We present an open-source computer program written in Python language for quantum measurement and related issues. In our program, quantum states and operators, including quantum gates, can be developed into a quantum-object function represented by a matrix. Build into the program are several measurement schemes, including von Neumann measurement and weak measurement. Various numerical simulation methods

SModelS is an automatized tool enabling the fast interpretation of simplified model results from the LHC within any model of new physics respecting a Z2 symmetry. We here present a new version of SModelS, which can use the full likelihoods now provided by ATLAS in the form of pyhf JSON files. This much improves the statistical evaluation and therefore also the limit setting on new physics scenarios

The Green’s function method was applied to solve the one-dimensional positron diffusion equation for a system consisting of up to four layers that contain defects with different trapping rates. These allow us to obtain the analytical relationships valid for the evaluation of data obtained from variable energy positron measurements. They have been implemented in user-friendly free computer code available

We report the development of SOMAFOAM, a finite volume framework for performing continuum simulations of low-temperature plasmas. The primary goal of this work is to discuss the features of SOMAFOAM along with representative results provided as examples for a range of operating conditions and geometries. This includes plasma and plasma–dielectric systems operating in direct current, radio frequency

The study of strongly out-of-equilibrium states and their time evolution towards thermalization is critical to the understanding of an ever widening range of physical processes. We present a numerical method that for the first time allows for the numerical solution of the most difficult part of the time-dependent Boltzmann equation: the full scattering term. Any number of bands (and quasiparticles)

The Quantum Self-Consistent Ab-Initio Lattice Dynamics package (QSCAILD) is a python library that computes temperature-dependent effective 2nd and 3rd order interatomic force constants in crystals, including anharmonic effects. QSCAILD’s approach is based on the quantum statistics of a harmonic model. The program requires the forces acting on displaced atoms of a solid as an input, which can be obtained

Modelling neutral beam injection (NBI) in fusion reactors requires computing the trajectories of large ensembles of particles. Slowing down times of up to one second combined with nanosecond time steps make these simulations computationally very costly. This paper explores the performance of BGSDC, a new numerical time stepping method, for tracking ions generated by NBI in the DIII-D and JET reactors

The program presented in this paper aims to simplify formulas involving products of a large amount of Wigner 3j-symbols summed over various magnetic quantum numbers. The algorithm used in our program is based on the graphical techniques originally developed by Yutsis, Levinson, and Vanagas, and later revised by some others. The output of our program is expressed as a weighted sum of products of 3j-

In the context of intra-cluster medium turbulence, it is essential to be able to split the turbulent velocity field in a compressive and a solenoidal component. We describe and implement a new method for this aim, i.e., performing a Helmholtz–Hodge decomposition, in multi-grid, multi-resolution descriptions, focusing on (but not being restricted to) the outputs of AMR cosmological simulations. The

We present an efficient program for the exact diagonalization solution of the pairing Hamiltonian in spherical systems with rotational invariance based on the SU(2) quasi-spin algebra. The basis vectors with quasi-spin symmetry considered are generated by using an iterative algorithm. Then the Hamiltonian matrix constructed on this basis is diagonalized with the Lanczos algorithm. All non-zero matrix

We present TB2J, a Python package for the automatic computation of magnetic interactions, including exchange and Dzyaloshinskii-Moriya, between atoms of magnetic crystals from the results of density functional calculations. The program is based on the Green’s function method with the local rigid spin rotation treated as a perturbation. As input, the package uses the output of either Wannier90, which

In this paper we present a high-accuracy charge conservation scheme of current assignment for particle-in-cell (PIC) simulations in two dimensional space. The current continuity integral equation is applied to set up a linear equation set about the assigned currents on edges of the cells through which a particle moves during a time step. The currents on the edges can be very accurately assigned by

We construct a novel fully-decoupled and second-order accurate time marching numerical scheme with unconditional energy stability for the Cahn-Hilliard-Darcy phase-field model of the two-phase Hele-Shaw flow, in which, the key idea to realize the full decoupling structure is to use the so-called “zero-energy-contribution” function and design a special ordinary differential equation to deal with the

A common way to evaluate electronic integrals for polyatomic molecules is to use Becke’s partitioning scheme (Becke and Chem, 1988) in conjunction with overlapping grids centered at each atomic site. The Becke scheme was designed for integrands that fall off rapidly at large distances, such as those approximating bound electronic states. When applied to states in the electronic continuum, however,

The parameters tuning of event generators is a research topic characterized by complex choices: the generator response to parameter variations is difficult to obtain on a theoretical basis, and numerical methods are hardly tractable due to the long computational times required by generators. Event generator tuning has been tackled by parametrization-based techniques, with the most successful one being

In this paper, we describe an efficient, massively parallel GPU implementation strategy for speeding up one-dimensional electrostatic plasma simulations based on the Particle-in-Cell method with Monte-Carlo collisions. Relying on the Roofline performance model, we identify performance-critical points of the program and provide optimised solutions. We use four benchmark cases to verify the correctness

A computer code for the computation of the phase shift in atom-atom and electron-atom potential scattering is presented. The phase shift is the central quantity required for the calculation of all types of scattering cross sections. The program uses the Variable Phase Approach (VPA). This is the only exact method for the direct calculation of the scattering phase shift. All other methods are based

We present a numerical algorithm that enables a phase-space adaptive Eulerian Vlasov–Fokker–Planck (VFP) simulation of inertial confinement fusion (ICF) capsule implosions. The approach relies on extending a recent mass, momentum, and energy conserving phase-space moving-mesh adaptivity strategy to spherical geometry. In configuration space, we employ a mesh motion partial differential equation (MMPDE)

Paris (PArallel, Robust, Interface Simulator) is a finite volume code for simulations of immiscible multifluid or multiphase flows. It is based on the “one-fluid” formulation of the Navier–Stokes equations where different fluids are treated as one material with variable properties, and surface tension is added as a singular interface force. The fluid equations are solved on a regular structured staggered

Software to analyse very large sets of experimental data often relies on a pipeline of irregular computational tasks with decisions to remove irrelevant data from further processing. A user-centred framework was designed and deployed, HEP-Frame, which aids domain experts to develop applications for scientific data analyses and to monitor and control their efficient execution. The key feature of HEP-Frame

The finite-time dynamical method is an effective tool studying phase transition in many-body systems. We design a parallel version of this method based on replica exchange whose probability is deduced from Langevin equation. The configuration swaps between different replicas enhance the importance sampling in parallel and control the fluctuation, leading to the conspicuous improvement for the simulation

Study of far-from-equilibrium thermalisation dynamics in quantum materials, including the dynamics of different types of quasiparticles, is becoming increasingly crucial. However, the inherent complexity of either the full quantum mechanical treatment or the solution of the scattering integral in the Boltzmann approach, has significantly limited the progress in this domain. In our previous work we

This work begins with the discretization of the governing equations of magnetic field for different type of magnetic media over a two-dimensional rectangular domain using a Cartesian grid system. The basic rules that the coefficients of the discretization equation should obey, to ensure physical realism and overall balance, are discussed. In order to satisfy the rule, “consistency at control-volume

Ultra-violet photoemission spectroscopy is a widely-used experimental technique to investigate the valence electronic structure of surfaces and interfaces. When detecting the intensity of the emitted electrons not only as a function of their kinetic energy, but also depending on their emission angle, as is done in angle-resolved photoemission spectroscopy (ARPES), extremely rich information about the

Neutrino models based on flavour symmetries provide a natural way to explain the origin of tiny neutrino masses. At the dawn of precision measurements of neutrino oscillation parameters, neutrino mass models can be constrained and examined by on-going and up-coming neutrino experiments. We present a supplemental tool Flavour Symmetry Embedded (FaSE) for General Long Baseline Experiment Simulator (GLoBES)

High-energy-density (HED) hydrodynamics studies such as those relevant to inertial confinement fusion and astrophysics require highly disparate densities, temperatures, viscosities, and other diffusion parameters over relatively short spatial scales. This presents a challenge for high-order accurate methods to effectively resolve the hydrodynamics at these scales, particularly in the presence of highly

We present STREAmS, an in-house high-fidelity solver for direct numerical simulations (DNS) of canonical compressible wall-bounded flows, namely turbulent plane channel, zero-pressure gradient turbulent boundary layer and supersonic oblique shock-wave/boundary layer interaction. The solver incorporates state-of-the-art numerical algorithms, specifically designed to cope with the challenging problems

The global impurity transport code (GITR - pronounced “guitar”) has been developed as a high-performance Monte Carlo particle (neutral atom and ion) tracking code to simulate the erosion, ionization, migration, and redistribution of plasma-facing components in magnetically confined fusion devices. The trace impurity assumption allows for a highly parallel computational model that enables increased

In this paper, a Petrov–Galerkin finite element interface method (PGFEIM) is proposed to compute the band structures of 2D photonic crystals (PtCs) with complex scatterer geometry, which is formulated as a generalized eigenvalue problem (GEP) for given wave vectors. The key idea of this method is to choose a piecewise linear function satisfying the jump conditions across the interface to be the solution

A novel mapping of the semi-bounded (R,Z) domain to a finite computational domain is used to solve the free-boundary axisymmetric equilibrium problem for tokamaks. Using this new mapping technique, the nonlinear Grad-Shafranov (GS) equation can be solved using only the “inner iterations” but with the actual boundary condition at infinity. Eliminating the outer iterations of the traditional algorithms

A new version release (4.0) of the molecular simulation tool ms2 (Deublein et al. 2011; Glass et al. 2014; Rutkai et al. 2017) is presented. Version 4.0 of ms2 features two additional potential functions to address the repulsive and dispersive interactions in a more versatile way, i.e. the Mie potential and the Tang–Toennies potential. This version further introduces Kirkwood–Buff integrals based on

Due to its rising importance in science and technology in recent years, particle tracking in videos presents itself as a tool for successfully acquiring new knowledge in the field of life sciences and physics. Accordingly, different particle tracking methods for various scenarios have been developed. In this article, we present a particle tracking application implemented in Python for, in particular

Non-Newtonian fluid flows, especially in three dimensions (3D), arise in numerous settings of interest to physics. Prior studies using the lattice Boltzmann method (LBM) of such flows have so far been limited mainly to two dimensions and used less robust collision models. In this paper, we develop a new 3D cascaded LBM based on central moments and multiple relaxation times (MRT) on a three-dimensional

The Graphical User Interface for Density Functional Theory (GUI4dft) is a new software for users of SIESTA. It is a free cross-platform software with a graphical user interface. GUI4dft allows the user to work with standard SIESTA files and prepare manuscript-quality figures of the atomic structure and properties such as three-dimensional charge density distributions, DOS, PDOS, and band structure

This paper describes the Jas4pp framework for exploring physics cases and for detector-performance studies of future particle collision experiments. Jas4pp is a multi-platform Java program for numeric calculations, scientific visualization in 2D and 3D, storing data in various file formats and displaying collision events and detector geometries. It also includes complex data-analysis algorithms for

picFoam is a fully kinetic electrostatic Particle-in-Cell (PIC) solver, including Monte Carlo Collisions (MCC), for non-equilibrium plasma research in the open-source framework of OpenFOAM. The solver’s modular design, based on the same principles used in OpenFOAM, makes it highly flexible, by allowing the user to choose different methods at run time, and extendable, by building upon templated modular

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

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

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

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

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

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

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

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

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 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

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

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

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 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