标签等效连接分量标记方法的变体与行进平方算法相结合,用于精确的晶界检测。利用提取的颗粒形状,以每个颗粒的质心和等效半径作为加权因子,进行加性加权Voronoi镶嵌(AWVT)。AWVT边界与实验数据非常吻合,优于传统的Voronoi和Laguerre镶嵌。此外,还讨论了AWVT与曲率驱动晶粒生长模型之间的关系,证明了该方法在改进微观结构表征和晶粒生长分析方面的潜力。
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引用次数: 0
Mixed Cayley and Cartesian sampling for fast and accurate coverage and configurational entropy computation 混合凯利和笛卡尔采样快速和准确的覆盖和配置熵计算
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-07 DOI: 10.1016/j.cpc.2025.109979
Yichi Zhang , Meera Sitharam
This article describes Uniform Cartesian (UC), an efficient deterministic methodology for computing configurational entropy, via relative volume of energy basins. The methodology is specifically tailored for short-ranged and hard-sphere pair-potential assembly systems, but adapts to longer ranged pair potentials. UC both leverages and significantly extends EASAL (Efficient Atlasing and Sampling of Assembly Landscapes), a recent methodology based on modern discrete geometry concepts including topological roadmapping and atlasing. Unique distance-based Cayley coordinate parametrization achieves sampling of nonlinear constrained regions of intrinsic dimension much lower than ambient degrees of freedom, while avoiding gradient descent and retraction maps. Thereby, EASAL navigates the interacting twin curses of dimensionality and topological complexity of nearly disconnected and highly separated configurational regions. Additionally, UC iteratively maps between Cayley and Cartesian coordinates, avoiding illconditioning from Jacobian and Hessian computations; and guarantees correctness, optimal time and space complexity, and efficiency-accuracy tradeoffs using rigorous algorithmic analysis. Variants of UC accurately compute the relative volume of an energy basin for transmembrane protein assembly within hours, even without parallelization. This article’s emphasis is not extensive benchmark comparisons of large-scale parallel implementations or prevailing methods. Rather, proof-of-concept demonstrations of the unique features of UC are given along with test-case comparisons between the Markov Chain Monte Carlo (MCMC) method, the new UC variants, and the “vanilla” EASAL. A curated opensource software implementation is provided.
本文描述了均匀笛卡尔(UC),一种有效的确定性方法,计算构型熵,通过相对体积的能量盆地。该方法是专门为短程和硬球对电位装配系统量身定制的,但适用于较长距离的对电位。UC利用并显著扩展了EASAL(高效装配景观的地图集和采样),这是一种基于现代离散几何概念的最新方法,包括拓扑道路测绘和地图集。独特的基于距离的Cayley坐标参数化实现了对固有维数远低于环境自由度的非线性约束区域的采样,同时避免了梯度下降和收缩映射。因此,EASAL在几乎不连接和高度分离的构型区域的维数和拓扑复杂性的相互作用的孪生轨迹中导航。此外,UC在Cayley和Cartesian坐标系之间迭代映射,避免了雅可比和Hessian计算的不适;并通过严格的算法分析保证正确性、最佳的时间和空间复杂性以及效率和准确性之间的权衡。UC的变体可以在数小时内精确地计算跨膜蛋白组装的能量盆的相对体积,即使没有并行化。本文的重点不是大规模并行实现或流行方法的广泛基准比较。相反,本文给出了UC独特功能的概念验证演示,以及马尔可夫链蒙特卡罗(MCMC)方法、新的UC变体和“香草”EASAL之间的测试用例比较。提供了一个精心策划的开源软件实现。
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引用次数: 0
A molecular dynamics postprocessing tool for analyzing the structure and dynamics of materials 用于分析材料结构和动力学的分子动力学后处理工具
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-06 DOI: 10.1016/j.cpc.2025.109982
Mayanak K Gupta
Machine learning and computing advancements have made it possible to carry out simulations over longer lengths and timescales. This has opened up new opportunities for understanding materials in different thermodynamic conditions. These large-scale simulations help analyze experimental measurements such as inelastic scattering and study diffusion in solid electrolytes for potential use in future batteries. However, analyzing these large datasets presents challenges in extracting useful thermodynamic and transport properties. To address these challenges, the Fortran-based code MDLAB has been developed. This code processes large-scale molecular dynamics simulation trajectories from various software and computes important quantities like mean squared displacements, phonon spectra, pair-distribution functions, simulated neutron/X-ray spectra and more. This comprehensive approach allows for a deeper understanding of material behavior, ultimately enhancing our overall grasp of condensed matter physics.
机器学习和计算技术的进步使得在更长的时间尺度上进行模拟成为可能。这为理解不同热力学条件下的材料开辟了新的机会。这些大规模的模拟有助于分析实验测量结果,如非弹性散射和研究固体电解质中的扩散,为未来电池的潜在应用提供帮助。然而,分析这些大型数据集在提取有用的热力学和输运性质方面提出了挑战。为了应对这些挑战,开发了基于fortran的代码MDLAB。该代码处理来自各种软件的大规模分子动力学模拟轨迹,并计算重要的量,如均方位移,声子谱,对分布函数,模拟中子/ x射线谱等。这种全面的方法可以更深入地了解材料的行为,最终增强我们对凝聚态物理的全面掌握。
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引用次数: 0
RelExt: A new dark matter tool for the exploration of dark matter models 释放:一个新的暗物质工具,用于探索暗物质模型
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-06 DOI: 10.1016/j.cpc.2025.109968
Rodrigo Capucha , Karim Elyaouti , Margarete Mühlleitner , Johann Plotnikov , Rui Santos
We present the C++ program RelExt for Standard Model (SM) extensions that feature a Dark Matter (DM) candidate. The tool allows to efficiently scan the parameter spaces of these models to find parameter combinations that lead to relic density values which are compatible with the measured value within the uncertainty specified by the user. The code computes the relic density for freeze-out (co-)annihilation processes. The user can choose between several pre-installed models or any arbitrary other model featuring a discrete Z2 symmetry, by solely providing the corresponding FeynRules model files. The code automatically generates the required (co-)annihilation amplitudes and thermally averaged cross sections, including the total widths in the s-channel mediators, and solves the Boltzmann equation to determine the relic density. It can easily be linked to other tools like e.g. ScannerS to check for the relevant theoretical and experimental constraints, or to BSMPT to investigate the phase history of the model and possibly related gravitational waves signals.
我们提出了标准模型(SM)扩展的c++程序RelExt,该扩展具有暗物质(DM)候选。该工具可以有效地扫描这些模型的参数空间,找到在用户指定的不确定度范围内与测量值兼容的遗物密度值的参数组合。该代码计算了冻结(共)湮灭过程的遗迹密度。用户可以通过单独提供相应的FeynRules模型文件,在几个预装模型或具有离散Z2对称性的任意其他模型之间进行选择。该代码自动生成所需(共)湮灭振幅和热平均截面,包括s通道介质的总宽度,并求解玻尔兹曼方程以确定遗迹密度。它可以很容易地连接到其他工具,例如扫描仪,以检查相关的理论和实验约束,或BSMPT,以调查模型的相位历史和可能相关的引力波信号。
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引用次数: 0
Multi-species Rosenbluth Fokker-Planck collision operator for discontinuous Galerkin method 不连续Galerkin方法的多种Rosenbluth - Fokker-Planck碰撞算子
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-06 DOI: 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.
我们提出了一种计算效率高的非线性rosenbluh - fokker - planck (RFP)碰撞算子,用于不连续Galerkin (DG)框架内的多物种动力学模拟。具有显著质量差异的物种间碰撞需要高阶高斯正交积分来精确解决慢速物种的Rosenbluth势的陡峭梯度。为了减少与大量正交点相关的计算开销,我们采用了预先计算的积分矩阵。由于DG方法的传统逆风格式与预先计算的矩阵不兼容,我们实现了Harten, Lax和van Leer (HLL)通量公式,用于单元边界的平流计算。利用从慢到快的物种碰撞作为参考状态,通过一个额外的累加扩散算子确保动量和能量的守恒。我们通过补偿项解决了平衡状态下人为不消失碰撞效应的数值挑战,从而实现了稳定的碰撞平衡状态。综合的数值基准验证了我们提出的方案的效率和准确性。特别是,我们的模型即使在极端质量差异和相对较低速度分辨率的条件下也能实现稳健的种间碰撞平衡。
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引用次数: 0
On the use of autoencoders to study the dynamics and the causality relations of complex systems with applications to nuclear fusion 用自编码器研究复杂系统的动力学和因果关系及其在核聚变中的应用
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-04 DOI: 10.1016/j.cpc.2025.109984
R. Rossi , A. Murari , T. Craciunescu , N. Rutigliano , I. Wyss , J. Vega , P. Gaudio , M. Gelfusa , on behalf of JET Contributors* and EUROfusion Tokamak Exploitation Team
Autoencoders are neural networks capable of learning compact representations of data through unsupervised learning. By encoding input data into a lower-dimensional space and subsequently reconstructing it, they enable efficient feature extraction, denoising, anomaly detection, and other applications. This work develops autoencoder-based methodologies tailored to time-dependent problems, specifically for reconstructing hidden dynamics, modelling governing equations, and detecting causal relationships.
A physics-informed autoencoder (PIC-AE) is introduced to impose physical or mathematical constraints on the latent representation, allowing the discovery of fundamental dynamics and model parameters. The PIC-AE effectively reconstructs equivalent dynamical systems from indirect measurements, as exemplified by numerical tests based on the Lotka-Volterra system of equations. It has been applied to edge-localized modes (ELMs) in nuclear fusion plasmas to assess whether they follow a Lotka-Volterra model and the results indicate the need for alternative sets of equations.
For causality detection, a novel autoencoder-based method has been developed to overcome the limitations of traditional techniques. This new approach accurately identifies causal relationships while providing a probabilistic measure of their strength. Applied to nuclear fusion data, it has confirmed the causal influence of ion cyclotron resonance heating (ICRH) on sawtooth crashes, reproducing previous findings obtained with different methodologies and extending the analysis to the spatio-temporal domain.
Although initially designed for nuclear fusion applications, the proposed methodologies are broadly applicable to any scientific and technological domain, in which time series analysis is crucial. Indeed, the developed tools have the representational capabilities of deep learning networks but are much less prone to overfitting and can be accurate even whit sparse data. Future work will explore alternative representations for ELMs and further validate the causality detection method across different datasets.
自编码器是能够通过无监督学习学习数据的紧凑表示的神经网络。通过将输入数据编码到低维空间并随后重建它,它们可以实现高效的特征提取,去噪,异常检测和其他应用。这项工作开发了基于自编码器的方法,专门针对时间相关问题,特别是用于重建隐藏动力学,建模控制方程和检测因果关系。引入物理信息自动编码器(PIC-AE)对潜在表示施加物理或数学约束,允许发现基本动力学和模型参数。基于Lotka-Volterra方程组的数值试验表明,PIC-AE可以有效地从间接测量中重建等效动力系统。它已被应用于核聚变等离子体中的边缘局域模式(elm),以评估它们是否遵循Lotka-Volterra模型,结果表明需要替代方程组。对于因果关系检测,一种新的基于自编码器的方法已经被开发出来,以克服传统技术的局限性。这种新方法准确地识别了因果关系,同时提供了对其强度的概率度量。应用于核聚变数据,它证实了离子回旋共振加热(ICRH)对锯齿碰撞的因果影响,再现了以前用不同方法获得的发现,并将分析扩展到时空域。虽然最初是为核聚变应用设计的,但所提出的方法广泛适用于任何科学和技术领域,其中时间序列分析是至关重要的。事实上,开发的工具具有深度学习网络的表示能力,但不太容易过度拟合,即使是稀疏数据也可以准确。未来的工作将探索elm的替代表示,并进一步验证跨不同数据集的因果关系检测方法。
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引用次数: 0
GeoDualSPHysics: a high-performance SPH solver for large deformation modelling of geomaterials with two-way coupling to multi-body systems geodualspphysics:一个高性能的SPH求解器,用于双向耦合到多体系统的岩土材料的大变形建模
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-02 DOI: 10.1016/j.cpc.2025.109965
Ruofeng Feng , Jidong Zhao , Georgios Fourtakas , Benedict D Rogers
<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
本文介绍了geodualspphysics,一个开源的图形处理单元(GPU)加速的光滑粒子流体动力学(SPH)求解器,用于模拟大变形地质材料及其与多体系统的相互作用。基于流行的开源SPH求解器dualspphysics,该求解器利用其由CUDA并行化授权的高度并行SPH方案,同时将其能力扩展到单个GPU上的颗粒高达10⁸的大变形地质力学问题。SPH地质力学模型通过一种无噪声应力处理技术得到增强,该技术可以稳定和准确地分解应力场,以及一种扩展的修正动态边界条件(mDBC),确保了固体边界模型的一阶一致性。此外,dualspphysics和多体动力学求解器Project Chrono之间的耦合接口适用于模拟岩土材料和多个相互作用的刚体之间的相互作用。基准验证证实了求解器在解决岩土工程失效、固体边界上的冲击力以及岩土材料-多体系统相互作用方面的准确性。新实现的CUDA内核的GPU分析表明,它们的性能指标与原始的dualspphysics求解器相似。性能评估表明,与现有的SPH地质力学求解器相比,它节省了30-50%的内存使用,提高了计算效率,实现了具有数千万粒子的系统的实际模拟速度,与优化的多核CPU实现相比,速度提高了180倍。这些进步使geodualspphysics成为复杂岩土系统高保真仿真的通用、高效工具。程序摘要程序标题:geodualspphysics scpc库链接到程序文件:https://doi.org/10.17632/z4sh62y97g.1Licensing条款:GNU较弱通用公共许可证编程语言:c++和cuda问题的性质:模拟大变形的地质材料及其与可移动或固定的固体体的相互作用是解决工程挑战,如滑坡,土壤-机器相互作用,和越野车辆的机动性至关重要。虽然光滑粒子流体动力学(SPH)方法非常适合在这些情况下对基于连续体的岩土材料行为进行建模,但关键的计算障碍仍然存在,包括:(1)大变形状态下的数值不稳定性和非物理噪声,(2)在将模拟缩放到真实系统的数百万粒子时效率低下,以及(3)可变形岩土材料和多体系统之间鲁棒的双向耦合框架不足。克服这些限制需要稳定的SPH公式、高性能计算架构以及与多体动力学求解器的双向耦合。解决方法:geodualspphysics求解器解决了上述挑战,它结合了(1)一个稳定的地质材料SPH公式,具有无噪声应力处理,以消除大变形中的伪振荡,以及一个扩展的修改动态边界条件(mDBC),用于一阶一致的固体边界建模;(2)继承了dualphysics的基于cuda的高性能GPU并行化,实现对数千万个粒子的高效模拟;(3)通过DSPHChronoLib库与Project Chrono进行双向耦合,该库集成了碰撞检测、摩擦接触模型和关节约束,以解决可变形岩土材料与多体系统之间的相互作用。
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引用次数: 0
PWACG: Partial wave analysis code generator supporting Newton-conjugate gradient method 部分波分析代码生成器支持牛顿共轭梯度法
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-02 DOI: 10.1016/j.cpc.2025.109963
Xiang Dong , Yu-Chang Sun , Chu-Cheng Pan , Ao-Yan Cheng , Ao-Bo Wang , Hao Cai , Kai Zhu
This paper introduces a novel Partial Wave Analysis Code Generator (PWACG) that automatically generates high-performance partial wave analysis codes. This is achieved by leveraging the JAX automatic differentiation library and the jinja2 template engine. The resulting code is constructed using the high-performance API of JAX, and includes support for the Newton’s Conjugate Gradient optimization method, as well as the full utilization of parallel computing capabilities offered by GPUs. By harnessing these advanced computing techniques, PWACG demonstrates a significant advantage in efficiently identifying global optimal points compared to conventional partial wave analysis software packages.
PROGRAM SUMMARY
Program Title: PWACG: Partial Wave Analysis Code Generator
CPC Library link to program files: https://doi.org/10.17632/47ppcnx77x.1
Licensing provisions: This software is distributed under the MIT License.
Programming language: Python
External routines/libraries: jaxlib, jax, jinja2, matplotlib, numpy, scipy
Nature of problem: The program addresses the need for high-performance computational tools in high-energy physics partial wave analysis (PWA). It introduces the Newton-conjugate gradient method for optimization, enhancing the accuracy and stability of fits.
Solution method: PWACG employs code generation and automatic differentiation techniques to automate the creation of PWA code. It leverages the computational capabilities of JAX for efficient execution and supports advanced features such as multi-GPU computation.
GitHub repository: https://github.com/caihao/PWACG
介绍了一种能自动生成高性能部分波分析代码的部分波分析代码发生器(pacg)。这是通过利用JAX自动区分库和jinja2模板引擎实现的。生成的代码使用JAX的高性能API构建,并包括对牛顿共轭梯度优化方法的支持,以及对gpu提供的并行计算能力的充分利用。通过利用这些先进的计算技术,与传统的部分波分析软件包相比,pwag在有效识别全局最优点方面具有显着优势。•程序标题:PWACG:部分波分析代码生成器•CPC库链接到程序文件:https://doi.org/10.17632/47ppcnx77x.1•许可条款:本软件在麻省理工学院许可下分发。•外部例程/库:jaxlib, jax, jinja2, matplotlib, numpy, scipy•问题性质:该程序解决了高能物理分波分析(PWA)中高性能计算工具的需求。引入牛顿共轭梯度法进行优化,提高了拟合的精度和稳定性。•解决方法:pwag采用代码生成和自动区分技术,自动创建PWA代码。它利用JAX的计算能力进行高效执行,并支持多gpu计算等高级特性。•GitHub存储库:https://github.com/caihao/PWACG
{"title":"PWACG: Partial wave analysis code generator supporting Newton-conjugate gradient method","authors":"Xiang Dong ,&nbsp;Yu-Chang Sun ,&nbsp;Chu-Cheng Pan ,&nbsp;Ao-Yan Cheng ,&nbsp;Ao-Bo Wang ,&nbsp;Hao Cai ,&nbsp;Kai Zhu","doi":"10.1016/j.cpc.2025.109963","DOIUrl":"10.1016/j.cpc.2025.109963","url":null,"abstract":"<div><div>This paper introduces a novel Partial Wave Analysis Code Generator (PWACG) that automatically generates high-performance partial wave analysis codes. This is achieved by leveraging the JAX automatic differentiation library and the jinja2 template engine. The resulting code is constructed using the high-performance API of JAX, and includes support for the Newton’s Conjugate Gradient optimization method, as well as the full utilization of parallel computing capabilities offered by GPUs. By harnessing these advanced computing techniques, PWACG demonstrates a significant advantage in efficiently identifying global optimal points compared to conventional partial wave analysis software packages.</div><div><strong>PROGRAM SUMMARY</strong></div><div>• <strong>Program Title:</strong> PWACG: Partial Wave Analysis Code Generator</div><div>• <strong>CPC Library link to program files:</strong> <span><span>https://doi.org/10.17632/47ppcnx77x.1</span><svg><path></path></svg></span></div><div>• <strong>Licensing provisions:</strong> This software is distributed under the MIT License.</div><div>• <strong>Programming language:</strong> Python</div><div>• <strong>External routines/libraries:</strong> jaxlib, jax, jinja2, matplotlib, numpy, scipy</div><div>• <strong>Nature of problem:</strong> The program addresses the need for high-performance computational tools in high-energy physics partial wave analysis (PWA). It introduces the Newton-conjugate gradient method for optimization, enhancing the accuracy and stability of fits.</div><div>• <strong>Solution method:</strong> PWACG employs code generation and automatic differentiation techniques to automate the creation of PWA code. It leverages the computational capabilities of JAX for efficient execution and supports advanced features such as multi-GPU computation.</div><div>• <strong>GitHub repository:</strong> <span><span>https://github.com/caihao/PWACG</span><svg><path></path></svg></span></div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109963"},"PeriodicalIF":3.4,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145786464","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}
引用次数: 0
Scalable, cloud-based simulations of blood flow and targeted drug delivery in retinal capillaries 可扩展的,基于云的模拟血液流动和视网膜毛细血管靶向药物输送
IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2025-12-01 DOI: 10.1016/j.cpc.2025.109967
Lucas Amoudruz , Sergey Litvinov , Riccardo Murri , Volker Eyrich , Jens Zudrop , Costas Bekas , Petros Koumoutsakos
We investigate the capabilities of cloud computing for large-scale, tightly-coupled simulations of biological fluids in complex geometries, traditionally performed in supercomputing centers. We demonstrate scalable and efficient simulations in the public cloud. We perform meso-scale simulations of blood flow in image-reconstructed capillaries, and examine targeted drug delivery by artificial bacterial flagella (ABFs). The simulations deploy dissipative particle dynamics (DPD) with two software frameworks, Mirheo(developed by our team) and LAMMPS. Mirheoexhibits remarkable weak scalability for up to 512 GPUs. Similarly, LAMMPS demonstrated excellent weak scalability for pure solvent as well as for blood suspensions and ABFs in reconstructed retinal capillaries. In particular, LAMMPS maintained weak scaling above 90 % on the cloud for up to 2000 cores. Our findings demonstrate that cloud computing can support tightly coupled, large-scale scientific simulations with competitive performance.
我们研究了云计算在复杂几何中对生物流体进行大规模、紧密耦合模拟的能力,这些模拟传统上是在超级计算中心进行的。我们在公共云中演示了可扩展和高效的模拟。我们进行了图像重建毛细血管血流的中尺度模拟,并检查了人工细菌鞭毛(ABFs)的靶向药物递送。模拟使用两个软件框架,Mirheo(由我们的团队开发)和LAMMPS部署耗散粒子动力学(DPD)。mirheo表现出显著的弱可扩展性,最多可支持512个gpu。同样,LAMMPS在纯溶剂以及重建视网膜毛细血管中的血液悬浮液和abf中表现出优异的弱可扩展性。特别是,LAMMPS在高达2000核的云中保持了90%以上的弱扩展。我们的研究结果表明,云计算可以支持紧密耦合的、具有竞争力性能的大规模科学模拟。
{"title":"Scalable, cloud-based simulations of blood flow and targeted drug delivery in retinal capillaries","authors":"Lucas Amoudruz ,&nbsp;Sergey Litvinov ,&nbsp;Riccardo Murri ,&nbsp;Volker Eyrich ,&nbsp;Jens Zudrop ,&nbsp;Costas Bekas ,&nbsp;Petros Koumoutsakos","doi":"10.1016/j.cpc.2025.109967","DOIUrl":"10.1016/j.cpc.2025.109967","url":null,"abstract":"<div><div>We investigate the capabilities of cloud computing for large-scale, tightly-coupled simulations of biological fluids in complex geometries, traditionally performed in supercomputing centers. We demonstrate scalable and efficient simulations in the public cloud. We perform meso-scale simulations of blood flow in image-reconstructed capillaries, and examine targeted drug delivery by artificial bacterial flagella (ABFs). The simulations deploy dissipative particle dynamics (DPD) with two software frameworks, Mirheo(developed by our team) and LAMMPS. Mirheoexhibits remarkable weak scalability for up to 512 GPUs. Similarly, LAMMPS demonstrated excellent weak scalability for pure solvent as well as for blood suspensions and ABFs in reconstructed retinal capillaries. In particular, LAMMPS maintained weak scaling above 90 % on the cloud for up to 2000 cores. Our findings demonstrate that cloud computing can support tightly coupled, large-scale scientific simulations with competitive performance.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109967"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681671","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}
引用次数: 0
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Computer Physics Communications
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