Computer Physics Communications

SDGMPS is a Fortran program that calculates differential cross sections of elastic proton-nucleus scattering at intermediate energies based on the spin-dependent Glauber model. In the program, the Glauber model explicitly takes into account spin effects by using the spin-dependent nucleon-nucleon scattering amplitude, where the spin-orbit amplitude parameters are needed as input. It is particularly useful for analyses of the elastic proton scattering at both low and high momentum transfers and studies of the inner density distributions in nuclei. Such studies are an important part of the physics research program of the radiation beam facilities, such as the Heavy Ion Research Facility in Lanzhou (HIRFL).

A new parallelized simulation code is presented, which uses a Monte Carlo method to determine particle spectra in the KATRIN source. Reaction chains are generated from the decay of tritium within the source. The code includes all relevant processes: elastic scattering, ionization, excitation (electric, vibrational, rotational), recombination and various clustering processes. The main emphasis of the code is the calculation of particle spectra and particle densities and currents at specific points within the source. It features a new technique to determine these quantities. It also calculates target fields for the interaction of particles with each other as it is needed for recombination processes. The code has been designed for the KATRIN experiment but is easily adaptable for other tritium based experiments like Project 8. Geometry and background tritium gas flow can be given as user input. The code is parallelized using MPI and writes output using HDF5. Input to the simulation is read from a JSON description.

We present an efficient solver for massively-parallel simulations of convective, wall-bounded and incompressible porous media flows. The algorithm consists of a second-order finite-difference pressure-correction scheme, allowing the use of an efficient FFT-based solver in problems with different boundary conditions. The parallelization method is implemented in a two-dimensional pencil-like domain decomposition, which enables efficient parallel large-scale simulations. The original version of the code presented by van der Poel et al. (2015) [35] has been modified to solve the Darcy equation for the momentum transport, representative of porous media flows driven by buoyancy. Two schemes are implemented to treat the diffusive term of the advection-diffusion equation, namely a fully implicit and semi-implicit formulation. Despite exhibiting a higher computational cost per time step, the fully implicit scheme allows an efficient simulation of transient flows, leading to a smaller time-to-solution compared to the semi-implicit scheme. The implementation was verified against different canonical flows, and the computational performance was examined. To show the code's capabilities, the maximal driving strength explored has been doubled as compared to state-of-art simulations, corresponding to an increase of the associated computational effort of about 8 to 16 times. Excellent strong scaling performance is demonstrated for both schemes developed and for domains with more than 10^10 spatial degrees of freedom.

We present PolyMorph, a lightweight standalone C++ program that extends its predecessor PolyHoop by a finite-difference solver for multi-component reaction-advection-diffusion equations. PolyMorph simulates two integral parts of tissue morphogenesis in two dimensions: 1) the mechanics of cellular deformation, growth and proliferation, and 2) transport and reaction of an arbitrary number of chemical species. Both of these components are bidirectionally coupled, allowing cells to base their behavior on local information on concentrations and flow, and allowing the chemical transport and reaction kinetics to depend on spatial information such as the local cell type. This bidirectional feedback makes PolyMorph a versatile tool to study a variety of cellular morphogenetic processes such as chemotaxis, cell sorting, tissue patterning with morphogen gradients, Turing patterning, and diffusion- or supply-limited growth with sub-cellular resolution.

We introduce COLOSS, a program designed to address the scattering problem using a bound-state technique known as complex scaling. In this method, the oscillatory boundary conditions of the wave function are transformed into exponentially decaying ones, accommodating the long-range Coulomb interaction. The program implements the general local optical potential and the Perey-Buck non-local optical potential, with all potential parameters included in a well-designed input format for ease of use. The design offers users direct access to compute S-matrices and cross-sections for scattering processes involving a projectile of any spin interacting with a spin-0 target. We provide thorough discussions on the precision of Lagrange functions and their benefits in evaluating matrix elements. Additionally, COLOSS incorporates two distinct rotation methods, making it adaptable to potentials without analytical expressions. Comparative results demonstrate that COLOSS achieves high accuracy when compared with the direct integration method, Numerov, underscoring its utility and effectiveness in scattering calculations.

We present an extensive review of the two-dimensional finite difference Hartree–Fock (FD HF) method, and present its implementation in the newest version of x2dhf, the FD HF program for atoms and diatomic molecules. The program was originally published in this journal in 1996, and was last revised in 2013. x2dhf can be used to obtain HF limit values of total energies and multipole moments for a wide range of diatomic molecules and their ions, using either point nuclei or a finite nuclear model. Polarizabilities (α_zz) and hyperpolarizabilities (β_zzz, γ_zzzz, A_z,zz, B_zz,zz) can also be computed by the program with the finite-field method. x2dhf has been extensively used in the literature to assess the accuracy of existing atomic basis sets and to help in developing new ones. As a new feature since the last revision, the program can now also perform Kohn–Sham density functional calculations with local and generalized gradient exchange-correlation functionals with the Libxc library of density functionals, enabling new types of studies. Furthermore, the initialization of calculations has been greatly simplified. As before, x2dhf can also perform one-particle calculations with (smooth) Coulomb, Green–Sellin–Zachor and Krammers–Henneberger potentials, while calculations with a superposition of atomic potentials have been added as a new feature. The program is easy to install from the GitHub repository and build via CMake using the x2dhfctl script that facilitates creating its single- and multiple-threaded versions, as well as building in Libxc support. Calculations can be carried out with x2dhf in double- or quadruple-precision arithmetic.

The calculation of irreducible (co-)representations of energy bands at high-symmetry points (HSPs) is essential for high-throughput research on topological materials based on symmetry-indicators or topological quantum chemistry. However, existing computational packages usually require transforming crystal structures adapted to specific conventions, thus hindering extensive application, especially to materials whose symmetries are yet to be identified. To address this issue, we developed a Mathematica package, ToMSGKpoint, capable of determining the little groups and irreducible (co-)representations of little groups of HSPs, high-symmetry lines (HSLs), and high-symmetry planes (HSPLs) for any nonmagnetic and magnetic crystalline materials in two and three dimensions, with or without considering spin-orbit coupling. To the best of our knowledge, this is the first package to achieve such functionality. The package also provides magnetic space group operations, supports the analysis of irreducible (co-)representations of energy bands at HSPs, HSLs, and HSPLs using electronic wavefunctions obtained from ab initio calculations interfaced with VASP. Designed for user convenience, the package generates results in a few simple steps and presents all relevant information in a clear tabular format. Its versatility is demonstrated through applications to nonmagnetic topological insulator Bi2Se3 and Dirac semimetal Na3Bi, as well as the antiferromagnetic topological material MnBi2Te4. Suitable for any crystal structure, this package can be conveniently applied in a streamlined study once magnetic space group varies with various symmetry-breakings caused by phase transitions.

The dynamics of light-matter interactions in the realm of strong-field ionization has been a focal point and has attracted widespread interest. We present the eTraj.jl program package, designed to implement established classical/semiclassical trajectory-based methods to determine the photoelectron momentum distribution resulting from strong-field ionization of both atoms and molecules. The program operates within a unified theoretical framework that separates the trajectory-based computation into two stages: initial-condition preparation and trajectory evolution. For initial-condition preparation, we provide several methods, including the Strong-Field Approximation with Saddle-Point Approximation (SFA-SPA), SFA-SPA with Non-adiabatic Expansion (SFA-SPANE), and the Ammosov-Delone-Krainov theory (ADK), with atomic and molecular variants, as well as the Weak-Field Asymptotic Theory (WFAT) for molecules. For trajectory evolution, available options are Classical Trajectory Monte-Carlo (CTMC), which employs purely classical electron trajectories, and the Quantum Trajectory Monte-Carlo (QTMC) and Semi-Classical Two-Step model (SCTS), which include the quantum phase during trajectory evolution. The program is a versatile, efficient, flexible, and out-of-the-box solution for trajectory-based simulations for strong-field ionization. It is designed with user-friendliness in mind and is expected to serve as a valuable and powerful tool for the community of strong-field physics.

PyFR is an open-source cross-platform computational fluid dynamics framework based on the high-order Flux Reconstruction approach, specifically designed for undertaking high-accuracy scale-resolving simulations in the vicinity of complex engineering geometries. Since the initial release of PyFR v0.1.0 in 2013, a range of new capabilities have been added to the framework, with a view to enabling industrial adoption. In this work, we provide details of these enhancements as released in PyFR v2.0.3, including improvements to cross-platform performance (new backends, extensions of the DSL, new matrix multiplication providers, improvements to the data layout, use of task graphs) and improvements to numerical stability (modal filtering, anti-aliasing, artificial viscosity, entropy filtering), as well as the addition of prismatic, tetrahedral and pyramid shaped elements, improved domain decomposition support for mixed element grids, improved handling of curved element meshes, the addition of an adaptive time-stepping capability, the addition of incompressible Euler and Navier-Stokes solvers, improvements to file formats and the development of a plugin architecture. We also explain efforts to grow an engaged developer and user community and provided a range of examples that show how our user base is applying PyFR to solve a wide range of fundamental, applied and industrial flow problems. Finally, we demonstrate the accuracy of PyFR v2.0.3 for a supersonic Taylor-Green vortex case, with shocks and turbulence, and provided latest performance and scaling results on up to 1024 AMD Instinct MI250X accelerators of Frontier at ORNL (each with two GCDs) and up to 2048 Nvidia GH200 GPUs of Alps at CSCS. We note that absolute performance of PyFR accounting for the totality of both hardware and software improvements has, conservatively, increased by almost 50× over the last decade.

Recent improvements in the ZKCM and ZKCM_QC libraries are presented in this announcement. ZKCM was released as a C++ library for multiprecision matrix computation and ZKCM_QC was developed as its extension for matrix-product-state (MPS) simulation of quantum circuits. Their parallel processing extensions using OpenMP and CUDA were briefly reported in a previous contribution [A. SaiToh, to appear in Proc. CCP2023]. Here, their most recent developments are reported, which include the employments of advanced FFT and Moore-Penrose inverse routines. The previous version of this program (AEPI_v1_0) may be found here https://doi.org/10.1016/j.cpc.2013.03.022.