Computer Physics Communications最新文献

{"title":"HFBTHO-AD: Differentiation of a nuclear energy density functional code","authors":"Laurent Hascoët ,&nbsp;Matt Menickelly ,&nbsp;Sri Hari Krishna Narayanan ,&nbsp;Jared O’Neal ,&nbsp;Nicolas Schunck ,&nbsp;Stefan M. Wild","doi":"10.1016/j.cpc.2025.109955","DOIUrl":"10.1016/j.cpc.2025.109955","url":null,"abstract":"<div><div>The HFBTHO code implements a nuclear energy density functional solver to model the structure of atomic nuclei. HFBTHO has previously been used to calibrate energy functionals and perform sensitivity analysis by using derivative-free methods. To enable derivative-based optimization and uncertainty quantification approaches, we must compute the derivatives of HFBTHO outputs with respect to the parameters of the energy functional, which are a subset of all input parameters of the code. We use the algorithmic/automatic differentiation (AD) tool Tapenade to differentiate HFBTHO. We compare the derivatives obtained using AD against finite-difference approximation and examine the performance of the derivative computation.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109955"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Software for simulation and analysis of far-field diffraction patterns in transient grating spectroscopy","authors":"Andrii Goloborodko ,&nbsp;Myhailo Kotov ,&nbsp;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}

{"title":"GeoDualSPHysics: a high-performance SPH solver for large deformation modelling of geomaterials with two-way coupling to multi-body systems","authors":"Ruofeng Feng ,&nbsp;Jidong Zhao ,&nbsp;Georgios Fourtakas ,&nbsp;Benedict D Rogers","doi":"10.1016/j.cpc.2025.109965","DOIUrl":"10.1016/j.cpc.2025.109965","url":null,"abstract":"&lt;div&gt;&lt;div&gt;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.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Program summary&lt;/h3&gt;&lt;div&gt;Program title: GeoDualSPHysics&lt;/div&gt;&lt;div&gt;CPC Library link to program files: &lt;span&gt;&lt;span&gt;https://doi.org/10.17632/z4sh62y97g.1&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;Licensing provisions: GNU Lesser General Public License&lt;/div&gt;&lt;div&gt;Programming language: C++ and CUDA&lt;/div&gt;&lt;div&gt;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}

{"title":"QUASAR: A flexible QM-MM method for biomolecular systems based on restraining spheres","authors":"Christoph Gorgulla ,&nbsp;Alejandro J. Garza ,&nbsp;Venkat Kapil ,&nbsp;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}

{"title":"OpenSn: A massively parallel, open-source simulation environment for discrete ordinates radiation transport","authors":"David Andrs ,&nbsp;Zachary Hardy ,&nbsp;Daryl Hawkins ,&nbsp;Jim Morel ,&nbsp;Dinh Quoc Dang Nguyen ,&nbsp;Jean C. Ragusa","doi":"10.1016/j.cpc.2025.110001","DOIUrl":"10.1016/j.cpc.2025.110001","url":null,"abstract":"&lt;div&gt;&lt;div&gt;OpenSn is an open-source, massively parallel deterministic radiation transport code for solving the discrete-ordinates (S&lt;sub&gt;&lt;em&gt;N&lt;/em&gt;&lt;/sub&gt;) form of the Boltzmann transport equation on unstructured, arbitrary polyhedral meshes. It supports high-fidelity simulations involving steady-state, eigenvalue, and adjoint problems for neutral particles (e.g., neutrons, photons, multi-particles), using the multigroup approximation in energy.&lt;/div&gt;&lt;div&gt;OpenSn combines angular discretization via discrete ordinates with a discontinuous Galerkin finite element method (DGFEM) in space, enabling accurate resolution of transport physics on arbitrary polyhedral cells, included locally refined spatial grids. It includes multiple angular quadrature types, including locally refined angular quadratures.&lt;/div&gt;&lt;div&gt;Written in modern C++ with a Python API, OpenSn runs efficiently on platforms ranging from laptops to supercomputers. The transport sweep algorithm is implemented using a task-based, directed-acyclic-graph (DAG) approach for each angle and supports asynchronous parallelism across thousands of MPI ranks. Group-set aggregation improves compute intensity, and synthetic acceleration techniques (e.g., diffusion synthetic acceleration, second-moment method) enhance solver convergence.&lt;/div&gt;&lt;div&gt;OpenSn has been verified on reactor physics problems and demonstrated excellent weak and strong scaling performance on more than 32,768 processes, making it a versatile and robust platform for large-scale transport simulations in complex geometries.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;PROGRAM SUMMARY&lt;/strong&gt;&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Program Title:&lt;/strong&gt; OpenSn&lt;/div&gt;&lt;div&gt;&lt;strong&gt;CPC Library link to program files:&lt;/strong&gt; &lt;span&gt;&lt;span&gt;https://doi.org/10.17632/gvrs69dzcv.1&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Developer’s repository link:&lt;/strong&gt; &lt;span&gt;&lt;span&gt;https://github.com/Open-Sn/OpenSn&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Licensing provisions:&lt;/strong&gt; MIT license&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Programming language:&lt;/strong&gt; C++ (core), Python (API)&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Supplementary material:&lt;/strong&gt; User manual, theory documentation, and tutorial notebooks available at &lt;span&gt;&lt;span&gt;https://open-sn.github.io/opensn/&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Nature of problem:&lt;/strong&gt;Radiation transport simulations are central to numerous applications in physics and engineering, including reactor analysis, shielding, radiography, and detector modeling. Solving the linear Boltzmann transport equation in its discrete-ordinates form (S&lt;sub&gt;&lt;em&gt;N&lt;/em&gt;&lt;/sub&gt;) on complex geometries requires robust numerical methods and scalable parallel algorithms. Many existing codes are closed-source, lack support for polyhedral meshes, or do not efficiently exploit modern HPC systems. A flexible, open-source tool is needed to address these challenges while supporting methodological innovation and large-scale computation.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Solution method:&lt;/strong&gt;","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110001"},"PeriodicalIF":3.4,"publicationDate":"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}

{"title":"Pyrometheus: Symbolic abstractions for XPU and automatically differentiated computation of combustion kinetics and thermodynamics","authors":"Esteban Cisneros–Garibay ,&nbsp;Henry Le Berre ,&nbsp;Dimitrios Adam ,&nbsp;Spencer H. Bryngelson ,&nbsp;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}

{"title":"Dofulator: A tool for calculating degrees of freedom of atoms in molecules with geometry constraints","authors":"Stephen Sanderson ,&nbsp;Sobin Alosious ,&nbsp;Debra J. Searles","doi":"10.1016/j.cpc.2025.110003","DOIUrl":"10.1016/j.cpc.2025.110003","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Recently, we proposed a method for calculating per-atom and per-direction degrees of freedom (DoF) in the presence of geometric constraints, enabling fine-grained local kinetic temperature calculations. Here, we discuss relevant implementation details for various constraint geometries, including those which feature kinematic loops (e.g. benzene with rigid bond lengths). Furthermore, by analyzing the effects of deformation of semi-rigid molecules on the DoF of each constituent atom, we gain insight into conditions under which atomic DoF may vary significantly during a simulation. This provides some guidance towards cases where local DoF should be calculated dynamically to obtain reliable local temperature measurements, and cases where using the atomic DoF of the equilibrium geometry as a constant throughout the simulation would be sufficient. We have implemented the presented algorithms in an open-source C library, &lt;span&gt;dofulator&lt;/span&gt;, which can be used on its own or through a Python interface that includes compatibility with the popular MDAnalysis package.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Program summary&lt;/strong&gt; &lt;em&gt;Program Title:&lt;/em&gt; &lt;span&gt;dofulator&lt;/span&gt; &lt;em&gt;CPC Library link to program files:&lt;/em&gt; (to be added by Technical Editor) &lt;em&gt;Developer’s repository link:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://github.com/CTCMS-UQ/dofulator&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt; &lt;em&gt;Licensing provisions:&lt;/em&gt; MPL-2.0 &lt;em&gt;Programming language:&lt;/em&gt; C, Python&lt;/div&gt;&lt;div&gt;&lt;em&gt;Nature of problem:&lt;/em&gt; In molecular simulations with geometry constraints, determining the degrees of freedom (DoF) associated with a local kinetic temperature measurement can become non-trivial when constraints include atoms both inside and outside the local subset of interest [1]. The (fractional) DoF of atoms in a rigid body depends on their masses and the molecular geometry. If constraints do not form a rigid body, but instead a semi-rigid fragment, then the partitioning of atomic DoF can vary as the fragment deforms. Furthermore, if directional kinetic temperatures are required, DoF along each direction must be determined, which additionally depend on the orientation of the rigid body or semi-rigid fragment.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Solution method:&lt;/em&gt; Atomic DoF can be calculated by the relative contribution of each atom to the inertia of each mode of motion [1]. This software allows rigid bodies and semi-rigid fragments to be defined, from which a plan is constructed for determining said modes and contributions. Once constructed, a plan can be applied repeatedly to calculate atomic DoF on required frames of a molecular dynamics trajectory.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Additional comments including restrictions and unusual features:&lt;/em&gt; The core &lt;span&gt;dofulator&lt;/span&gt; library is provided as a C API, depending only on a BLAS and LAPACK implementation and suitable for direct integration with a molecular dynamics engine (possibly with some modifications). For convenience, a thin Python wrapper is also provided, and this","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 110003"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SimOS: A Python framework for simulations of optically addressable spins","authors":"Laura A. Völker ,&nbsp;John M. Abendroth ,&nbsp;Christian L. Degen ,&nbsp;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}

{"title":"INTW: A versatile modular environment for advanced treatment of electronic structure and electron-phonon related properties","authors":"Haritz Garai-Marin ,&nbsp;María Blanco-Rey ,&nbsp;Idoia G. Gurtubay ,&nbsp;Jon Lafuente-Bartolome ,&nbsp;Asier Eiguren","doi":"10.1016/j.cpc.2025.109991","DOIUrl":"10.1016/j.cpc.2025.109991","url":null,"abstract":"&lt;div&gt;&lt;div&gt;We present &lt;span&gt;INTW&lt;/span&gt;, a modular software environment designed for advanced electronic structure calculations. Developed in Fortran95, &lt;span&gt;INTW&lt;/span&gt; is capable of reading self-consistent field (SCF) results, such as electron energies, wave functions, and potentials, generated by the &lt;span&gt;Quantum ESPRESSO&lt;/span&gt; and &lt;span&gt;SIESTA&lt;/span&gt; codes. Using these SCF results as input, &lt;span&gt;INTW&lt;/span&gt; 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. &lt;span&gt;INTW&lt;/span&gt; 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 &lt;span&gt;SIESTA&lt;/span&gt;, and plane-wave codes like &lt;span&gt;Quantum ESPRESSO&lt;/span&gt;. These capabilities make &lt;span&gt;INTW&lt;/span&gt; unique, offering a versatile approach that effectively combines the use of symmetry with both localized basis sets and plane-wave methods.&lt;/div&gt;&lt;div&gt;&lt;strong&gt;Program summary&lt;/strong&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;Program Title:&lt;/em&gt; &lt;span&gt;INTW&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;CPC Library link to program files:&lt;/em&gt; (to be added by Technical Editor)&lt;/div&gt;&lt;div&gt;&lt;em&gt;Developer’s repository link:&lt;/em&gt; &lt;span&gt;&lt;span&gt;https://github.com/eiguren/intw&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;&lt;/div&gt;&lt;div&gt;&lt;em&gt;Code Ocean capsule:&lt;/em&gt; (to be added by Technical Editor)&lt;/div&gt;&lt;div&gt;&lt;em&gt;Licensing provisions:&lt;/em&gt; GPL-3.0-or-later&lt;/div&gt;&lt;div&gt;&lt;em&gt;Programming language:&lt;/em&gt; Fortran95&lt;/div&gt;&lt;div&gt;&lt;em&gt;Nature of problem:&lt;/em&gt;&lt;/div&gt;&lt;div&gt;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 &lt;span&gt;Quantum ESPRESSO&lt;/span&gt; and &lt;span&gt;SIESTA&lt;/span&gt;. 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.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Solution method:&lt;/em&gt;&lt;/div&gt;&lt;div&gt;Electron and phonon states are calculated only in the irreducible Brillouin zone provided by &lt;span&gt;Quantum ESPRESSO&lt;/span&gt; and &lt;span&gt;SIESTA&lt;/span&gt;. &lt;span&gt;INTW&lt;/span&gt; interfaces with these codes to generate electron (spinor) states and phonon induced (spinor) potentials at arbitrary momenta using symmetry operations. &lt;span&gt;INTW&lt;/span&gt; efficiently calculates the nearest-neighbor overlap matrices for Wannier functions by exploiting symmetry. In &lt;span&gt;SIESTA&lt;/span&gt;, phonons are calculated using the supercell method, although &lt;span&gt;INTW&lt;/span&gt; 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}

{"title":"Multi-species Rosenbluth Fokker-Planck collision operator for discontinuous Galerkin method","authors":"Janghoon Seo ,&nbsp;Gahyung Jo ,&nbsp;Jae-Min Kwon ,&nbsp;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}