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MADHAT: Model-Agnostic Dark Halo Analysis Tool Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 Kimberly K. Boddy; Stephen Hill; Jason Kumar; Pearl Sandick; Barmak Shams Es Haghi
We present the Model-Agnostic Dark Halo Analysis Tool (MADHAT), a numerical tool which implements a Fermi-LAT data-driven, model-independent analysis of gamma-ray emission from dwarf satellite galaxies and dwarf galaxy candidates due to dark matter annihilation, dark matter decay, or other nonstandard or unknown astrophysics. This tool efficiently provides statistical upper bounds on the number of
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Conservation laws and spin system modeling through principal component analysis Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-14 David Yevick
This paper examines several applications of principal component analysis (PCA) to physical systems. The central result demonstrates that the PCA can identify from the recorded system trajectories conserved quantities that take the form of polynomials in the system variables in an easily programmed and straightforward fashion. In particular, a data record composed of the positions and velocities generated
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Wang-Landau sampling for estimation of the reliability of physical networks Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-14 Wanyok Atisattapong; Pasin Marupanthorn
Modern physical networks, for example in communication and transportation, can be interpreted as directed graphs. Network models are used to identify the probability that given nodes are connected, and therefore the effect of a failure at a given link. This is essential for network design, optimization, and reliability. In this study, we investigated three alternative ensembles for estimating network
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An algorithm for estimating kinetic parameters of atomistic rare events using finite-time temperature programmed molecular dynamics trajectories Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-14 Saurabh Shivpuje; Manish Kumawat; Abhijit Chatterjee
A new variation of the temperature programmed molecular dynamics (TPMD) algorithm, called finite-time TPMD (FT-TPMD), is presented. In this variation, a collection of independent molecular dynamics (MD) trajectories is generated, such that each trajectory is of a fixed duration of time and a transition from a given state of the system may/may not occur in a trajectory. This eliminates the requirement
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A new software implementation of the Oslo method with rigorous statistical uncertainty propagation Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-13 Jørgen E. Midtbø; Fabio Zeiser; Erlend Lima; Ann-Cecilie Larsen; Gry M. Tveten; Magne Guttormsen; Frank Leonel Bello Garrote; Anders Kvellestad; Therese Renstrøm
The Oslo method comprises a set of analysis techniques designed to extract nuclear level density and average γ-decay strength function from a set of excitation-energy tagged γ-ray spectra. Here we present a new software implementation of the entire Oslo method, called OMpy. We provide a summary of the theoretical basis and derive the essential equations used in the Oslo method. In addition to the functionality
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PyR@TE 3 Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-02 Lohan Sartore; Ingo Schienbein
We present a new version of PyR@TE, a Python tool for the computation of renormalization group equations for general, non-supersymmetric gauge theories. Its new core relies on a recent paper by Poole & Thomsen (2019) to compute the β-functions. In this framework, gauge kinetic mixing is naturally implemented, and the Weyl consistency relations between gauge, quartic and Yukawa couplings are automatically
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ARC 3.0: An expanded Python toolbox for atomic physics calculations Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-01 E.J. Robertson; N. Šibalić; R.M. Potvliege; M.P.A. Jones
ARC 3.0 is a modular, object-oriented Python library combining data and algorithms to enable the calculation of a range of properties of alkali and divalent atoms. Building on the initial version of the ARC library (Šibalić et al., 2017), which focused on Rydberg states of alkali atoms, this major upgrade introduces support for divalent atoms. It also adds new methods for working with atom–surface
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A variant of stabilized-scalar auxiliary variable (S-SAV) approach for a modified phase-field surfactant model Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-08 Junxiang Yang; Junseok Kim
In this article, we develop a new linear, decoupled, second-order accurate, and energy stable numerical method for a modified phase-field surfactant model (Xu et al., 2020). The proposed scheme is a simple and efficient variant of stabilized-scalar auxiliary variable (S-SAV) method. The proposed scheme not only retains all advantages of S-SAV method but also simplifies the solution algorithm. The phase-field
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OpenNTP: Implementation of the SN method in cartesian 2D geometry and the CP method in cylindrical and spherical 1D geometry Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 M. Lahdour; T. El Bardouni; O. El Hajjaji; E. Chakir; H. Ziani; Jamal Al Zain; E. Chham; M. El Barbari
This paper presents the implementation of the discrete ordinates method (SN) in 2D cartesian geometry and the collision probability method (CP) in cylindrical and spherical 1D geometry in OpenNTP code (Open Neutron Transport Package). This code is a pedagogical tool for computer analysis of nuclear reactors. Its main features are as follows: a free software with an open source, it solves the neutron
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PyXtal: A Python library for crystal structure generation and symmetry analysis Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 Scott Fredericks; Kevin Parrish; Dean Sayre; Qiang Zhu
We present PyXtal, a new package based on the Python programming language, used to generate structures with specific symmetry and chemical compositions for both atomic and molecular systems. This software provides support for various systems described by point, rod, layer, and space group symmetries. With only the inputs of chemical composition and symmetry group information, PyXtal can automatically
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Calculation of coefficients of transformations between three-particle hyperspherical harmonics Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 Victor D. Efros
New versions of the program to calculate the three-particle hyperspherical brackets 〈l1′l2′|l1l2〉KLφ are presented. Whereas the previous program, Efros (2020), computes the sets of brackets existing at given l1, l2, K, and L values, one of the present programs produces the set of all the brackets existing at L values in a range from Lmin up to Lmax and all K values of a given parity up to some Kmax
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On the delta function broadening in the Kubo–Greenwood equation Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-13 Pavlo Bulanchuk
Understanding DC electrical conductivity is crucial for the study of materials. Macroscopic DC conductivity can be calculated from first principles using the Kubo–Greenwood equation. The procedure involves finding the thermodynamic limit of the current response to an electric field that is slowly switched on, and then taking the limit of the switching rate to zero. We introduce a nonlinear extrapolation
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Irvsp: To obtain irreducible representations of electronic states in the VASP Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-23 Jiacheng Gao; Quansheng Wu; Clas Persson; Zhijun Wang
We present an open-source program irvsp, to compute irreducible representations of electronic states for all 230 space groups with an interface to the Vienna ab-initio Simulation Package. This code is fed with plane-wave-based wavefunctions (e.g. WAVECAR) and space group operators (listed in OUTCAR), which are generated by the VASP package. This program computes the traces of matrix presentations and
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JaSTA-3: Light scattering simulations for heterogeneous aggregate Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-01 Prithish Halder
This article announces the development of the third version of the Java Superposition T-matrix App (JaSTA-3), to study the light scattering properties of heterogeneous aggregate particles. It has been developed using Netbeans 7.1.2, which is a Java integrated development environment (IDE). The JaSTA uses double precision superposition codes for multi-sphere clusters in random orientation, developed
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Strategies for particle resampling in PIC simulations Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-07 A. Muraviev; A. Bashinov; E. Efimenko; V. Volokitin; I. Meyerov; A. Gonoskov
In particle-in-cell simulations, excessive or even unfeasible computational demands can be caused by the growth of the number of particles in the course of prolific ionization or cascaded pair production due to the effects of quantum electrodynamics. Here we discuss how one can organize a dynamic rearrangement of the ensemble to reduce the number of macroparticles, while maintaining acceptable sampling
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Open-source modelling of aerosol dynamics and computational fluid dynamics: Nodal method for nucleation, coagulation, and surface growth Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-11 Mino Woo; Robert T. Nishida; Mario A. Schriefl; Marc E.J. Stettler; Adam M. Boies
Understanding formation, growth and transport of aerosols is critical to processes ranging from cloud formation to disease transmission. In this work, a numerical algorithm of aerosol dynamics including nucleation, coagulation, and surface growth was coupled with flow and heat transfer equations enabling the solution of three-dimensional multi-physics aerosol processes in an open-source platform. The
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Implicit highly-coupled single-ion Hall-MHD formulation for hybrid particle-in-cell codes Comput. Phys. Commun. (IF 3.627) Pub Date : 2021-01-06 C. Thoma; D.R. Welch; D.V. Rose
The rudiments of a particle-based single-fluid two-temperature magnetohydrodynamic (MHD) algorithm have been outlined in Thoma et al. (2013). The extension of this algorithm to include the effect of Hall physics is described in this paper. An implicit leapfrog version of the algorithm, which allows timesteps large compared to the resistive decay time and other relevant timescales, has recently been
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Deep learning approach to Hubble parameter Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-30 H. Tilaver; M. Salti; O. Aydogdu; E.E. Kangal
The main purpose of this work is to show that machine learning algorithms (MLAs) can be used to improve the abilities of cosmological models and to make meaningful astrophysical predictions. As a preliminary step, we construct an expression for the Hubble parameter in the caloric variable Chaplygin gas (cVCG) framework including a particle creation scenario. Then, making use of a set of updated observational
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Density matrix embedding theory of excited states for spin systems Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-13 Jie Qiao; Quanlin Jie
We use cluster density matrix embedding theory (CDMET) to calculate the excited states for quantum spin systems. The bath states are a set of block-product states and optimized by the variational method. By considering the symmetry in the form of penalty function, the degeneracy of excited eigenstates can be reduced. We prove the accuracy of our method by obtaining different excited states of square
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X-ray spectrometer simulation code with a detailed support of mosaic crystals Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 Michal Šmíd; Xiayun Pan; Kateřina Falk
We present a newly developed ray tracing code called mmpxrt, dedicated to study and design x-ray crystal optics, with a special focus on mosaic crystal spectrometers. Its main advantage over other currently available ray tracing codes is that it includes a detailed and benchmarked algorithm to treat mosaic crystals, especially HOPG and HAPG (Highly Oriented/Annealed Pyrolitic Graphite). The code is
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GPU-acceleration of the ELPA2 distributed eigensolver for dense symmetric and hermitian eigenproblems Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 Victor Wen-zhe Yu; Jonathan Moussa; Pavel Kůs; Andreas Marek; Peter Messmer; Mina Yoon; Hermann Lederer; Volker Blum
The solution of eigenproblems is often a key computational bottleneck that limits the tractable system size of numerical algorithms, among them electronic structure theory in chemistry and in condensed matter physics. Large eigenproblems can easily exceed the capacity of a single compute node, thus must be solved on distributed-memory parallel computers. We here present GPU-oriented optimizations of
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ULYSSES: Universal leptogenesis equation solver Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 A. Granelli; K. Moffat; Y.F. Perez-Gonzalez; H. Schulz; J. Turner
ULYSSES is a python package that calculates the baryon asymmetry produced from leptogenesis in the context of a type-I seesaw mechanism. The code solves the semi-classical Boltzmann equations for points in the model parameter space as specified by the user. We provide a selection of predefined Boltzmann equations as well as a plugin mechanism for externally provided models of leptogenesis. Furthermore
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FaVAD: A software workflow for characterisation and visualizing of defects in crystalline structures Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-31 Udo von Toussaint; F.J. Domínguez-Gutiérrez; Michele Compostella; Markus Rampp
The analysis of defects and defect dynamics in crystalline materials is important for fundamental science and for a wide range of applied engineering. With increasing system size the analysis of molecular-dynamics simulation data becomes non-trivial. Here, we present a workflow for semi-automatic identification and classification of defects in crystalline structures, combining a new approach for defect
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RESPACK: An ab initio tool for derivation of effective low-energy model of material Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-11 Kazuma Nakamura; Yoshihide Yoshimoto; Yusuke Nomura; Terumasa Tadano; Mitsuaki Kawamura; Taichi Kosugi; Kazuyoshi Yoshimi; Takahiro Misawa; Yuichi Motoyama
RESPACK is a first-principles calculation software for evaluating the interaction parameters of materials and is able to calculate maximally localized Wannier functions, response functions based on the random phase approximation and related optical properties, and frequency-dependent electronic interaction parameters. RESPACK receives its input data from a band-calculation code using norm-conserving
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DMFTwDFT: An open-source code combining Dynamical Mean Field Theory with various density functional theory packages Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 Vijay Singh; Uthpala Herath; Benny Wah; Xingyu Liao; Aldo H. Romero; Hyowon Park
Dynamical Mean Field Theory (DMFT) is a successful method to compute the electronic structure of strongly correlated materials, especially when it is combined with density functional theory (DFT). Here, we present an open-source computational package (and a library) combining DMFT with various DFT codes interfaced through the Wannier90 package. The correlated subspace is expanded as a linear combination
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A simple variational quantum Monte Carlo-effective mass approach for excitons and trions in quantum dots Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-16 Josep Planelles; Juan I. Climente
A computational model is presented to calculate the ground state energy of neutral and charged excitons confined in semiconductor quantum dots. The model is based on the variational Quantum Monte Carlo method and effective mass Hamiltonians. Through an iterative Newton–Raphson process, minimizing the local energy, and (optional) parallelization of random walkers, fast and accurate estimates of both
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HTR-1.2 solver: Hypersonic Task-based Research solver version 1.2 Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Mario Di Renzo; Sergio Pirozzoli
We present an updated version of the open-source Hypersonics Task-based Research (HTR) solver for hypersonic aerothermodynamics. The solver, whose first version was presented in Di Renzo et al. (2020), is designed for direct numerical simulation (DNS) of canonical hypersonic flows at high Reynolds numbers in which thermo-chemical effects induced by high temperatures are relevant. The solver relies
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Simulation of quantum many-body systems on Amazon cloud Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-28 Justin A. Reyes; Dan C. Marinescu; Eduardo R. Mucciolo
Quantum many-body systems (QMBs) are some of the most challenging physical systems to simulate numerically. Methods involving approximations for tensor network (TN) contractions have proven to be viable alternatives to algorithms such as quantum Monte Carlo or simulated annealing. However, these methods are cumbersome, difficult to implement, and often have significant limitations in their accuracy
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Algorithm for replica redistribution in an implementation of the population annealing method on a hybrid supercomputer architecture Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-23 Alexander Russkov; Roman Chulkevich; Lev N. Shchur
The population annealing method is a promising approach for large-scale simulations because it is potentially scalable on any parallel architecture. We present an implementation of the algorithm on a hybrid program architecture combining CUDA and MPI. The problem is to keep all general-purpose graphics processing unit devices as busy as possible by efficiently redistributing replicas. We provide details
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Mammography and breast tomosynthesis simulator for virtual clinical trials Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 Andreu Badal; Diksha Sharma; Christian G. Graff; Rongping Zeng; Aldo Badano
Computer modeling and simulations are increasingly being used to predict the clinical performance of x-ray imaging devices in silico, and to generate synthetic patient images for training and testing of machine learning algorithms. We present a detailed description of the computational models implemented in the open source GPU-accelerated Monte Carlo x-ray imaging simulation code MC-GPU. This code
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minimal-lagrangians: Generating and studying dark matter model Lagrangians with just the particle content Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-13 Simon May
minimal-lagrangians is a Python program which allows one to specify the field content of an extension of the Standard Model of particle physics and, using this information, to generate the most general renormalizable Lagrangian that describes such a model. As the program was originally created for the study of minimal dark matter models with radiative neutrino masses, it can handle additional scalar
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Arbitrarily high-order structure-preserving schemes for the Gross–Pitaevskii equation with angular momentum rotation Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 Jin Cui; Yushun Wang; Chaolong Jiang
In this paper, we design a novel class of arbitrarily high-order structure-preserving numerical schemes for the time-dependent Gross–Pitaevskii equation with angular momentum rotation. Based on the idea of the scalar auxiliary variable approach which is proposed in the recent papers [J. Comput. Phys., 353 (2018) 407–416 and SIAM Rev., 61(2019) 474–506] for developing energy stable schemes for gradient
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A quasi-static particle-in-cell algorithm based on an azimuthal Fourier decomposition for highly efficient simulations of plasma-based acceleration: QPAD Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-15 Fei Li; Weiming An; Viktor K. Decyk; Xinlu Xu; Mark J. Hogan; Warren B. Mori
The three-dimensional (3D) quasi-static particle-in-cell (PIC) algorithm is a very efficient method for modeling short-pulse laser or relativistic charged particle beam–plasma interactions. In this algorithm, the plasma response, i.e., plasma wave wake, to a non-evolving laser or particle beam is calculated using a set of Maxwell’s equations based on the quasi-static approximate equations that exclude
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Elastic3rd: A tool for calculating third-order elastic constants from first-principles calculations Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 Mingqing Liao; Yong Liu; Shun-Li Shang; Fei Zhou; Nan Qu; Yichuan Chen; Zhonghong Lai; Zi-Kui Liu; Jingchuan Zhu
The third-order elastic constants (TOECs) are fundamental to describe crystal’s nonlinear response to stress, and can be applied to explore anharmonic properties of crystals such as Grüneisen parameters, thermal expansion coefficient, and the effect of pressure on second-order elastic constants (SOECs). Here, we report an open-source python package, Elastic3rd, which is able to calculate the SOECs
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Heterogeneous Multi-Rate mass transfer models in OpenFOAM® Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 Federico Municchi; Nicodemo Di Pasquale; Marco Dentz; Matteo Icardi
We implement the Multi-Rate Mass Transfer (MRMT) model for mobile–immobile transport in porous media (Haggerty and Gorelick, 1995; Municchi and Icardi, 2019 [1]) within the open-source finite volume library OpenFOAM® (Foundation, 2014). Unlike other codes available in the literature (Geiger et al., 2011 [2]; Silva et al., 2009), we propose an implementation that can be applied to complex three-dimensional
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The bi-Lebedev scheme for the Maxwell eigenvalue problem with 3D bi-anisotropic complex media Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 Xing-Long Lyu; Tiexiang Li; Tsung-Ming Huang; Wen-Wei Lin; Heng Tian
This paper focuses on studying the eigenstructure of generalized eigenvalue problems (GEPs) arising in the three-dimensional source-free Maxwell equations for bi-anisotropic complex media with a 3-by-3 permittivity tensor ε>0, a permeability tensor μ>0, and scalar magnetoelectric coupling constants ξ=ζ̄=ıγ. The bi-Lebedev scheme is appealing because it preserves the symmetry inherent to the Maxwell
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Crystal field module for the general relativistic atomic structure package Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-10 G. Gaigalas; D. Kato
The latest version of the grasp2018 package [Froese Fischer et al. (2019)], based on the multiconfigurational Dirac–Hartree–Fock method, is extended to account for effects of crystal fields in complex systems. Instead of using the simplified treatment of the crystal field effects based on the Stevens’ operator-equivalent method the program uses the fully ab-initio method in which the external ions
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A Maple package for combinatorial aspects of Bethe Ansatz Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-12-05 Paweł Jakubczyk; Andrzej Wal; Michał Kaczor; Dorota Jakubczyk; Mirosław Łabuz; Jan Milewski
ComBethAns is a Maple module developed to enable calculations concerning spin systems using combinatorial Bethe Ansatz approach. This method of spin system analysis is based on representation theory and combinatorics. It allows to consider one-dimensional spin systems with periodic boundary conditions. The module ComBethAns offers tools to define the different bases for such quantum system, to carry
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Integrating state of the art compute, communication, and autotuning strategies to multiply the performance of ab initio molecular dynamics on massively parallel multi-core supercomputers Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-29 Tobias Klöffel; Gerald Mathias; Bernd Meyer
The development in today’s supercomputer hardware is that the compute power of the individual nodes grows much faster than the speed of their interconnects. To benefit from this evolution in computer hardware, the challenge in modernization of simulation software is to increase the computational load on the nodes and to reduce simultaneously the inter-node communication. Here, we demonstrate the implementation
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Fast and robust algorithm for energy minimization of spin systems applied in an analysis of high temperature spin configurations in terms of skyrmion density Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-30 A.V. Ivanov; V.M. Uzdin; H. Jónsson
An algorithm for the minimization of the energy of magnetic systems is presented and applied to the analysis of thermal configurations of a ferromagnet to identify inherent structures, i.e. the nearest local energy minima, as a function of temperature. Over a rather narrow temperature interval, skyrmions appear and reach a high temperature limit for the skyrmion density. In addition, the performance
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From Feynman rules to conserved quantum numbers, III Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-23 P. Nogueira
The present article complements the earlier ones in this series. The first part contains various results on the constituent system Cκ(M) of a graph model M, and on its feasibility system Iη(M) (which comprises a number of identities that define the number conservation rules). Those results include the general form of the (particle) number conservation rules in models without explicit propagator mixing
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Brute-forcing spin-glass problems with CUDA Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Konrad Jałowiecki; Marek M. Rams; Bartłomiej Gardas
We demonstrate how to compute the low energy spectrum for small (N≤50), but otherwise arbitrary, spin-glass instances using modern Graphics Processing Units or similar heterogeneous architecture. Our algorithm performs an exhaustive (i.e., brute-force) search of all possible configurations to select S≪2N lowest ones together with their corresponding energies. We mainly focus on the Ising model defined
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Benchmark of the KGMf with a coupled Boltzmann equation solver Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-30 Janez Krek; Yangyang Fu; Guy M. Parsey; John P. Verboncoeur
The Kinetic Global Model framework (KGMf) is an open-source general-purpose global model (spatially averaged) simulation code developed to explore the reaction kinetics and pathways in plasma discharge systems. It contains species continuity and electron energy balance equations, with a time-dependent evaluated electron energy distribution function (EEDF) for electron impact reactions. The EEDF is
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Large-scale first-principles quantum transport simulations using plane wave basis set on high performance computing platforms Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-23 Meng Ye; Xiangwei Jiang; Shu-Shen Li; Lin-Wang Wang
As the characteristic lengths of advanced electronic devices are approaching the atomic scale, ab initio simulation method, with full consideration of quantum mechanical effects, becomes essential to study the quantum transport phenomenon in them. The widely used non-equilibrium Green’s function (NEGF) combined with the density functional theory (DFT) approach prefers a localized basis set. As many
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PaScaL_TDMA: A library of parallel and scalable solvers for massive tridiagonal systems Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Ki-Ha Kim; Ji-Hoon Kang; Xiaomin Pan; Jung-Il Choi
The aim of this study is to devise an efficient and scalable computational procedure to solve the many tridiagonal systems in multi-dimensional partial differential equations. The modified Thomas algorithm and a newly designed communication scheme were used to reduce the communication overhead encountered while solving the many tridiagonal systems. Benchmark test results reveal an advantage of the
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The Monte Carlo Program KKMC, for the Lepton or Quark Pair Production at LEP/SLC Energies—Updates of electroweak calculations Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-21 A. Arbuzov; S. Jadach; Z. Wa̧s; B.F.L. Ward; S.A. Yost
Since the KKMC program was published for the first time over 20 years ago, it has gained popularity and was exploited in a broad spectrum of applications. The core part of the program itself did not change much. In contrast, some of the libraries have evolved substantially. The aim of this publication is to archive four versions, alternative to the one published 20 years ago versions of the electroweak
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Hybrid Large Eddy Simulation for low-order Discontinuous Galerkin methods using an explicit filter Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-19 A.C.W. Creech; A. Jackson
In this paper we present a simple, easily implemented and effective approach for explicitly-filtered Large Eddy Simulation with a Discontinuous Galerkin (DG) discretisation for velocity. DG formulations are often desirable due to their stability and increased accuracy, however this can come at greater computational expense due to the additional degrees of freedom in the velocity field. Additionally
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Variational inequality transport model on the sphere by the active-set reduced-space algorithm Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-21 Haijian Yang; Chao Yang; Jizu Huang
The simulation of the transport problem on the sphere is crucial in the numerical modeling of the transport of trace constituents in atmospheric models. One major issue in the numerical simulation is the ability of the solver to obtain accurate constraint-preserving solutions, i.e., ensuring the predicted solution to stay within the physical range. In this paper, we develop and study a variational
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Cyclically parallelized treecode for fast computations of electrostatic interactions on molecular surfaces Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-23 Jiahui Chen; Weihua Geng; Daniel R. Reynolds
We study the parallelization of a flexible order Cartesian treecode algorithm for evaluating electrostatic potentials of charged particle systems in which N particles are located on the molecular surfaces of biomolecules such as proteins. When the well-separated condition is satisfied, the treecode algorithm uses a far-field Taylor expansion to compute O(NlogN) particle–cluster interactions to replace
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QSW_MPI: A framework for parallel simulation of quantum stochastic walks Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Edric Matwiejew; Jingbo Wang
QSW_MPI is a Python package developed for time-series simulation of continuous-time quantum stochastic walks. This model allows for the study of Markovian open quantum systems in the Lindblad formalism, including a generalisation of the continuous-time random walk and continuous-time quantum walk. Consisting of a Python interface accessing parallelised Fortran libraries utilising sparse data structures
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FEMS – A Mechanics-oriented Finite Element Modeling Software Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Modesar Shakoor
This paper is a presentation of a Finite Element Modeling Software named FEMS that integrates mesh generation and adaption features in order to alleviate significantly the difficulty of designing a Finite Element (FE) mesh for a particular problem. FEMS is targeted at engineers and scientists addressing localization problems in mechanics, although it should be suited to many other applications. FEMS
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UNDI: An open-source library to simulate muon-nuclear interactions in solids Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Pietro Bonfà; Jonathan Frassineti; Muhammad Maikudi Isah; Ifeanyi John Onuorah; Samuele Sanna
We present UNDI, an open-source program to analyze the time dependent spin polarization of an isolated muon interacting with the surrounding nuclear magnetic dipoles in the context of standard muon spin rotation and relaxation spectroscopy experiments. The code can perform both exact and approximated estimates of the muon polarization function in presence of external fields and electric field gradients
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Hybrid seeding: A standalone track reconstruction algorithm for scintillating fibre tracker at LHCb Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-10 S. Aiola; Y. Amhis; P. Billoir; B. Kishor Jashal; L. Henry; A. Oyanguren Campos; C. Marin Benito; F. Polci; R. Quagliani; M. Schiller; M. Wang
We describe the Hybrid seeding, a stand-alone pattern recognition algorithm aiming at finding charged particle trajectories for the LHCb upgrade. A significant improvement to the charged particle reconstruction efficiency is accomplished by exploiting the knowledge of the LHCb magnetic field and the position of energy deposits in the scintillating fibre tracker detector. Moreover, we achieve a low
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PARCE: Protocol for Amino acid Refinement through Computational Evolution Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-20 Rodrigo Ochoa; Miguel A. Soler; Alessandro Laio; Pilar Cossio
The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their interactions with protein targets. In this work, we present PARCE, an open source Protocol for Amino acid Refinement through Computational Evolution that implements an advanced
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Perturbation approach to ab initio effective mass calculations Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-17 Oleg Rubel; Fabien Tran; Xavier Rocquefelte; Peter Blaha
A degenerate perturbation k⋅p approach for effective mass calculations is implemented in the all-electron density functional theory (DFT) package WIEN2k. The accuracy is tested on major group IVA, IIIA-VA, and IIB-VIA semiconductor materials. Then, the effective mass in graphene and CuI with defects is presented as illustrative applications. For states with significant Cu-d character additional local
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AMMCR: Ab initio model for mobility and conductivity calculation by using Rode Algorithm Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-10-28 Anup Kumar Mandia; Bhaskaran Muralidharan; Jung-Hae Choi; Seung-Cheol Lee; Satadeep Bhattacharjee
We present a module to calculate the mobility and conductivity of semiconducting materials using Rode’s algorithm. This module uses a variety of electronic structure inputs derived from the Density Functional Theory (DFT). We have demonstrated good agreement with experimental results for the case of Cadmium Sulfide (CdS). We also provide a comparison with the widely used method, the so-called relaxation
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LBfoam: An open-source software package for the simulation of foaming using the Lattice Boltzmann Method Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-10-28 Mohammadmehdi Ataei; Vahid Shaayegan; Franco Costa; Sejin Han; Chul B. Park; Markus Bussmann
This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated bubbles, bubble dynamics and coalescence, surface tension, the stabilizing disjoining pressure between bubbles, and Newtonian and non-Newtonian rheological models. The
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A new method to dispatch split particles in Particle-In-Cell codes Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-11-07 Roch Smets; Nicolas Aunai; Andrea Ciardi; Matthieu Drouin; Martin Campos-Pinto; Philip Deegan
Particle-In-Cell codes are widely used for plasma physics simulations. It is often the case that particles within a computational cell need to be split to improve the statistics or, in the case of non-uniform meshes, to avoid the development of fictitious self-forces. Existing particle splitting methods are largely empirical and their accuracy in preserving the distribution function has not been evaluated
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DFMSPH22: A C-code for the double folding interaction potential of two spherical nuclei Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-10-26 Igor I. Gontchar; Maria V. Chushnyakova; Natalya A. Khmyrova
This is a new version of the DFMSPH (DFMSPH14, DFMSPH19) code published earlier. The new version is designed to obtain the nucleus–nucleus potential between two spherical nuclei using the double folding model (DFM). In particular, the code enables one to find the Coulomb barrier. Using the new version, one can employ three types of effective nucleon–nucleon interaction: the M3Y, Migdal, and relativistic
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SudoDEM: Unleashing the predictive power of the discrete element method on simulation for non-spherical granular particles Comput. Phys. Commun. (IF 3.627) Pub Date : 2020-10-22 Shiwei Zhao; Jidong Zhao
This paper presents a novel open-source discrete element code, SudoDEM, for efficient modeling of both 2D and 3D non-spherical particles under a GPL v3 or later license. Built upon a popular open-source code YADE, our code inherits the core of a classic DEM framework empowered by OpenMP acceleration, and further offers unique features of a rich library of prime particle shapes, including poly-superellipsoids
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