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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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