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Computer Physics Communications

ISSN: 0010-4655

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  • SuperScreen: An open-source package for simulating the magnetic response of two-dimensional superconducting devices
    Quantitative understanding of the spatial distribution of magnetic fields and Meissner screening currents in two-dimensional (2D) superconductors and mesoscopic thin film superconducting devices is critical to interpreting the results of magnetic measurements of such systems. Here, we introduce SuperScreen, an open-source Python package for simulating the response of 2D superconductors to trapped flux and applied time-independent or quasi-DC magnetic fields for any value of the effective magnetic penetration depth, Λ. Given an applied magnetic field, SuperScreen solves the 2D London equation using an efficient matrix inversion method [1], [2] to obtain the Meissner currents and magnetic fields in and around structures composed of one or more superconducting thin films of arbitrary geometry. SuperScreen can be used to model screening effects and calculate self- and mutual-inductance in thin film superconducting devices.
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  • SporTran: A code to estimate transport coefficients from the cepstral analysis of (multivariate) current time series
    SporTran is a Python utility designed to estimate generic transport coefficients in extended systems, based on the Green-Kubo theory of linear response and the recently introduced cepstral analysis of the current time series generated by molecular dynamics simulations. SporTran can be applied to univariate as well as multivariate time series. Cepstral analysis requires minimum discretion from the user, in that it weakly depends on two parameters, one of which is automatically estimated by a statistical model-selection criterion that univocally determines the resulting accuracy. In order to facilitate the optimal refinement of these parameters, SporTran features an easy-to-use graphical user interface. A command-line interface and a Python API, easy to embed in complex data-analysis workflows, are also provided.
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  • QuGIT: A numerical toolbox for Gaussian quantum states
    Simulating quantum states on a classical computer is hard, typically requiring prohibitive resources in terms of memory and computational power. Efficient simulation, however, can be achieved for certain classes of quantum states, in particular the so-called Gaussian quantum states of continuous variable systems. In this work we introduce QuGIT - a python numerical toolbox based on symplectic methods specialized in efficiently simulating multimode Gaussian states and operations. QuGIT is exact, requiring no truncation of Hilbert space, and provides a wide range of Gaussian operations on arbitrary Gaussian states, including unitaries, partial traces, tensor products, general-dyne measurements, conditional and unconditional dynamics. To illustrate the toolbox, several examples of usage relevant to quantum optics and optomechanics are described.
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  • Efficient CPU and GPU implementations of multicenter integrals over long-range operators using Cartesian Gaussian functions
    We present a library for evaluating multicenter integrals over polarization operators of the form x^{m_x}y^{m_y}z^{m_z}r^{-k}C(r) using Cartesian Gaussian basis functions. m_x, m_y, m_z >= 0, k>2 are integers, while the cutoff function, C(r) = (1 - e^{-αr^2})^q, with α ∈ R_+ and certain integer values of q ensures the existence of the integrals. The formulation developed by Schwerdtfeger and Silberbach [Phys. Rev. A 37, 2834 (1988)] is implemented in an efficient and stable way taking into account a recent fix in one of the equations. A cheap upper bound is presented that allows negligible integrals to be prescreened. The correctness of the analytical integrals was verified by numerical integration. The library provides separate codes for serial CPU and parallel GPU architectures and can be wrapped into a python module.
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  • Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures
    An open-source data-analysis framework 2DMAT has been developed for experimental measurements of two-dimensional material structures. 2DMAT offers five analysis methods: (i) Nelder-Mead optimization, (ii) grid search, (iii) Bayesian optimization, (iv) replica exchange Monte Carlo method, and (v) population-annealing Monte Carlo method. Methods (ii) through (v) are implemented by parallel computation, which is efficient not only for personal computers but also for supercomputers. The current version of 2DMAT is applicable to total-reflection high-energy positron diffraction (TRHEPD), surface X-ray diffraction (SXRD), and low-energy electron diffraction (LEED) experiments by installing corresponding forward problem solvers that generate diffraction intensity data from a given dataset of the atomic positions. The analysis methods are general and can be applied also to other experiments and problems.
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  • libdlr: Efficient imaginary time calculations using the discrete Lehmann representation
    We introduce libdlr, a library implementing the recently introduced discrete Lehmann representation (DLR) of imaginary time Green's functions. The DLR basis consists of a collection of exponentials chosen by the interpolative decomposition to ensure stable and efficient recovery of Green's functions from imaginary time or Matsubara frequency samples. The library provides subroutines to build the DLR basis and grids, and to carry out various standard operations. The simplicity of the DLR makes it straightforward to incorporate into existing codes as a replacement for less efficient representations of imaginary time Green's functions, and libdlr is intended to facilitate this process. libdlr is written in Fortran, provides a C header interface, and contains a Python module pydlr. We also introduce a stand-alone Julia implementation, Lehmann.jl.
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  • LIBAMI: Implementation of algorithmic Matsubara integration
    We present libami, a lightweight implementation of algorithmic Matsubara integration (AMI) written in C++. AMI is a tool for analytically resolving the sequence of nested Matsubara integrals that arise in virtually all Feynman perturbative expansions.
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  • DFT-FE 1.0: A massively parallel hybrid CPU-GPU density functional theory code using finite-element discretization
    We present DFT-FE 1.0, building on DFT-FE 0.6 Motamarri et al. (2020) [28], to conduct fast and accurate large-scale density functional theory (DFT) calculations (reaching ~100,000 electrons) on both many-core CPU and hybrid CPU-GPU computing architectures. This work involves improvements in the real-space formulation—via an improved treatment of the electrostatic interactions that substantially enhances the computational efficiency—as well high-performance computing aspects, including the GPU acceleration of all the key compute kernels in DFT-FE. We demonstrate the accuracy by comparing the ground-state energies, ionic forces and cell stresses on a wide-range of benchmark systems against those obtained from widely used DFT codes. Further, we demonstrate the numerical efficiency of our GPU acceleration, which yields ∼20× speed-up on hybrid CPU-GPU nodes of the Summit supercomputer. Notably, owing to the parallel-scaling of the GPU implementation, we obtain wall-times of 80 - 140 seconds for full ground-state calculations, with stringent accuracy, on benchmark systems containing ~6,000 - 15,000 electrons using 64 - 224 nodes of the Summit supercomputer.
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  • Models of advanced recording systems: A multi-timescale micromagnetic code for granular thin film magnetic recording systems
    Micromagnetic modelling provides the ability to simulate large magnetic systems reliably without the computational cost limitation imposed by atomistic modelling. Through micromagnetic modelling it is possible to simulate systems consisting of thousands of grains over a time range of nanoseconds to years, depending upon the solver used. Here we present the creation and release of an open-source multi-timescale micromagnetic code combining three key solvers: Landau-Lifshitz-Gilbert; Landau-Lifshitz-Bloch; Kinetic Monte Carlo. This code, called MARS (Models of Advanced Recording Systems), is capable of accurately simulating the magnetisation dynamics in large and structurally complex single- and multi-layered granular systems as is shown by comparison to established atomistic simulation results. The short timescale simulations are achieved for systems far from and close to the Curie point via the implemented Landau-Lifshitz-Gilbert and Landau-Lifshitz-Bloch solvers respectively. This enables read/write simulations for general perpendicular magnetic recording and also state of the art heat assisted magnetic recording (HAMR). The long timescale behaviour is simulated via the Kinetic Monte Carlo solver, enabling investigations into signal-to-noise ratio and data longevity. The combination of these solvers opens up the possibility of multi-timescale simulations within a single software package. For example the entire HAMR process from initial data writing and data read back to long term data storage is possible via a single simulation using MARS. The use of atomistic parameterisation for the material input of MARS enables highly accurate material descriptions which provide a bridge between atomistic simulation and real world experimentation. Thus MARS is capable of performing simulations for all aspects of recording media research and development. This ranges from material characterisation and optimisation to system design and implementation. The object orientated nature of MARS is structured to facilitate quick and simple development and easy implementation of user defined custom simulation types which can utilise either timescale or a combination of both timescales.
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  • KSSOLV 2.0: An efficient MATLAB toolbox for solving the Kohn-Sham equations with plane-wave basis set
    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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