Computer Physics Communications - Mendeley Data (2022)

  • KSSOLV 2.0: An efficient MATLAB toolbox for solving the Kohn-Sham equations with plane-wave basis set

    Shizhe Jiao, Zhenlin Zhang, Kai Wu, Lingyun Wan, Huanhuan Ma et al

    Published 25 July 2022 | Mendeley Data

    KSSOLV (Kohn-Sham Solver) is a MATLAB toolbox for performing Kohn-Sham density functional theory (DFT) calculations with a plane-wave basis set. KSSOLV 2.0 preserves the design features of the original KSSOLV software to allow users and developers to easily set up a problem and perform ground-state calculations as well as to prototype and test new algorithms. Furthermore, it includes new functionalities such as new iterative diagonalization algorithms, k-point sampling for electron band structures, geometry optimization and advanced algorithms for performing DFT calculations with local, semi-local, and hybrid exchange-correlation functionals. It can be used to study the electronic structures of both molecules and solids. We describe these new capabilities in this work through a few use cases. We also demonstrate the numerical accuracy and computational efficiency of KSSOLV on a variety of examples.

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  • HP – A code for the calculation of Hubbard parameters using density-functional perturbation theory

    Iurii Timrov, Nicola Marzari, Matteo Cococcioni

    Published 25 July 2022 | Mendeley Data

    We introduce HP, an implementation of density-functional perturbation theory, designed to compute Hubbard parameters (on-site U and inter-site V) in the framework of DFT+U and DFT+U+V. The code does not require the use of computationally expensive supercells of the traditional linear-response approach; instead, unit cells are used with monochromatic perturbations that significantly reduce the computational cost of determining Hubbard parameters. HP is an open-source software distributed under the terms of the GPL as a component of Quantum ESPRESSO. As with other components, HP is optimized to run on a variety of different platforms, from laptops to massively parallel architectures, using native mathematical libraries (LAPACK and FFTW) and a hierarchy of custom parallelization layers built on top of MPI. The effectiveness of the code is showcased by computing Hubbard parameters self-consistently for the phospho-olivine LixMn1/2Fe1/2PO4 (x = 0, 1/2, 1) and by highlighting the accuracy of predictions of the geometry and Li intercalation voltages.

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  • DAMQT 3: Advanced suite for the analysis of molecular density and related properties in large systems

    Anmol Kumar, Rafael Lopez, Frank Martínez, Guillermo Ramírez, Ignacio Ema et al

    Published 25 July 2022 | Mendeley Data

    A new version of the DAMQT package specially developed for large systems is reported. The graphical part has been entirely redesigned, using new OpenGL libraries (versions 3.3 or higher) for 3D display. Several 2D plotters and 3D viewers can be launched now in the same session and more than one molecule can be loaded in the same 3D window. Algorithms have been rescaled and modified to work with densities coming from ZDO computations in very big molecular systems (up to thousands of atoms) at a very moderate cost. New functionalities have been added including computation of molecular electrostatic potential over a molecular surface determined as a user-defined density isosurface. The method of Electrostatics for Intermolecular Complexation has been added to the package to serve as an auxiliary tool for cluster geometry optimization. Examples are provided which prove the good performance of the algorithms.

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  • Parallelized discrete exterior calculus for three-dimensional elliptic problems

    Pieter Boom, Ashley Seepujak, Odysseas Kosmas, Lee Margetts, Andrey Jivkov

    Published 25 July 2022 | Mendeley Data

    A formulation of elliptic boundary value problems is used to develop the first discrete exterior calculus (DEC) library for massively parallel computations with 3D domains. This can be used for steady-state analysis of any physical process driven by the gradient of a scalar quantity, e.g. temperature, concentration, pressure or electric potential, and is easily extendable to transient analysis. In addition to offering this library to the community, we demonstrate one important benefit from the DEC formulation: effortless introduction of strong heterogeneities and discontinuities. These are typical for real materials, but challenging for widely used domain discretization schemes, such as finite elements. Specifically, we demonstrate the efficiency of the method for calculating the evolution of thermal conductivity of a solid with a growing crack population. Future development of the library will deal with transient problems, and more importantly with processes driven by gradients of vector quantities.

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  • Gaussian dispersion analysis in the time domain: Efficient conversion with Padé approximants

    Ludmila Prokopeva, Samuel Peana, Alexander V. Kildishev

    Published 20 July 2022 | Mendeley Data

    We present an approach for adapting the Gaussian dispersion analysis (GDA) of optical materials to time-domain simulations. Within a GDA model, the imaginary part of a measured dielectric function is presented as a sum of Gaussian absorption terms. Such a simple model is valid for materials where inhomogeneous broadening is substantially larger than the homogeneous linewidth. The GDA model is the essential broadband approximation for the dielectric function of many glasses, polymers, and other natural and artificial materials with disorder. However, efficient implementation of this model in time-domain full-wave electromagnetic solvers has never been fully achieved. We start with a causal form of an isolated oscillator with Gaussian-type absorption — Causal Dawson-Gauss oscillator. Then, we derive explicit analytical formulas to implement the Gaussian oscillator in a finite-difference time-domain (FDTD) solver with minimal use of memory and floating point operations. The derivation and FDTD implementation employ our generalized dispersive material (GDM) model — a universal, modular approach to describing optical dispersion with Padé approximants. We share the FDTD prototype codes that include automated generation of the approximants and a universal FDTD dispersion implementation that employs various second-order accurate numerical schemes. The codes can be used with non-commercial solvers and commercial software for time-domain simulations of light propagation in dispersive media, which are experimentally characterized with GDA models.

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  • UCNS3D: An open-source high-order finite-volume unstructured CFD solver

    Antonios Antoniadis, Dimitris Drikakis, Pericles S. Farmakis, Lin Fu, Ioannis Kokkinakis et al

    Published 20 July 2022 | Mendeley Data

    UCNS3D is an open-source computational solver for compressible flows on unstructured meshes. State-of-the-art high-order methods and their associated benefits can now be implemented for industrial-scale CFD problems due to the flexibility and highly-automated generation offered by unstructured meshes. We present the governing equations of the physical models employed in UCNS3D, and the numerical framework developed for their solution. The code has been designed so that extended to other systems of equations and numerical models is straightforward. The employed methods are validated towards a series of stringent well-established test problems against experimental or analytical solutions, where the full capabilities of UCNS3D in terms of applications spectrum, robustness, efficiency, and accuracy are demonstrated.

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  • CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff

    Leandro Martínez

    Published 20 July 2022 | Mendeley Data

    N-body simulations and trajectory analysis rely on the calculation of attributes that depend on pairwise particle distances within a cutoff. Interparticle potential energies, forces, distribution functions, neighbor lists, and distance-dependent distributions, for example, must be calculated. Cell lists are widely used to avoid computing distances outside the cutoff. However, efficient cell list implementations are difficult to customize. Here, we provide a fast and parallel implementation of cell lists in Julia that allows the mapping of custom functions dependent on particle positions in 2 or 3 dimensions. Arbitrary periodic boundary conditions are supported. Automatic differentiation and unit propagation can be used. The implementation provides a framework for the development of new analysis tools and simulations with custom potentials. The performance of resulting computations is comparable to state-of-the-art implementations of neighbor list algorithms and cell lists, available in specialized software. Examples are provided for the computation of potential energies, forces, distribution of pairwise velocities, neighbor lists and other typical calculations in molecular and astrophysical simulations. The Julia package is freely available at http://m3g.github.io/CellListMap.jl. Interfacing with Python and R with minimal overhead is possible.

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  • RDM: An R interface for high-throughput simulation of ion-material interactions using TRIM

    Ivan Prearo, Arnaldo L. Lixandrão Filho, Sandro Guedes

    Published 20 July 2022 | Mendeley Data

    The quantitative estimation of the damage caused by ion-material interaction is carried out using Monte Carlo codes as, for instance, TRIM (TRansport of Ions in Matter). Some studies require multiple simulations to be run, varying the ion energy, mass, and charge, or changing the target material. Natural radiation damage in minerals due to the alpha decays in the three natural series is an example. In such applications, the task of calculating the ion damage on the material becomes very time-consuming. The R language code presented in this paper, Radiation Damage in Materials (RDM), is designed to serve as an interface to set parameters, start, collect, and treat the results of multiple TRIM simulations. The main outputs of RDM are the dpa (displacements per atom) and dpa profiles for ion beam irradiation, and, if needed, the natural radiation dpa for any materials to be used in a given study. The fluence of an artificially accelerated ion beam matching the natural radiation dpa is also calculated for studies in which swift heavy ions are used as proxies for natural radiation damage.

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  • FORTRESS: FORTRAN programs to solve coupled Gross-Pitaevskii equations for spin-orbit coupled spin-f Bose-Einstein condensate with spin f = 1 or 2

    Paramjeet Banger, Pardeep Makkar, Arko Roy, Sandeep Gautam

    Published 20 June 2022 | Mendeley Data

    We provide here the updated versions of OpenMP parallelized FORTRAN 90/95 programs to numerically study the ground states and/or the dynamics of homogeneous or trapped spin-1 or spin-2 Bose-Einstein condensates (BECs) with anisotropic spin-orbit (SO) coupling. The coupled sets of three or five Gross-Pitaevskii (GP) equations, respectively, for a spin-1 or a spin-2 Bose-Einstein condensate (BEC) are solved using a time-splitting Fourier spectral method.

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  • FELINE: Finite element solver for hydrodynamic lubrication problems using the inexact Newton method

    Alexandre Silva, Veniero Lenzi, Albano Cavaleiro, Sandra Carvalho, Luís Marques

    Published 16 June 2022 | Mendeley Data

    In this work we present FELINE, a C++ solver of the Reynolds equation for treating hydrodynamic lubrication problems. To correctly describe cavitation regions, FELINE implements the inexact Newton iteration (INE) algorithm within a finite element method (FEM) framework. The solver was tested and validated against known cases in literature and industrially relevant cases of dimpled textures. Furthermore, we provide a benchmark for a complex dimpled texture case to evaluate the performance and robustness of the implementation. FELINE performs very fast when compared with existing implementations and shows a great degree of stability, while providing physically correct solutions thanks to the INE algorithm.

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