Pub Date : 2025-11-19DOI: 10.1016/j.cpc.2025.109955
Laurent Hascoët , Matt Menickelly , Sri Hari Krishna Narayanan , Jared O’Neal , Nicolas Schunck , Stefan M. Wild
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.
{"title":"HFBTHO-AD: Differentiation of a nuclear energy density functional code","authors":"Laurent Hascoët , Matt Menickelly , Sri Hari Krishna Narayanan , Jared O’Neal , Nicolas Schunck , 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":"2025-11-19","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}
Pub Date : 2025-11-19DOI: 10.1016/j.cpc.2025.109935
Javier López Miras, Fuensanta Vilches
We introduce mosca, a Mathematica package designed to facilitate on-shell calculations in effective field theories (EFTs). This initial release focuses on the reduction of Green’s bases to physical bases, as well as transformations between arbitrary operator bases. The core of the package is based on a diagrammatic on-shell matching procedure, grounded in the equivalence of physical observables derived from both redundant and non-redundant Lagrangians. mosca offers a complete set of tools for performing basis transformations, diagram isomorphism detection, numerical substitution of kinematic configurations, and symbolic manipulation of algebraic expressions. Planned future developments include extension to one-loop computations, thus providing support for EFT renormalization directly in a physical basis and automated computation of one-loop finite matching, including contributions from evanescent operators.
PROGRAM SUMMARYProgram Title: mosca CPC Library link to program files: (to be added by Technical Editor) Developer’s repository link:https://gitlab.com/matchingonshell/moscaLicensing provisions: GPLv3 Programming language: Mathematica Nature of problem: Matching calculations in effective field theories are traditionally performed off-shell, involving complicated basis reductions through non-trivial field redefinitions to eliminate redundant operators. This process is algebraically intensive and prone to errors. Although on-shell matching, which focuses directly on physical observables, could simplify these steps by avoiding field redefinitions, it has been considered impractical due to the presence of apparent non-localities that must cancel precisely. Automating on-shell matching has therefore been a long-standing challenge. Solution method: Our approach is based on a numerical solution of the on-shell matching equations, which naturally and effortlessly enforces the delicate cancellation of non-local terms between the full theory and the effective theory. By employing rational on-shell kinematics, the method achieves an exact analytic solution despite using numerical techniques. This allows the matching to be performed entirely within a physical operator basis. Additional comments including restrictions and unusual features: The workflow for handling Lagrangians and Feynman diagrams in mosca is based on the integration of FeynArts and FeynCalc. Consequently, users need to provide specific FeynArts model files patched for compatibility with FeynCalc. Additionally, a specialized input format is required to define Wilson coefficients along with their corresponding EFT order (EFTOrder). These requirements ensure the correct processing of models and coefficients.
{"title":"Automation of a matching on-shell calculator","authors":"Javier López Miras, Fuensanta Vilches","doi":"10.1016/j.cpc.2025.109935","DOIUrl":"10.1016/j.cpc.2025.109935","url":null,"abstract":"<div><div>We introduce <span>mosca</span>, a <span>Mathematica</span> package designed to facilitate on-shell calculations in effective field theories (EFTs). This initial release focuses on the reduction of Green’s bases to physical bases, as well as transformations between arbitrary operator bases. The core of the package is based on a diagrammatic on-shell matching procedure, grounded in the equivalence of physical observables derived from both redundant and non-redundant Lagrangians. <span>mosca</span> offers a complete set of tools for performing basis transformations, diagram isomorphism detection, numerical substitution of kinematic configurations, and symbolic manipulation of algebraic expressions. Planned future developments include extension to one-loop computations, thus providing support for EFT renormalization directly in a physical basis and automated computation of one-loop finite matching, including contributions from evanescent operators.</div><div><strong>PROGRAM SUMMARY</strong> <em>Program Title:</em> mosca <em>CPC Library link to program files:</em> (to be added by Technical Editor) <em>Developer’s repository link:</em> <span><span>https://gitlab.com/matchingonshell/mosca</span><svg><path></path></svg></span> <em>Licensing provisions:</em> GPLv3 <em>Programming language:</em> Mathematica <em>Nature of problem:</em> Matching calculations in effective field theories are traditionally performed off-shell, involving complicated basis reductions through non-trivial field redefinitions to eliminate redundant operators. This process is algebraically intensive and prone to errors. Although on-shell matching, which focuses directly on physical observables, could simplify these steps by avoiding field redefinitions, it has been considered impractical due to the presence of apparent non-localities that must cancel precisely. Automating on-shell matching has therefore been a long-standing challenge. <em>Solution method:</em> Our approach is based on a numerical solution of the on-shell matching equations, which naturally and effortlessly enforces the delicate cancellation of non-local terms between the full theory and the effective theory. By employing rational on-shell kinematics, the method achieves an exact analytic solution despite using numerical techniques. This allows the matching to be performed entirely within a physical operator basis. <em>Additional comments including restrictions and unusual features:</em> The workflow for handling Lagrangians and Feynman diagrams in mosca is based on the integration of FeynArts and FeynCalc. Consequently, users need to provide specific FeynArts model files patched for compatibility with FeynCalc. Additionally, a specialized input format is required to define Wilson coefficients along with their corresponding EFT order (EFTOrder). These requirements ensure the correct processing of models and coefficients.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109935"},"PeriodicalIF":3.4,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681672","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 : 2025-11-17DOI: 10.1016/j.cpc.2025.109961
Jian Zhang , Ping Zhu , Chris C. Hegna
A hybrid spectral/finite-element code is developed to numerically solve the resistive finite-pressure magnetohydrodynamic equilibria without the necessity of postulating nested magnetic flux surfaces in the non-axisymmetric toroidal systems. The adopted approach integrates a hyperbolic parallel damping equation for pressure updating, along with a dynamic resistive relaxation for magnetic field. To address the non-axisymmetry in toroidal geometry, a pseudo flux mapping is employed to relate the axisymmetric computational domain to the physical domain. On the computational mesh, an isoparametric C1-continuous triangular element is utilized to discretize the poloidal plane, which is complemented with a Fourier decomposition in the toroidal direction. The versatility of the code is demonstrated through its application to several different non-axisymmetric toroidal systems, including the inherently three-dimensional equilibria in stellarators, the helical-core equilibrium states in tokamak plasmas, and the quasi-single-helicity states in a reversed-field pinch.
{"title":"Numerical solutions of resistive finite-pressure magnetohydrodynamic equilibria for stellarator and non-axisymmetric toroidal plasmas","authors":"Jian Zhang , Ping Zhu , Chris C. Hegna","doi":"10.1016/j.cpc.2025.109961","DOIUrl":"10.1016/j.cpc.2025.109961","url":null,"abstract":"<div><div>A hybrid spectral/finite-element code is developed to numerically solve the resistive finite-pressure magnetohydrodynamic equilibria without the necessity of postulating nested magnetic flux surfaces in the non-axisymmetric toroidal systems. The adopted approach integrates a hyperbolic parallel damping equation for pressure updating, along with a dynamic resistive relaxation for magnetic field. To address the non-axisymmetry in toroidal geometry, a pseudo flux mapping is employed to relate the axisymmetric computational domain to the physical domain. On the computational mesh, an isoparametric C1-continuous triangular element is utilized to discretize the poloidal plane, which is complemented with a Fourier decomposition in the toroidal direction. The versatility of the code is demonstrated through its application to several different non-axisymmetric toroidal systems, including the inherently three-dimensional equilibria in stellarators, the helical-core equilibrium states in tokamak plasmas, and the quasi-single-helicity states in a reversed-field pinch.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109961"},"PeriodicalIF":3.4,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145571120","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 : 2025-11-17DOI: 10.1016/j.cpc.2025.109949
Christoph Gorgulla , Alejandro J. Garza , Venkat Kapil , Konstantin Fackeldey
Quantum mechanical models of molecules theoretically offer unprecedented accuracy in predicting values associated with these systems, including the free energy of interaction between two molecules. However, high-accuracy quantum mechanical methods are computationally too expensive to be applied to larger systems, including most biomolecular systems such as proteins. To circumvent this challenge, the hybrid quantum mechanics/molecular mechanics (QM/MM) method was developed, allowing one to treat only the most important part of the system on the quantum mechanical level and the remaining part on the classical level. To date, QM/MM simulations for biomolecular systems have been carried out almost exclusively on the electronic structure level, neglecting nuclear quantum effects (NQEs). Yet NQEs can play a major role in biomolecular systems [1]. Here, we present i-QI, a QM/MM client for the path integral molecular dynamics (PIMD) software i-PI [2, 3, 4]. i-QI allows for carrying out QM/MM simulations simultaneously, allowing for the inclusion of electronic as well as NQEs. i-QI implements a new QM/MM scheme based on constraining potentials called QUASAR, which allows handling diffusive systems, such as biomolecules solvated in water solvent. The QUASAR method is suitable in particular when the properties of interest are equilibrium properties, such as the free energy of binding. i-QI is freely available and open source, and we demonstrate it on a test system.
{"title":"QUASAR: A flexible QM-MM method for biomolecular systems based on restraining spheres","authors":"Christoph Gorgulla , Alejandro J. Garza , Venkat Kapil , Konstantin Fackeldey","doi":"10.1016/j.cpc.2025.109949","DOIUrl":"10.1016/j.cpc.2025.109949","url":null,"abstract":"<div><div>Quantum mechanical models of molecules theoretically offer unprecedented accuracy in predicting values associated with these systems, including the free energy of interaction between two molecules. However, high-accuracy quantum mechanical methods are computationally too expensive to be applied to larger systems, including most biomolecular systems such as proteins. To circumvent this challenge, the hybrid quantum mechanics/molecular mechanics (QM/MM) method was developed, allowing one to treat only the most important part of the system on the quantum mechanical level and the remaining part on the classical level. To date, QM/MM simulations for biomolecular systems have been carried out almost exclusively on the electronic structure level, neglecting nuclear quantum effects (NQEs). Yet NQEs can play a major role in biomolecular systems [1]. Here, we present i-QI, a QM/MM client for the path integral molecular dynamics (PIMD) software i-PI [2, 3, 4]. i-QI allows for carrying out QM/MM simulations simultaneously, allowing for the inclusion of electronic as well as NQEs. i-QI implements a new QM/MM scheme based on constraining potentials called QUASAR, which allows handling diffusive systems, such as biomolecules solvated in water solvent. The QUASAR method is suitable in particular when the properties of interest are equilibrium properties, such as the free energy of binding. i-QI is freely available and open source, and we demonstrate it on a test system.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109949"},"PeriodicalIF":3.4,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-16DOI: 10.1016/j.cpc.2025.109960
Xiaofei Jia , Qun Wei , Wenpeng Zhang , Han Wang , Liang He
In recent years, Monte Carlo simulation has been increasingly applied as a particle-based technique for microscopic device reliability analysis. This stochastic method solves physical and mathematical problems through statistical sampling and has become instrumental in noise characterization of nanoscale field-effect transistors. However, prior simulations of channel current noise were predominantly one-dimensional and neglected quantum effects arising from dimensional scaling. Therefore, this paper proposes a two-dimensional and three-dimensional Monte Carlo simulation current noise method for metal-oxide-semiconductor field-effect transistors (MOSFET) at the nanoscale. This method is based on the list method and an approximate method for quickly processing anisotropic scattering final states; it uses the successive over-relaxation (SOR) iteration method to iteratively solve the Poisson equation for the divided grid areas, and each node applies a multi-grid method to solve the Poisson equation at each grid point within the sub-area. At the same time, the effective potential method is used to quantum-correct each grid point, and the simulation tracks the accelerated flight and random scattering motion of a group of charged particles, keeping the load on all nodes always balanced. Benchmark results demonstrate that the Monte Carlo simulation framework not only reduces overall CPU time requirements but also validates the effectiveness of predicted MOSFET noise disturbance patterns. The conclusions exhibit excellent agreement with established theories and experimental data, thereby facilitating design and reliability analysis of nanoscale field-effect transistors
{"title":"Noise reliability evaluation of nanoscale metal-oxide-semiconductor field-effect transistors based on Monte Carlo simulation and soft computing","authors":"Xiaofei Jia , Qun Wei , Wenpeng Zhang , Han Wang , Liang He","doi":"10.1016/j.cpc.2025.109960","DOIUrl":"10.1016/j.cpc.2025.109960","url":null,"abstract":"<div><div>In recent years, Monte Carlo simulation has been increasingly applied as a particle-based technique for microscopic device reliability analysis. This stochastic method solves physical and mathematical problems through statistical sampling and has become instrumental in noise characterization of nanoscale field-effect transistors. However, prior simulations of channel current noise were predominantly one-dimensional and neglected quantum effects arising from dimensional scaling. Therefore, this paper proposes a two-dimensional and three-dimensional Monte Carlo simulation current noise method for metal-oxide-semiconductor field-effect transistors (MOSFET) at the nanoscale. This method is based on the list method and an approximate method for quickly processing anisotropic scattering final states; it uses the successive over-relaxation (SOR) iteration method to iteratively solve the Poisson equation for the divided grid areas, and each node applies a multi-grid method to solve the Poisson equation at each grid point within the sub-area. At the same time, the effective potential method is used to quantum-correct each grid point, and the simulation tracks the accelerated flight and random scattering motion of a group of charged particles, keeping the load on all nodes always balanced. Benchmark results demonstrate that the Monte Carlo simulation framework not only reduces overall CPU time requirements but also validates the effectiveness of predicted MOSFET noise disturbance patterns. The conclusions exhibit excellent agreement with established theories and experimental data, thereby facilitating design and reliability analysis of nanoscale field-effect transistors</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"319 ","pages":"Article 109960"},"PeriodicalIF":3.4,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145576743","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 : 2025-11-16DOI: 10.1016/j.cpc.2025.109953
Pengfei Zhao, Lei Ye, Xiaotao Xiao
The Numerical Lie Transform approach for gyrokinetic simulation has been extended to the electromagnetic model through integration with the mixed-variable and pull-back scheme. We developed a hybrid spectral semi-Lagrangian method for solving the gyrokinetic equation in toroidal geometry. The nonlinear Vlasov equation is expressed in a convective formalism aligned with unperturbed gyrocenter trajectories. Combined with toroidal spectral decomposition, this reformulation enables efficient semi-Lagrangian solutions through fixed-point interpolation method with 3D B-splines. The implemented algorithm in the NLT code facilitates electromagnetic turbulence simulations in tokamak plasmas. Verification was achieved through systematic benchmarking against electromagnetic instabilities including ion temperature gradient (ITG) modes, trapped electron modes (TEM), kinetic ballooning modes (KBM), toroidal Alfvén eigenmodes (TAE), and energetic particle-driven modes (EPM).
{"title":"Hybrid spectral semi-Lagrangian method for electromagnetic gyrokinetic simulations of Tokamak plasma","authors":"Pengfei Zhao, Lei Ye, Xiaotao Xiao","doi":"10.1016/j.cpc.2025.109953","DOIUrl":"10.1016/j.cpc.2025.109953","url":null,"abstract":"<div><div>The Numerical Lie Transform approach for gyrokinetic simulation has been extended to the electromagnetic model through integration with the mixed-variable and pull-back scheme. We developed a hybrid spectral semi-Lagrangian method for solving the gyrokinetic equation in toroidal geometry. The nonlinear Vlasov equation is expressed in a convective formalism aligned with unperturbed gyrocenter trajectories. Combined with toroidal spectral decomposition, this reformulation enables efficient semi-Lagrangian solutions through fixed-point interpolation method with 3D B-splines. The implemented algorithm in the NLT code facilitates electromagnetic turbulence simulations in tokamak plasmas. Verification was achieved through systematic benchmarking against electromagnetic instabilities including ion temperature gradient (ITG) modes, trapped electron modes (TEM), kinetic ballooning modes (KBM), toroidal Alfvén eigenmodes (TAE), and energetic particle-driven modes (EPM).</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109953"},"PeriodicalIF":3.4,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145571121","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}
This paper introduces PolyDiM, an open-source C++ library tailored for the development and implementation of polytopal discretization methods for partial differential equations. The library provides robust and modular tools to support advanced numerical techniques, with a focus on the Virtual Element Method in both 2D and 3D settings. PolyDiM is designed to address a wide range of challenging problems, including those involving non-convex geometries, domain decomposition and mixed-dimensional coupling applications. It is integrated with the geometry library GeDiM, and offers interfaces for MATLAB and Python to enhance accessibility. Distinguishing features include support for multiple polynomial bases, advanced stabilization strategies, and efficient local-to-global assembly procedures. PolyDiM aims to serve both as a research tool and a foundation for scalable scientific computing in complex geometrical settings.
{"title":"POLYDIM: A C++ library for POLYtopal DIscretization Methods","authors":"Stefano Berrone , Andrea Borio , Gioana Teora , Fabio Vicini","doi":"10.1016/j.cpc.2025.109937","DOIUrl":"10.1016/j.cpc.2025.109937","url":null,"abstract":"<div><div>This paper introduces PolyDiM, an open-source C++ library tailored for the development and implementation of polytopal discretization methods for partial differential equations. The library provides robust and modular tools to support advanced numerical techniques, with a focus on the Virtual Element Method in both 2D and 3D settings. PolyDiM is designed to address a wide range of challenging problems, including those involving non-convex geometries, domain decomposition and mixed-dimensional coupling applications. It is integrated with the geometry library GeDiM, and offers interfaces for MATLAB and Python to enhance accessibility. Distinguishing features include support for multiple polynomial bases, advanced stabilization strategies, and efficient local-to-global assembly procedures. PolyDiM aims to serve both as a research tool and a foundation for scalable scientific computing in complex geometrical settings.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109937"},"PeriodicalIF":3.4,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681670","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 : 2025-11-15DOI: 10.1016/j.cpc.2025.109950
Tyler C. Sterling
The linear combination of atomic orbitals (LCAO) method uses a small basis set in exchange for expensive matrix element calculations. The most efficient approximation for the matrix element calculations is the two-center approximation (2CA) in tight binding (TB). In the 2CA, a variety of matrix elements are neglected with only “two-center integrals” (2CI) remaining. The 2CI are calculated efficiently by rotating to symmetrical coordinates where the integral is parameterized. This makes TB fast in exchange for diminished transferability. An ideal electronic structure method has both the efficiency of TB and the transferability of ab-initio methods. In this work, I expand the full crystal potential into multipoles where the resulting matrix elements are transformed into the form of 2CI between high angular momentum functions. The usual Slater-Koster formulae for TB are limited to l ≤ 3; to enable efficient evaluation of the full crystal potential 2CI, I derive a Wigner matrix based convolution algorithm (WMCA) that works for arbitrary angular momentum. Given a suitable method for generating a local ab-initio Kohn-Sham potential, the algorithm for calculating matrix elements is applicable to fully ab-initio LCAO methods (this is the subject of forthcoming work). In this paper, I apply the WMCA to silicon using a model crystal potential.
{"title":"A Wigner matrix based convolution algorithm for matrix elements in the LCAO method","authors":"Tyler C. Sterling","doi":"10.1016/j.cpc.2025.109950","DOIUrl":"10.1016/j.cpc.2025.109950","url":null,"abstract":"<div><div>The linear combination of atomic orbitals (LCAO) method uses a small basis set in exchange for expensive matrix element calculations. The most efficient approximation for the matrix element calculations is the two-center approximation (2CA) in tight binding (TB). In the 2CA, a variety of matrix elements are neglected with only “two-center integrals” (2CI) remaining. The 2CI are calculated efficiently by rotating to symmetrical coordinates where the integral is parameterized. This makes TB fast in exchange for diminished transferability. An ideal electronic structure method has both the efficiency of TB and the transferability of ab-initio methods. In this work, I expand the full crystal potential into multipoles where the resulting matrix elements are transformed into the form of 2CI between high angular momentum functions. The usual Slater-Koster formulae for TB are limited to <em>l</em> ≤ 3; to enable efficient evaluation of the full crystal potential 2CI, I derive a Wigner matrix based convolution algorithm (WMCA) that works for arbitrary angular momentum. Given a suitable method for generating a local ab-initio Kohn-Sham potential, the algorithm for calculating matrix elements is applicable to fully ab-initio LCAO methods (this is the subject of forthcoming work). In this paper, I apply the WMCA to silicon using a model crystal potential.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109950"},"PeriodicalIF":3.4,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145555177","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 : 2025-11-14DOI: 10.1016/j.cpc.2025.109951
Amani Kiruga , Charles Cheung , Dmytro Filin , Parinaz Barakhshan , Akshay Bhosale , Vipul Badhan , Bindiya Arora , Rudolf Eigenmann , Marianna S. Safronova
We’ve developed a scalable and sustainable online atomic data portal with an automated interface for easy update and addition of new data. The current portal provides energies, transition matrix elements, transition rates, radiative lifetimes, branching ratios, polarizabilities, hyperfine constants, and other data, for 28 atoms and ions. It also features an interactive polarizability plotting interface for neutral atoms and singly-charged ions. The data production is supported by recent developments of open-access atomic software based on our research codes, including new workflow algorithms, which allow large volumes of such data to be generated with automated accuracy assessments. This entails a new method of comparing our calculated values with data from the NIST Atomic Spectra Database. All calculated values include estimated uncertainties. Data for more systems will be added in the future. Experimental values are included with references, where high-precision data are available.
{"title":"Portal for high-precision atomic data and computation","authors":"Amani Kiruga , Charles Cheung , Dmytro Filin , Parinaz Barakhshan , Akshay Bhosale , Vipul Badhan , Bindiya Arora , Rudolf Eigenmann , Marianna S. Safronova","doi":"10.1016/j.cpc.2025.109951","DOIUrl":"10.1016/j.cpc.2025.109951","url":null,"abstract":"<div><div>We’ve developed a scalable and sustainable online atomic data portal with an automated interface for easy update and addition of new data. The current portal provides energies, transition matrix elements, transition rates, radiative lifetimes, branching ratios, polarizabilities, hyperfine constants, and other data, for 28 atoms and ions. It also features an interactive polarizability plotting interface for neutral atoms and singly-charged ions. The data production is supported by recent developments of open-access atomic software based on our research codes, including new workflow algorithms, which allow large volumes of such data to be generated with automated accuracy assessments. This entails a new method of comparing our calculated values with data from the NIST Atomic Spectra Database. All calculated values include estimated uncertainties. Data for more systems will be added in the future. Experimental values are included with references, where high-precision data are available.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"319 ","pages":"Article 109951"},"PeriodicalIF":3.4,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145576712","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 : 2025-11-14DOI: 10.1016/j.cpc.2025.109947
Daniela Moreno-Chaparro , Florencio Balboa Usabiaga , Nicolas Moreno , Marco Ellero
Fluid-structure interactions are commonly modeled using no-slip boundary conditions. However, small deviations from these conditions can significantly alter the dynamics of suspensions and particles, especially at the micro and nano scales. This work presents a robust implicit solvent method for simulating non-colloidal suspensions with non-homogeneous Navier slip boundary conditions. Our approach is based on a regularized boundary integral formulation, enabling accurate and efficient computation of hydrodynamic interactions. This makes the method well-suited for large-scale simulations. We validate the method by comparing computed drag forces on homogeneous and Janus particles with analytical results. Additionally, we consider the effective viscosity of suspensions with varying slip lengths, benchmarking against available analytical no-slip and partial-slip theories.
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