A new method based on a time diffusion technique is developed to mitigate the numerical instability induced by the high frequency electrostatic shear Alfvén wave (ωH mode) in the gyrokinetic simulation of electrostatic turbulence. It can preserve fully drift-kinetic electron effects and can be incorporated efficiently with explicit time integration scheme. This method has been implemented in the semi-Lagrangian

Numerical simulations of nonhydrostatic atmospheric flow, based on linearly decoupled semi-implicit or fully-implicit techniques, usually solve linear systems by a pre-conditioned Krylov method without preserving the skew-symmetry of convective operators. We propose to perform atmospheric simulations in such a fully-implicit manner that the difference operators preserve both the skew-symmetry and the

This paper discusses the algorithmic generation of Feynman graphs for QFT models that have some form of explicit propagator mixing, including some related theoretical background. Primarily, it is shown that an ordinary Feynman graph generator — ie one that is able to deal with models without mixed propagators — can be employed to simulate the former, more general type of graph generation. Most of the

We give a detailed presentation of the theory and numerical implementation of an expression for the adiabatic energy flux in extended systems, derived from density-functional theory. This expression can be used to estimate the heat conductivity from equilibrium ab initio molecular dynamics, using the Green-Kubo linear response theory of transport coefficients. Our expression is implemented in an open-source

In this paper, a new cell-centered positivity-preserving finite volume scheme is proposed for the 3D anisotropic diffusion problems on distorted meshes. The primary unknowns and auxiliary unknowns are used in this scheme. First, the one-sided flux on each cell facet is discretized by a fixed stencil. Then, the nonlinear two-point flux approximation is applied to get the cell-centered discrete scheme

No area of computing is hungrier for performance than High Performance Computing (HPC), the demands of which continue to be a major driver for processor performance and adoption of accelerators, and also advances in memory, storage, and networking technologies. A key feature of the Intel processor domination of the past decade has been the extensive adoption of GPUs as coprocessors, whilst more recent

Automatic Defect Analysis and Qualification (ADAQ) is a collection of automatic workflows developed for high-throughput simulations of magneto-optical properties of point defects in semiconductors. These workflows handle the vast number of defects by automating the processes to relax the unit cell of the host material, construct supercells, create point defect clusters, and execute calculations in

Recently, there has been considerable interest in solving optimization problems by mapping these onto a binary representation, sparked mostly by the use of quantum annealing machines. Such binary representation is reminiscent of a discrete physical two-state system, such as the Ising model. As such, physics-inspired techniques—commonly used in fundamental physics studies—are ideally suited to solve

The CGMF code implements the Hauser-Feshbach statistical nuclear reaction model to follow the de-excitation of fission fragments by successive emissions of prompt neutrons and γ rays. The Monte Carlo technique is used to facilitate the analysis of complex distributions and correlations among the prompt fission observables. Starting from initial configurations for the fission fragments in mass, charge

Lattice models consisting of high-dimensional local degrees of freedom without global particle-number conservation constitute an important problem class in the field of strongly correlated quantum many-body systems. For instance, they are realized in electron-phonon models, cavities, atom-molecule resonance models, or superconductors. In general, these systems elude a complete analytical treatment

The simulation of beam energy transfer and medium dynamics is essential in nuclear studies and designs involving the beam loading on targets. Although the existing methods are relatively mature in simulating the thermohydrodynamics of a solid or liquid target coupled with an energetic beam, they may not be entirely applicable to a complex porous medium such as granular materials with massive discrete

Particle physics experiments entail the collection of large data samples of complex information. In order to produce and detect low probability processes of interest (signal), a huge number of particle collisions must be carried out. This type of experiments produces huge sets of observations where most of them are of no interest (background). For this reason, a mechanism able to differentiate rare

Avoidance of the harmful effects of runaway electrons (REs) in plasma-terminating disruptions is pivotal in the design of safety systems for magnetic fusion devices. Here, we describe a computationally efficient numerical tool, that allows for self-consistent simulations of plasma cooling and associated RE dynamics during disruptions. It solves flux-surface averaged transport equations for the plasma

In electrical engineering and physics, Maxwell's equations play a very important role and have a variety of applications. In this paper, we propose and analyse a novel class of time domain conservative schemes in rectangular coordinate to solve Maxwell's equations with periodic boundary conditions. This class of methods is explicit and easy to implement with low computational cost and memory storage

The Maxwell-Bloch equations are a valuable tool to model light-matter interaction, where the application examples range from the description of pulse propagation in two-level media to the elaborate simulation of optoelectronic devices, such as the quantum cascade laser (QCL). In this work, we present mbsolve, an open-source solver tool for the Maxwell-Bloch equations. Here, we consider the one-dimensional

multiUQ is a novel tool that simulates gas-liquid multiphase flows and quantifies uncertainty in results due to variability about fluid properties and initial/boundary conditions. The benefit over a typical deterministic solver is that inexact information, such as variability in fluid properties or flow rates, can be included to determine the affect on simulation solutions. It is common to deploy non-intrusive

The last ten years have witnessed fast spreading of massively parallel computing clusters, from leading supercomputing facilities down to the average university computing center. Many companies in the private sector have undergone a similar evolution. In this scenario, the seamless integration of software and middleware libraries is a key ingredient to ensure portability of scientific codes and guarantees

GroupMath is a Mathematica package which performs several calculations related to semi-simple Lie algebras and the permutation groups, both of which are important in various areas of physics. Having in mind the specific needs of theoretical particle physicists, the program computes several basis-independent quantities (such as roots, weights, decomposition of products of representations, branching

In this paper, exponential propagator (EP) is introduced to the discontinuous Galerkin finite element method (DG-FEM) for solving transient electromagnetic problems. As a kind of explicit time-stepping method, the proposed EP has fourth order accuracy in time and requires only one storage unit for each of the degrees-of-freedom. It provides an attractive alternative to the high-order low-storage explicit

The tight-binding (TB) model is complementary to the ab-initio methods that can be represented by the well-known Density Functional Theory since the empirical nature of a TB model enables the scope of electronic structure simulations to include realistically sized nanoscale structures that are normally made up of several million atoms. As the major computational hotspot of TB simulations comes from

Recently the drift-reduced Landau fluid six-field turbulence model within the BOUT++ framework [1] has been upgraded. In particular, this new model employs a new normalization, adds a volumetric flux-driven source option, the Landau fluid closure for parallel heat flux and a Laplacian inversion solver which is able to capture n=0 axisymmetric mode evolution in realistic tokamak configurations. These

In atomic structure and collision theory, the efficient spin-angular integration is known to be crucial and often decides, how accurate the properties and behavior of atoms can be predicted numerically. Various methods have been developed in the past to keep the computation (and implementation) of the spin-angular integration feasible for complex shell structures, including open d- and f-shell elements

We show how the well-known Wang-Landau method can be modified to produce non-flat distributions. Through the choice of a suitable profile this can lead to an increase in efficiency for some systems. Examples for such an enhancement are provided.

We present the first public version of Caravel, a C++17 framework for the computation of multi-loop scattering amplitudes in quantum field theory, based on the numerical unitarity method. Caravel is composed of modules for the D-dimensional decomposition of integrands of scattering amplitudes into master and surface terms, the computation of tree-level amplitudes in floating point or finite-field arithmetic

We present SpectrumSDT – a program for calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems. Large-amplitude vibrational motion is treated

The NCrystal library provides a range of models for simulation of both elastic and inelastic scattering of thermal neutrons in a range of material structures. This article presents the available models for elastic scattering, and includes detailed discussion of their theoretical background, their implementation, and in particular their validation. The lineup includes a model for Bragg diffraction in

This is a revised and updated version of the package GammaCHI. The package includes routines for computing and inverting the gamma and chi-square cumulative distribution functions (central and noncentral). Additionally, the package also provides routines for computing the gamma function, the error function and other functions related to the gamma function (the logarithm of the gamma function, the regulated

We present a robust analysis code developed in the Python language and incorporating libraries of the ROOT data analysis framework for the state-of-the-art mass spectrometry method called phase-imaging ion-cyclotron-resonance (PI-ICR). A step-by-step description of the dataset construction and analysis algorithm is given. The code features a new phase-determination approach that offers up to 10 times

The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix (Cij) obtained from any ab-initio density-functional theory (DFT) code. The current version of this package reads the output of VASP, ABINIT, and Quantum Espresso codes (but it can be easily generalized to any other DFT code) and performs the appropriate post-processing

The Wu-Wentzcovitch semi-analytical method (SAM) is a concise and predictive formalism to calculate the high-pressure and high-temperature (high-PT) thermoelastic tensor (Cij) of crystalline materials. This method has been successfully applied to materials across different crystal systems in conjunction with ab initio calculations of static elastic coefficients and phonon frequencies. Such results

We present VAH, a (3+1)–dimensional simulation that evolves the far-from-equilibrium quark-gluon plasma produced in ultrarelativistic heavy-ion collisions with anisotropic fluid dynamics. We solve the hydrodynamic equations on an Eulerian grid using the Kurganov–Tadmor algorithm in combination with a new adaptive Runge–Kutta method. Our numerical scheme allows us to start the simulation soon after

We present ComCTQMC, a GPU accelerated quantum impurity solver. It uses the continuous-time quantum Monte Carlo (CTQMC) algorithm wherein the partition function is expanded in terms of the hybridisation function (CT-HYB). ComCTQMC supports both partition and worm-space measurements, and it uses improved estimators and the reduced density matrix to improve observable measurements whenever possible.

Computational load imbalance is a well-known performance issue in multiprocessor reacting flow simulations utilizing directly integrated chemical kinetics. We introduce an open-source dynamic load balancing model named DLBFoam to address this issue within OpenFOAM, an open-source C++ library for Computational Fluid Dynamics (CFD). Due to the commonly applied operator splitting practice in reactive

Understanding the intricate properties of one-dimensional quantum systems coupled to multiple reservoirs poses a challenge to both analytical approaches and simulation techniques. Fortunately, density matrix renormalization group-based tools, which have been widely used in the study of closed systems, have also been recently extended to the treatment of open systems. We present an implementation of

In this paper, we present an open-source multi-resolution and multi-physics library, SPHinXsys, which is released under the Apache License (2.0). Along with the source code, a complete documentation is also distributed for easy compilation and execution. SPHinXsys aims at modeling coupled multi-physics industrial dynamic systems within a unified SPH framework. It has two important features, namely

A quadrature-based moment method for the approximate solution of the generalized population balance equation (GPBE) governing the evolution of the joint size-velocity number density function (NDF) of a particle population is formulated and tested. The proposed method relies on the third-order hyperbolic conditional quadrature method of moments developed for velocity distribution transport. This approach

Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts

Equation of motion method has proven efficient for electronic structure calculations of very large systems, i.e. containing several million atoms. In this work, we redesign its previously published implementation and hereby release a revised software tool, EQMO, now capable of solving a crystalline TiO2 test sample of nearly a quarter of a billion atoms on NEC SX-Aurora TSUBASA vector computer. The

We present a new improved version of BiconeDrag, a code that allows one to obtain the values of interfacial dynamic moduli from dynamic experiments performed in rotational interfacial shear rheometers with bicone probes. The general structure of the program remains the same: starting from the values of the torque/angular displacement amplitude ratio, and by using the equations of the hydrodynamic field

OpenSBLI is an open-source code-generation system for compressible fluid dynamics (CFD) on heterogeneous computing architectures. Written in Python, OpenSBLI is an explicit high-order finite-difference solver on structured curvilinear meshes. Shock-capturing is performed by a choice of high-order Weighted Essentially Non-Oscillatory (WENO) or Targeted Essentially Non-Oscillatory (TENO) schemes. OpenSBLI

We present an open-source code for the simulation of electron and ion transport for user-defined gas mixtures with static uniform electric and magnetic fields. The program provides microscopic interaction simulation and is interfaced with cross-section tables published by LXCat[1]. The framework was validated against drift velocity tables available in literature obtaining an acceptable match for atomic

The energy minimization involved in density functional calculations of electronic systems can be carried out using an exponential transformation that preserves the orthonormality of the orbitals. The energy of the system is then represented as a function of the elements of a skew-Hermitian matrix that can be optimized directly using unconstrained minimization methods. An implementation based on the

The REGINA code calculates the São Paulo potential version 2 (SPP2) and the Brazilian nuclear potential (BNP). The code also provides nuclear densities obtained from the Dirac-Hartree-Bogoliubov model, which are used to calculate the nuclear potentials. Elastic scattering cross sections are obtained within the context of the optical model, with different options for the real and imaginary parts of

Given a value of the Fermi-Dirac integral ∫0∞tjdtet−η+1, this routine returns the value of the parameter η for a given j with a relative error less than 10−13. The inversion is provided for η∈[−30,100] and for the following set of j values, {−1/2,1/2,3/2,5/2,1,2}. For η∈[−30,−2], an iterative method involving the McDougall and Stoner series is used. For the rest of the region of interest, a rational

Epidemic processes on random graphs or networks are marked by localization of activity that can trap the dynamics into a metastable state, confined to a subextensive part of the network, before visiting an absorbing configuration. Quasistationary (QS) method is a technique to deal with absorbing states for finite sizes and has played a central role in the investigation of epidemic processes on heterogeneous

Efficient numerical simulations of fluid flow on the pore scale allow for the numerical estimation of effective material properties of porous media like effective permeability or tortuosity, among others. In contrast to time-consuming and often expensive laboratory tests, pore scale-resolved numerical simulations further enable the computational quantification of anisotropy of inherent material properties

We present a new package for Mathematica system, called Libra. Its purpose is to provide convenient tools for the transformation of the first-order differential systems ∂ij=Mij for one or several variables. In particular, Libra is designed for the reduction to ϵ-form of the differential systems which appear in multiloop calculations. The package also contains some tools for the construction of general

We present novel roulette schemes for rare-event sampling that are both structure-preserving and unbiased. The boundaries where Monte Carlo markers are split and deleted are placed automatically and adapted during runtime. Extending existing codes with the new schemes is possible without severe changes because the equation of motion for the markers is not altered. These schemes can also be applied

The first-principles quantum perturbation theory, also called density-functional perturbation theory (DFPT), is the state-of-the-art formalism to directly link the experimental response properties of the materials with the quantum modeling of the electrons. Here in this work, we present an implementation of all-electron DFPT for massively parallel Sunway many-core architectures to accelerate DFPT calculation

We present the VASPKIT, a command-line program that aims at providing a robust and user-friendly interface to perform high-throughput analysis of a variety of material properties from the raw data produced by the VASP code. It consists of mainly the pre- and post-processing modules. The former module is designed to prepare and manipulate input files such as the necessary input files generation, symmetry

The Lattice Boltzmann Method algorithm is simplified by assuming constant numerical viscosity (the relaxation time is fixed at τ=1). This leads to the removal of the distribution function from the computer memory. To test the solver the Poiseuille and Driven Cavity flows are simulated and analyzed. The error of the solution decreases with the grid size L as L−2. Compared to the standard algorithm,

By developing a multilevel thermosolutal phase-field lattice-Boltzmann method, we achieve three-dimensional phase-field simulations of dendrite growth with realistic Lewis number (Le∼104) in equivalently over 108 uniform meshes. In addition to parallel computing and mesh adaptivity, the high-performance computing algorithm allows the time step enlarged by 2–3 orders of magnitude in an explicit scheme

We present the detailed formalism for stress calculations within the framework of numerical atomic orbital (NAO) bases, as implemented in the first-principles electronic code package ABACUS. The validity and numerical precision of our implementation are benchmarked against reference results obtained using the finite difference method as well as those calculated using plane wave (PW) bases. The equation

We present a high-energy neutrino event generator, called LeptonInjector, alongside an event weighter, called LeptonWeighter. Both are designed for large-volume Cherenkov neutrino telescopes such as IceCube. The neutrino event generator allows for quick and flexible simulation of neutrino events within and around the detector volume, and implements the leading Standard Model neutrino interaction processes

Optical properties of warm dense matter are computed within linear response theory using the Kubo-Greenwood formula in the framework of Density Functional Theory and the Projector Augmented–Wave (PAW) method. For transition metals, the effect of spin-orbit coupling (SOC) has to be taken into account. We present the theoretical framework to introduce SOC in the PAW formalism and then to compute optical

A Monte Carlo framework for solving optimal control problems governed by kinetic models is presented. The focus is on a kinetic model with Keilson-Storer linear collision term and the control mechanism is an external space-dependent force. The purpose of this control is to drive an ensemble of particles to acquire a desired mean velocity and position and to reach a desired final configuration in phase

The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the corresponding X-ray scattering response in one-dimensional samples, such as multilayers. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of element-specific physical