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Computer Physics Communications

ISSN: 0010-4655

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Datasets associated with articles published in Computer Physics Communications

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  • JRAF: A Julia package for computation of relativistic molecular auxiliary functions
    The evaluation of relativistic molecular integrals over exponential−type spinor orbitals requires the use of relativistic auxiliary functions in prolate spheroidal coordinates, and has been recently achieved (Bağcı and Hoggan (2015) [14]). This process is used in the solution of the molecular Dirac equation for electrons moving in a Coulomb potential. A series of papers on a method for fully analytical evaluation of relativistic auxiliary functions has been published [2, 3, 4] From the perspective of computational physics, these studies demonstrate how to deal with the integrals of the product of power functions with non−integer exponents and incomplete gamma functions. The computer program package used to calculate these auxiliary functions with high accuracy is presented. It is designed using the Julia programming language and yields highly accurate results for molecular integrals over a wide range of orbital parameters and quantum numbers. Additionally, the program package facilitates the efficient calculation of the angular momentum coefficients that arise from the product of two normalized Legendre functions centered at different atomic positions, and the determination of the rotation angular functions used for both complex and real spherical harmonics. Sample calculations are performed for two−center one−electron integrals over non−integer Slater−type orbitals, and the results prove the robustness of the package.
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  • ElasT: A toolkit for thermoelastic calculations
    A toolkit that simplifies the calculation of solid-state elastic properties at finite temperatures to a one-shot task is developed. We report the improvement and automation of the stress-strain method, which relies on the averaged stresses from ab initio or classical calculations. Stresses obtained from strained crystal lattices at zero and finite temperatures can be directly extracted to fit the strain-stress relationship and get the elastic constants. Furthermore, the finite-temperature elastic constants can also be obtained by solving a system of overdetermined linear equations directly under constant pressure dynamics (NPT, NPH, etc.) within the stress-strain method, which does not require the equilibrated lattice as a prior condition. It is shown that the elastic constants converge quickly in constant pressure dynamics. This approach proves to be robust and can significantly reduce computational cost.
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  • Medical module for Hyper-Fractal Analysis
    In Grossu (2022) [1] it was discussed the migration of Hyper-Fractal Analysis from Visual Basic 6 to C# .Net. The main goal of current work was developing a medical module for fractal analysis of computed tomography multi-channel images. A new tool for comparing images by RGB channels superposition was also considered. This could be of particular interest in medical image analysis (e.g. compare native with contrast CT slices).
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  • Pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries
    Creating and maintaining computer-readable geometries for use in Monte Carlo Radiation Transport (MCRT) simulations is an error-prone and time-consuming task. Simulating a system often requires geometry from different sources and modelling environments, including a range of MCRT codes and computer-aided design (CAD) tools. Pyg4ometry is a Python library that enables users to rapidly create, manipulate, display, debug, read, and write Geometry Description Markup Language (GDML)-based geometry used in MCRT simulations. Pyg4ometry provides importation of CAD files to GDML tessellated solids, conversion of GDML geometry to FLUKA and conversely from FLUKA to GDML. The implementation of Pyg4ometry is explained in detail in this paper and includes a number of small examples to demonstrate some of its capabilities. The paper concludes with a complete example using most of Pyg4ometry's features and a discussion of possible extensions and future work.
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  • GETaLM: A generator for electron tagger and luminosity monitor for electron - proton and ion collisions
    The study of elastic bremsstrahlung and electron tagging in electron-proton or ion collisions is gaining importance with the planned construction of several experimental facilities focused on deep-inelastic scattering (DIS) measurements. This paper describes a program which generates bremsstrahlung photons in electron-proton and electron-ion interactions as well as scattered electrons in bremsstrahlung processes and in a quasi-real photon approximation to the general DIS process. The effects of electron beam divergence and the spread of the interaction vertex are implemented. The program can be used as an input to simulations of instrumentation for bremsstrahlung photon detection, luminosity measurements, electron tagging, and the determination of the cross sections of corresponding processes.
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  • Code O-SUKI-N 3D: Upgraded direct-drive fuel target 3D implosion code in heavy ion inertial fusion
    The Code O-SUKI-N 3D is an upgraded version of the 2D Code O-SUKI (Sato et al., 2019 [1]). Code O-SUKI-N 3D is an integrated 3-dimensional (3D) simulation program system for fuel implosion, ignition and burning of a direct-drive nuclear-fusion pellet in heavy ion beam (HIB) inertial confinement fusion (HIF). The Code O-SUKI-N 3D consists of the three programs of Lagrangian fluid implosion program, data conversion program, and Euler fluid implosion, ignition and burning program. The Code O-SUKI-N 3D can also couple with the HIB illumination and energy deposition program of OK3 (Ogoyski et al., 2010 [8]). The spherical target implosion 3D behavior is computed by the 3D Lagrangian fluid code until the time just before the void closure of the fuel implosion. After that, all the data by the Lagrangian implosion code are converted to the data for the 3D Eulerian code. In the 3D Euler code, the DT fuel compression at the stagnation, ignition and burning are computed. The Code O-SUKI-N 3D simulation system provides a capability to compute and to study the HIF target implosion dynamics.
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  • Real-fluid thermophysicalModels: An OpenFOAM-based library for reacting flow simulations at high pressure
    Although OpenFOAM is a widely-used open source computational fluid dynamics (CFD) tool, it is limited to numerical simulations of multi-dimensional reacting/nonreacting flows at relatively-low pressures. This is not only because real-fluid models that can evaluate thermophysical properties at high pressures are not available in the thermophysicalModels library of OpenFOAM, but also because the existing mixing model cannot handle various mixing rules of real-fluid models. In the present study, we develop a novel algorithm applicable for a mixture model incorporating various mixing rules in OpenFOAM. Based on the new algorithm, we update the thermophysicalModels library of OpenFOAM 6.0 by implementing a set of real-fluid models such as the Soave-Redlich-Kwong/Peng-Robinson equation of state, Chung's model for dynamic viscosity and thermal conductivity, mixture averaged model for mass diffusivity using Takahashi's correction for binary diffusion coefficients at high pressure. The new library is validated against experimental data and is further assessed for compressible reacting flows by performing two-dimensional numerical simulations of axisymmetric laminar non-premixed counterflow flames and one-dimensional numerical simulations of premixed CH_4/air flames at high pressures. The developed library can be used for any reacting flow solvers in OpenFOAM 6.0 that adopt a set of implemented real-fluid models.
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  • EDIpack: A parallel exact diagonalization package for quantum impurity problems
    We present EDIpack, an exact diagonalization package to solve generic quantum impurity problems. The algorithm includes a generalization of the look-up method introduced in Ref. [1] and enables a massively parallel execution of the matrix-vector linear operations required by Lanczos and Arnoldi algorithms. We show that a suitable Fock basis organization is crucial to optimize the inter-processors communication in a distributed memory setup and to reach sub-linear scaling in sufficiently large systems. We discuss the algorithm in details indicating how to deal with multiple orbitals and electron-phonon coupling. Finally, we outline the download, installation and functioning of the package.
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  • Automated tip functionalization via machine learning in scanning probe microscopy
    Auto-CO-AFM is an open-source software package for scanning probe microscopes that enables the automatic functionalization of scanning probe tips with carbon monoxide molecules. This enables machine operators to specify the quality of the tip needed utilizing a pre-trained library with off-the-shelf software. From a single image, the software package can determine which molecules on a surface are carbon monoxide, perform the necessary tip functionalization procedures, interface with microscope software to control the tip position, and determines the centeredness of the tip after a successful functionalization. This is of particular interest for atomic force microscopy imaging of molecules on surfaces, where the tip functionalization is a necessary and time consuming step needed for sub-molecular resolution imaging. This package is freely available under the MIT License.
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  • A brute-force code searching for cell of non-identical displacement for CSL grain boundaries and interfaces
    Atomic simulation of coincidence-site lattice (CSL) grain boundaries (GBs) and interfaces is of importance for understanding GBs in polycrystalline materials and for making functional films. A common process of high-throughput simulation for CSL GBs and interfaces is to explore rigid body translation (RBT) of one crystal respect to the other. Cell of non-identical displacement (CNID) is the minimum cell including all non-identical RBTs in the GB or interface plane and is important for effective sampling. This work proposes an algorithm to compute the CNID of any two-dimensional CSL GB or interface based on a reciprocity relation between the displacement shift complete (DSC) and CSL.
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