Computer Physics Communications

We present NAVIS (NAnochannel Velocity and thermal Interfacial Slip), a LAMMPS-Python scripted toolkit for computing the Navier (hydrodynamic) friction coefficient and Kapitza (thermal) resistance at arbitrary solid-fluid interfaces. NAVIS is based on equilibrium molecular dynamics (EMD) methods for calculating the linear response friction and thermal resistance at the interface, as well as the corresponding velocity and temperature slips. The methodology is based on our previous studies (Hansen, et al., Phys. Rev. E 84, 016,313 (2011); Varghese et al., J. Chem. Phys. 154, 184,707 (2021); Alosious, et al., J. Chem. Phys. 151, 194,502 (2019); Alosious, et al., Langmuir 37, 2355–2361 (2021)), and in this work we provide a pedagogical framework for the implementation of this toolkit on two systems: (i) a water-graphene system (for hydrodynamic slip) and (ii) a water-CNT system (for thermal slip). We provide detailed instructions for performing the EMD simulations using the LAMMPS package and processing the simulation outputs using Python modules to obtain the desired quantities of interest. We expect the toolkit to be useful for computational researchers studying interfacial friction and thermal transport, key factors for efficient and practical applications of nanofluidic systems.

We present BRAHMS, a cross-platform (Linux/Windows) graphical user interface, with GPU (CUDA) and CPU (OpenMP) backends, for the efficient and accurate simulation of three-wave mixing processes involving focused and pulsed Gaussian beams. The package solves the coupled 𝜒^(2) nonlinear Schrödinger equations, including diffraction, dispersion, walk-off, and phase-mismatch effects simultaneously, in full (3+1)D. To our knowledge, this is the first open-source package that solves the complete second-order (three-wave-mixing) nonlinear-optics problem in (3+1)D while fully exploiting the parallel capabilities of modern GPUs, with an equivalent CPU backend available for users without GPU hardware. The GPU implementation is inherently scalable thanks to its Thrust-based design. The package provides a valuable tool for experimental design and for studying three-dimensional field propagation in nonlinear three-wave interactions, supporting applications such as second-harmonic generation (SHG), sum-frequency generation (SFG), and optical parametric generation (OPG). Its GUI requires no programming experience, so that users can readily set up simulations and interpret their results.

Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are computationally intensive. We introduce exaPD, a user-friendly workflow that enables simultaneous sampling of multiple phases across a fine mesh of temperature and composition for free energy calculations. The package employs standard molecular dynamics (MD) and Monte Carlo (MC) sampling techniques, as implemented in the LAMMPS package. Various interatomic potentials are supported, including the neural network potentials with near ab initio accuracy. A global controller, built with Parsl, manages the MD/MC jobs to achieve massive parallelization with near ideal scalability. The resulting free energies of both liquid and solid phases, including solid solutions, are integrated into CALPHAD modeling using the PYCALPHAD package for constructing the phase diagram.

The Fortran program qsolver is designed to solve a system of coupled radial Schrödinger equations for both bound and resonant (quasi-bound) energy levels. To search for energies and widths of resonant states, the program utilizes the exterior complex scaling method. The potential-energy matrix V(r) and the optional radial-coupling matrix B(r) are supplied by the user as either real or complex functions of the radial coordinate r. For resonant-state calculations qsolver can also automatically extrapolate the real-valued multiplicative Vmn(r) and Bmn(r) functions into the complex plane. An exact analytical transformation 𝑥=𝑓⁡(𝑟) maps the modified coupled-channel (CC) equations from a semi-infinite r ∈ [a, ∞) or infinite 𝑟 ∈ (−∞,+∞) interval onto a finite domain x ∈ [a, b], enabling their numerical solution via polynomial collocation methods that exhibit an exponential convergence rate. The program is able to identify spurious (”ghost”) resonant states by examining their eigenfunctions in a spectral basis as well as to evaluate partial derivatives of both real and complex eigenvalues with respect to Hamiltonian parameters, including the reduced mass μ. Built around a modern Fortran 2003 interface in which most arguments are optional, qsolver is straightforward to use and to incorporate into the user’s code. The qsolver program can effectively find energies and widths of the resonant states with an accuracy of up to 13-14 significant digits in double-precision (real*8) arithmetic, as confirmed by numerical tests.

Reliable time-domain nanoplasmonic calculations require separate verification of the dispersive material model, explicit field update, charge bookkeeping, electromagnetic normalization, boundary treatment and spatial refinement. We present NanoTD-Audit, a documented validation package for local Drude–Lorentz auxiliary-differential-equation finite-difference time-domain (ADE–FDTD) calculations, with separate component diagnostics for hard-wall hydrodynamic Drude-model (HDM) and quantum-corrected-model (QCM) extensions. The supplied three-dimensional solver implements the local-response branch only; it contains neither a finite-geometry hard-wall HDM update nor a QCM gap-current or coupled HDM–QCM nanogap solver. The package combines a nonnegative-residue gold fit, explicit Yee/ADE update and stability checks, a four-level local-Au sphere FDTD–Mie audit on one common physical configuration whose boundary sensitivity is independently checked at ℎ=12nm, acquisition-window and Courant studies, an operator-consistent Gauss-law audit, and a closed source-free, absorber-free bulk Yee/ADE energy audit. Over 480–820 nm, the finest ℎ=4.5nm sphere errors are 3.31%, 13.76% and 11.18% for extinction, absorption and scattering, respectively; scattering is already plateaued between 6 and 4.5 nm, so neither asymptotic convergence nor the proposed two-percent predictive gate is claimed. The literature QCM table is retained only as a geometry-integrated effective metric carrying the source-reported S/m label, not as an independently established three-dimensional pointwise constitutive conductivity. NanoTD-Audit is therefore a reproducible local-response verification tool with separate HDM and QCM diagnostics rather than a full nonlocal-tunnelling solver.

Bayesian optimization (BO) is widely used to accelerate physics and materials research, where objective function evaluations are computationally or experimentally expensive. While many BO frameworks focus on algorithmic efficiency, practical usability and portability are equally critical for sustained use in real research environments. PHYSBO is a Bayesian optimization library designed to address these needs by enabling optimization over user-defined candidate pools and by supporting domain-specific problem settings. This paper presents the major updates introduced in PHYSBO versions 2 and 3, with a focus on improvements in usability, portability, and practical deployment rather than on new optimization algorithms. In PHYSBO version 2, the software license was changed from GPL to MPL to improve compatibility with a wider range of research and software ecosystems. Building on this revision, PHYSBO version 3 introduces a set of implementation-oriented updates aimed at improving usability and portability, without modifying the core optimization algorithms. These updates include improvements in computational performance and scalability, extended support for multi-objective optimization, the introduction of range-based policies for continuous-variable optimization, the removal of environment-dependent components such as tightly coupled Cython modules, and compatibility with NumPy 2. These improvements reduce the technical and organizational burden on users, enabling PHYSBO to be deployed across diverse computing environments and research workflows. By emphasizing portability and ease of integration while maintaining sufficient performance, PHYSBO version 3 is positioned as a sustainable research infrastructure for Bayesian optimization in physics and materials science.

We present BCA_modern, an open-source Python code for simulating low-energy ion scattering (LEIS) from crystalline surfaces using the binary collision approximation. The code implements pair-specific NLH interatomic potentials [1] for 70 ion–atom combinations (He+, Ne+, Ar+, Kr+, Xe+ on 14 target elements), position-dependent electronic stopping 𝑆𝑒 ⁡(𝑣, 𝜌), thermal lattice vibrations, and Hagstrum ion neutralisation. A universal crystal structure module supports 35 built-in structures (zincblende, wurtzite, rocksalt, corundum, cristobalite, FCC metals, BCC metals, diamond cubic), disordered alloys via partial site occupation, and CIF file input. A simulation with automatically generated material and model parameters can be initialised from three required inputs—ion atomic number, crystal name and beam energy—while the beam geometry, temperature, trajectory count and detector acceptance remain user-configurable and must be set to reproduce a specific experiment. We validate the code through: (i) kinematic factor verification yielding machine-precision agreement for 54 ion–target pairs; (ii) backscattering spectra for He+ → CaSiO3 under the normal-incidence, 145∘-detector geometry of a recent BCA/experiment study, recovering spectral features at the single-collision kinematic energies of Ca, Si, and O; (iii) statistical convergence analysis demonstrating ∼1% precision at 5000 trajectories; and (iv) comparison with published experimental LEIS conditions for He+ → Au and Cu at normal incidence, showing peak position agreement within 1% of the kinematic prediction. Applications to GaP, CdTe, GaAs, and Al2O3 are presented; a companion study applies the same code to detector-induced distortions in low-energy ion scattering [2].

Accurate electrochemical-thermal simulation of lithium-ion batteries (LIBs) is critical for improving performance, ensuring safety, and extending service life. However, conventional pseudo-two-dimensional (P2D) models often fail to capture in-plane inhomogeneities, particularly in large-format pouch cells, due to geometric simplifications. {While pseudo-four-dimensional (P4D) models can resolve such effects, their practical use is limited by the high computational cost associated with nonlinear iterative solution procedures.} {This study introduces a non-iterative electrochemical–thermal solution framework} based on a pseudo-four-dimensional (P4D) modeling approach, which incorporates full three-dimensional (3D) spatial resolution alongside a pseudo-dimension representing intra-particle lithium diffusion, enabling high-fidelity analysis of internal gradients in large-format LIBs. To mitigate the computational burden of P4D simulations, an efficient non-iterative numerical scheme is developed by combining staggered time integration, Taylor-series-based linearization, and an adaptive time-stepping strategy guided by output gradients. {The governing equations are reformulated into a sequence of linear subsystems, allowing the coupled system to be solved without nonlinear iterations.} Validation against experimental discharge data and commercial finite element simulations demonstrates that the proposed method achieves comparable accuracy while reducing computational time by up to 5-fold. The proposed method is further applied to analyze spatial inhomogeneities in large-format pouch cells under varying aspect ratios and charging conditions. Results show that spatial gradients in electrolyte concentration, electrode overpotential, and interfacial reaction rates become increasingly pronounced with larger cell geometries and higher C-rates. These in-plane non-uniformities significantly influence voltage dynamics and remain unresolved in lower-dimensional models such as the P2D model. In particular, the P4D framework enables precise identification of localized regions susceptible to lithium plating–insights inaccessible in conventional modeling approaches. {Overall, the results demonstrate that the proposed non-iterative framework enables efficient and scalable high-fidelity P4D simulations, providing a practical pathway for the design and analysis of large-format lithium-ion batteries.}

As ion irradiation techniques have increasingly extended from three-dimensional (3D) bulk targets to low-dimensional nanomaterials, there is a growing need for developing an efficient tool capable of simulating ion irradiation for materials of different dimensionalities. Here, we present a general framework ASIM (Atomic-scale Simulation on Ion Irradiation of Matter) to achieve full-cascade ion irradiation simulations of multi-dimensional systems, ranging from micrometer-scale 3D bulk to nanoscale two-dimensional (2D) one-dimensional (1D) and zero-dimensional (0D) structures, as well as their combined geometries. Based on binary collision approximation (BCA), ASIM describes both nuclear and electronic stopping, and simultaneous collision is also explicitly included. Importantly, ASIM offers a high degree of flexibility with a modular design, allowing variable displacement thresholds and customized irradiation conditions. The predictive accuracy is demonstrated by systematic comparisons with available experimental results and molecular dynamics calculations for irradiation of silicon, free-standing/supported graphene, carbon nanotube and fullerene with various incident ions, showing excellent agreement. We expect the developed framework to provide an attractive and versatile platform for interpreting, optimizing and designing irradiation-driven defect engineering strategies in emerging nanoscale materials and devices.

We describe libwignernj, a freely available, BSD-licensed library that evaluates Wigner 3j, 6j, and 9j symbols, Clebsch–Gordan, Racah W, Fano X, and Gaunt coefficients over both complex and real spherical harmonics in standards-compliant C99. libwignernj represents factorials by the vector of their signed prime-exponent decomposition—a prime-factorization technique introduced for the angular-momentum coefficients by Dodds and Wiechers (Comput.\ Phys.\ Commun.\ 4, 268 (1972)) and refined in a long line of subsequent work—and combines that representation with the multiword-integer Racah sum of Johansson and Forss\'en (SIAM J.\ Sci.\ Comput.\ 38, A376 (2016)), under which every intermediate quantity is an exact rational and all rounding is confined to the final floating-point conversion. Single-, double-, and long-double-precision results are correct to the last representable bit, and IEEE 754 binary128 evaluation through libquadmath and arbitrary-precision evaluation through the GNU Multiple-Precision Floating-Point Reliable (MPFR) library are optionally exposed. libwignernj has no mandatory runtime dependencies and no caller-side initialization step, making it easy to embed across the atomic, molecular, nuclear, and electromagnetic-scattering applications in which these coefficients arise. C++, CPython, and Fortran 90 bindings ship alongside the C library. Half-integer angular momenta are encoded exactly via integer 2⁢𝑗 arguments throughout the application programming interface (API). CMake-package and pkg-config files ship for drop-in integration into downstream projects, and a continuous-integration (CI) pipeline runs the full test suite on Linux (shared and static), macOS, and Windows on every push.