Pub Date : 2025-12-07DOI: 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.
{"title":"Tessellation-based grain boundary determination for X-ray orientation microscopies","authors":"Jaemyung Kim , Yujiro Hayashi , Sung Soo Ha , Makina Yabashi","doi":"10.1016/j.cpc.2025.109988","DOIUrl":"10.1016/j.cpc.2025.109988","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109988"},"PeriodicalIF":3.4,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145732949","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 : 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":"2025-12-06","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}
<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":"2025-12-02","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 : 2025-12-01DOI: 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.
{"title":"Scalable, cloud-based simulations of blood flow and targeted drug delivery in retinal capillaries","authors":"Lucas Amoudruz , Sergey Litvinov , Riccardo Murri , Volker Eyrich , Jens Zudrop , Costas Bekas , 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}
Pub Date : 2025-11-28DOI: 10.1016/j.cpc.2025.109966
Seokhwan Min, Jonghwa Shin
Controlling the scattering of waves from multi-shell spherical systems and particles is a crucial aspect in many applications in photonics such as superdirective antennae and structural coloring. Nevertheless, the effective design of such systems is non-trivial due to the coexistence of topological (number of shells and their material composition) and shape (shell thicknesses) parameters. Thus far, general-purpose algorithms such as parameter sweeps, gradient descent, differential evolution, and deep neural networks have been used to optimize particle shape under one or a few fixed topologies, limiting the complexity and effectiveness of the resulting designs. To address this shortcoming, we present a topology nucleation algorithm that allows the concurrent design of particle topology and shape through the use of a topology derivative expression derived from the transfer matrix formulation of the analytical Mie scattering theory. The principle behind our algorithm can readily be applied to the design of multi-shell spherical systems in other fields such as acoustics and quantum transport.
{"title":"Eschallot: A topology nucleation algorithm for designing stratified, spherically symmetric systems that exhibit complex angular scattering of electromagnetic waves","authors":"Seokhwan Min, Jonghwa Shin","doi":"10.1016/j.cpc.2025.109966","DOIUrl":"10.1016/j.cpc.2025.109966","url":null,"abstract":"<div><div>Controlling the scattering of waves from multi-shell spherical systems and particles is a crucial aspect in many applications in photonics such as superdirective antennae and structural coloring. Nevertheless, the effective design of such systems is non-trivial due to the coexistence of topological (number of shells and their material composition) and shape (shell thicknesses) parameters. Thus far, general-purpose algorithms such as parameter sweeps, gradient descent, differential evolution, and deep neural networks have been used to optimize particle shape under one or a few fixed topologies, limiting the complexity and effectiveness of the resulting designs. To address this shortcoming, we present a topology nucleation algorithm that allows the concurrent design of particle topology and shape through the use of a topology derivative expression derived from the transfer matrix formulation of the analytical Mie scattering theory. The principle behind our algorithm can readily be applied to the design of multi-shell spherical systems in other fields such as acoustics and quantum transport.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109966"},"PeriodicalIF":3.4,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733048","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 : 2025-11-27DOI: 10.1016/j.cpc.2025.109957
Nicolás F. Barrera , Javiera Cabezas-Escares , Mònica Calatayud , Francisco Munoz , Tatiana Gómez , Carlos Cárdenas
FukuiGrid is a Python-based code that calculates Fukui functions and Fukui potentials in systems with periodic boundary conditions, making it a valuable tool for solid-state chemistry. It focuses on chemical reactivity descriptors from Conceptual Density-Functional Theory (c-DFT) and enables the calculation of Fukui functions through methods such as finite differences and interpolation. FukuiGrid addresses the challenges associated with periodic boundary conditions when calculating the electrostatic potential of a Fukui function (known as the Fukui potential) by integrating various corrections to alleviate the compensating background of charge. These corrections include the electrode approach and self-consistent potential correction as post-processing techniques. This package is compatible with VASP outputs and specifically designed to study the reactivity of surfaces and adsorbates. It generates surface reactivity maps and provides insights into adsorption site preferences, as well as regions prone to electron donation or withdrawal. FukuiGrid has been designed to make c-DFT easier for the surface chemistry community.
{"title":"FukuiGrid: A Python code for c-DFT in solid-state chemistry","authors":"Nicolás F. Barrera , Javiera Cabezas-Escares , Mònica Calatayud , Francisco Munoz , Tatiana Gómez , Carlos Cárdenas","doi":"10.1016/j.cpc.2025.109957","DOIUrl":"10.1016/j.cpc.2025.109957","url":null,"abstract":"<div><div>FukuiGrid is a Python-based code that calculates Fukui functions and Fukui potentials in systems with periodic boundary conditions, making it a valuable tool for solid-state chemistry. It focuses on chemical reactivity descriptors from Conceptual Density-Functional Theory (c-DFT) and enables the calculation of Fukui functions through methods such as finite differences and interpolation. FukuiGrid addresses the challenges associated with periodic boundary conditions when calculating the electrostatic potential of a Fukui function (known as the Fukui potential) by integrating various corrections to alleviate the compensating background of charge. These corrections include the electrode approach and self-consistent potential correction as post-processing techniques. This package is compatible with VASP outputs and specifically designed to study the reactivity of surfaces and adsorbates. It generates surface reactivity maps and provides insights into adsorption site preferences, as well as regions prone to electron donation or withdrawal. FukuiGrid has been designed to make c-DFT easier for the surface chemistry community.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109957"},"PeriodicalIF":3.4,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681707","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 : 2025-11-27DOI: 10.1016/j.cpc.2025.109959
Zhixin Lu, Guo Meng, Roman Hatzky, Philipp Lauber, Matthias Hoelzl
The features of the TRIMEG-GKX code are described with emphasis on the exploration using novel/different schemes compared to other gyrokinetic codes, particularly the use of object-oriented programming, filter/buffer-free treatment, and a high-order piecewise field-aligned finite element method. The TRIMEG-GKX code solves the electromagnetic gyrokinetic equation using the particle-in-cell scheme, taking into account multi-species effects and shear Alfvén physics. The mixed-variable/pullback scheme has been implemented to enable electromagnetic studies. This code is parallelized using particle decomposition and domain cloning among computing nodes, replacing traditional domain decomposition techniques. The applications to study the micro- and macro-instabilities are demonstrated, including the energetic-particle-driven Alfvén eigenmode, ion temperature gradient mode, and kinetic ballooning mode. Good performance is achieved in both ad hoc and experimentally reconstructed equilibria, such as those of the ASDEX Upgrade (AUG), Tokamak á configuration variable (TCV), and the Joint European Torus (JET). Future studies of edge physics using the high-order C1 finite element method for triangular meshes in the TRIMEG-C1 code will be built upon the same numerical methods.
{"title":"TRIMEG-GKX: An electromagnetic gyrokinetic particle code with a piecewise field-aligned finite element method for micro- and macro-instability studies in tokamak core plasmas","authors":"Zhixin Lu, Guo Meng, Roman Hatzky, Philipp Lauber, Matthias Hoelzl","doi":"10.1016/j.cpc.2025.109959","DOIUrl":"10.1016/j.cpc.2025.109959","url":null,"abstract":"<div><div>The features of the TRIMEG-GKX code are described with emphasis on the exploration using novel/different schemes compared to other gyrokinetic codes, particularly the use of object-oriented programming, filter/buffer-free treatment, and a high-order piecewise field-aligned finite element method. The TRIMEG-GKX code solves the electromagnetic gyrokinetic equation using the particle-in-cell scheme, taking into account multi-species effects and shear Alfvén physics. The mixed-variable/pullback scheme has been implemented to enable electromagnetic studies. This code is parallelized using particle decomposition and domain cloning among computing nodes, replacing traditional domain decomposition techniques. The applications to study the micro- and macro-instabilities are demonstrated, including the energetic-particle-driven Alfvén eigenmode, ion temperature gradient mode, and kinetic ballooning mode. Good performance is achieved in both ad hoc and experimentally reconstructed equilibria, such as those of the ASDEX Upgrade (AUG), Tokamak á configuration variable (TCV), and the Joint European Torus (JET). Future studies of edge physics using the high-order <em>C</em><sup>1</sup> finite element method for triangular meshes in the TRIMEG-C1 code will be built upon the same numerical methods.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109959"},"PeriodicalIF":3.4,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681673","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 : 2025-11-26DOI: 10.1016/j.cpc.2025.109954
Mehmet Ali Sarsıl , Mubashir Mansoor , Mert Saraçoğlu , Servet Timur , Onur Ergen
<div><div>The diverse spectrum of material characteristics, including band gap, mechanical moduli, color, phonon and electronic density of states, along with catalytic and surface properties, are intricately intertwined with the atomic structure and the corresponding interatomic bond lengths. This interconnection extends to the manifestation of interplanar spacings within a crystalline lattice. Analysis of these interplanar spacings and the comprehension of any deviations-whether it be lattice compression or expansion, commonly referred to as strain, hold paramount significance in unraveling various unknowns within the field. Transmission Electron Microscopy (TEM) is widely used to capture these atomic-scale ordering, facilitating direct investigation of interplanar spacings. However, creating critical contour maps for visualizing and interpreting lattice stresses in TEM images remains a challenging task. This study introduces an open-source, AI-assisted application, developed entirely in Python, for processing TEM images to facilitate strain analysis through advanced visualization techniques. This application is designed to process a diverse range of materials, including nanoparticles, 2D materials, pure crystals, and solid solutions. By converting local variations in interplanar spacings into contour maps, it provides a visual representation of lattice expansion and compression. With highly versatile settings, as detailed in this paper, the tool is readily accessible for TEM image-based material analysis. It facilitates an in-depth exploration of strain engineering by generating strain contour maps at the atomic scale, offering valuable insights into material properties. <strong>Program summary</strong> <em>Program Title:</em> PyNanoSpacing <em>CPC Library link to program files:</em> “<span><span>https://doi.org/10.17632/y864t5ykxx.1</span><svg><path></path></svg></span> ” <em>Developer’s repository link:</em> “<span><span>https://github.com/malisarsil/PyNanoSpacing</span><svg><path></path></svg></span> ” <em>Licensing provisions:</em> MIT license <em>Programming language:</em> Python 3.11 <em>Nature of problem:</em> Transmission Electron Microscopy (TEM) is widely used to analyze lattice structures in materials, but extracting quantitative strain information from TEM images remains challenging. Existing tools often lack automation, requiring manual calibration and region selection, leading to inconsistencies. Researchers need a user-friendly, automated solution to analyze local lattice strains and interplanar spacing variations efficiently. <em>Solution method:</em> The developed desktop application simplifies TEM image strain analysis by automating key steps. It extracts image details (such as scale and resolution) and detects atomic regions using AI-based segmentation. A correction step ensures proper alignment before measuring interlayer distances, which are then color-mapped to show strain variations. A smoothing technique is applied to re
{"title":"Mapping strain at the atomic scale with PyNanospacing: An AI-assisted approach to TEM image processing and visualization","authors":"Mehmet Ali Sarsıl , Mubashir Mansoor , Mert Saraçoğlu , Servet Timur , Onur Ergen","doi":"10.1016/j.cpc.2025.109954","DOIUrl":"10.1016/j.cpc.2025.109954","url":null,"abstract":"<div><div>The diverse spectrum of material characteristics, including band gap, mechanical moduli, color, phonon and electronic density of states, along with catalytic and surface properties, are intricately intertwined with the atomic structure and the corresponding interatomic bond lengths. This interconnection extends to the manifestation of interplanar spacings within a crystalline lattice. Analysis of these interplanar spacings and the comprehension of any deviations-whether it be lattice compression or expansion, commonly referred to as strain, hold paramount significance in unraveling various unknowns within the field. Transmission Electron Microscopy (TEM) is widely used to capture these atomic-scale ordering, facilitating direct investigation of interplanar spacings. However, creating critical contour maps for visualizing and interpreting lattice stresses in TEM images remains a challenging task. This study introduces an open-source, AI-assisted application, developed entirely in Python, for processing TEM images to facilitate strain analysis through advanced visualization techniques. This application is designed to process a diverse range of materials, including nanoparticles, 2D materials, pure crystals, and solid solutions. By converting local variations in interplanar spacings into contour maps, it provides a visual representation of lattice expansion and compression. With highly versatile settings, as detailed in this paper, the tool is readily accessible for TEM image-based material analysis. It facilitates an in-depth exploration of strain engineering by generating strain contour maps at the atomic scale, offering valuable insights into material properties. <strong>Program summary</strong> <em>Program Title:</em> PyNanoSpacing <em>CPC Library link to program files:</em> “<span><span>https://doi.org/10.17632/y864t5ykxx.1</span><svg><path></path></svg></span> ” <em>Developer’s repository link:</em> “<span><span>https://github.com/malisarsil/PyNanoSpacing</span><svg><path></path></svg></span> ” <em>Licensing provisions:</em> MIT license <em>Programming language:</em> Python 3.11 <em>Nature of problem:</em> Transmission Electron Microscopy (TEM) is widely used to analyze lattice structures in materials, but extracting quantitative strain information from TEM images remains challenging. Existing tools often lack automation, requiring manual calibration and region selection, leading to inconsistencies. Researchers need a user-friendly, automated solution to analyze local lattice strains and interplanar spacing variations efficiently. <em>Solution method:</em> The developed desktop application simplifies TEM image strain analysis by automating key steps. It extracts image details (such as scale and resolution) and detects atomic regions using AI-based segmentation. A correction step ensures proper alignment before measuring interlayer distances, which are then color-mapped to show strain variations. A smoothing technique is applied to re","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109954"},"PeriodicalIF":3.4,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681710","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}
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":"2025-11-25","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 : 2025-11-25DOI: 10.1016/j.cpc.2025.109956
Alessio Roccon
We present an extended version of MHIT36, a GPU-tailored solver for interface-resolved simulations of multiphase turbulence. The framework couples direct numerical simulation (DNS) of the Navier–Stokes equations, which describe the flow field, with a phase-field method to capture interfacial phenomena. In addition, the transport equation for a scalar can also be solved. The governing equations are discretized using a second-order finite difference scheme. The Navier–Stokes equations are time advanced with an explicit fractional-step method, and the resulting pressure Poisson equation is solved using a FFT-based method. The accurate conservative diffuse interface (ACDI) formulation is used to describe the transport of the phase-field variable. Simulations can be performed in two configurations: a triply-periodic cubic domain or a rectangular domain of arbitrary dimensions bounded by two walls. From a computational standpoint, MHIT36 employs a two-dimensional domain decomposition to distribute the workload across MPI tasks. The cuDecomp library is used to perform pencil transpositions and halo updates, while the cuFFT library and OpenACC directives are leveraged to offload the remaining computational kernels to the GPU. MHIT36 is developed using the managed memory feature and it provides a baseline code that is easy to further extend and modify. MHIT36 is released open source under the MIT license.
{"title":"MHIT36: Extension to wall-bounded turbulence and scalar transport equation","authors":"Alessio Roccon","doi":"10.1016/j.cpc.2025.109956","DOIUrl":"10.1016/j.cpc.2025.109956","url":null,"abstract":"<div><div>We present an extended version of MHIT36, a GPU-tailored solver for interface-resolved simulations of multiphase turbulence. The framework couples direct numerical simulation (DNS) of the Navier–Stokes equations, which describe the flow field, with a phase-field method to capture interfacial phenomena. In addition, the transport equation for a scalar can also be solved. The governing equations are discretized using a second-order finite difference scheme. The Navier–Stokes equations are time advanced with an explicit fractional-step method, and the resulting pressure Poisson equation is solved using a FFT-based method. The accurate conservative diffuse interface (ACDI) formulation is used to describe the transport of the phase-field variable. Simulations can be performed in two configurations: a triply-periodic cubic domain or a rectangular domain of arbitrary dimensions bounded by two walls. From a computational standpoint, MHIT36 employs a two-dimensional domain decomposition to distribute the workload across MPI tasks. The cuDecomp library is used to perform pencil transpositions and halo updates, while the cuFFT library and OpenACC directives are leveraged to offload the remaining computational kernels to the GPU. MHIT36 is developed using the managed memory feature and it provides a baseline code that is easy to further extend and modify. MHIT36 is released open source under the MIT license.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109956"},"PeriodicalIF":3.4,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616112","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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