Computer Physics Communications

We introduce a lattice dynamics package which calculates elastic, thermodynamic and thermal transport properties of crystalline materials from data on their force and potential energy as a function of atomic positions. The data can come from density functional theory (DFT) calculations or classical molecular dynamics runs performed in a supercell. First, the model potential parameters, which are anharmonic force constants are extracted from the latter runs. Then, once the anharmonic model is defined, thermal conductivity and equilibrium properties at finite temperatures can be computed using lattice dynamics, Boltzmann transport theories, and a variational principle respectively. In addition, the software calculates the mechanical properties such as elastic tensor, Gruneisen parameters and the thermal expansion coefficient within the quasi-harmonic approximation (QHA). Phonons, elastic constants and thermodynamic properties results applied to the germanium crystal will be illustrated. Using the force constants as a force field, one may also perform molecular dynamics (MD) simulations in order to investigate the combined effects of anharmonicity and defect scattering beyond perturbation theory.

We detail our implementation of the random-phase-approximation based functional (RPAF) derived in Ref. [1] for the QUANTUM ESPRESSO (QE) package. We also make available in the Computer Physics Communications library the source files which are required in order to apply this functional within QE. We also provide the corresponding RPAF projector augmented wave (PAW) and ultrasoft pseudopotentials for most elements. Lastly, we benchmark the performance of the RPAF by calculating the equilibrium lattice constant and bulk modulus of a set of the same 60 crystals used by other authors to benchmark other functionals for both PAW and ultrasoft pseudopotentials. We find that the RPAF performs better overall as compared to the other most popular functionals.

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.