Eigenvalues of the Hermitian Wilson–Dirac operator are of special interest in several lattice QCD simulations, e.g., for noise reduction when evaluating all-to-all propagators. In this paper we present a Davidson-type eigensolver that utilizes the structural properties of the Hermitian Wilson–Dirac operator Q to compute eigenpairs of this operator corresponding to small eigenvalues. The main idea is

The real-space density-functional perturbation theory (DFPT) for the computations of the response properties with respect to the atomic displacement and homogeneous electric field perturbation has been recently developed and implemented into the all-electron, numeric atom-centered orbitals electronic structure package FHI-aims. It is found that the bottleneck for large scale applications is the computation

First presented in 1993, Dissipative Particle Dynamics(DPD) has gained increasingly popularity in the scientific community due to its extensive potential to be employed in a broad range of mesoscale systems, such as polymers, colloids, surfactants and many other multi-phase systems. Although much research has been done in DPD systems, a challenge still persists when physical boundaries, such as the

This paper discusses a parallelized event reconstruction of the COMET Phase-I experiment. The experiment aims to discover charged lepton flavor violation by observing 104.97 MeV electrons from neutrinoless muon-to-electron conversion in muonic atoms. The event reconstruction of electrons with multiple helix turns is a challenging problem because hit-to-turn classification requires a high computation

We present an effective computer simulation method, called 3D object stochastic kinetic modelling framework (3DO-SKMF), to calculate atomic movements in 3D objects including surface segregation and Gibbs–Thomson effect (surface curvature). Objects with any kind of shapes can easily be considered thanks to the flexibility and versatility of the model and code. Accordingly, the model and the computer

The ALICE experiment at the CERN LHC focuses on studying the quark-gluon plasma produced by heavy-ion collisions. Starting from 2021, it will see its input data throughput increase a hundredfold, up to 3.5 TB/s. To cope with such a large amount of data, a new online-offline computing system, called O2, will be deployed. It will synchronously compress the data stream by a factor of 35 down to 100 GB/s

Hadron production at low transverse momenta in semi-inclusive deep inelastic scattering can be described by transverse momentum dependent (TMD) factorization. This formalism has also been widely used to study the Drell–Yan process and back-to-back hadron pair production in e+e− collisions. These processes are the main ones for extractions of TMD parton distribution functions and TMD fragmentation functions

Here we present a new code for modelling electron kinetics in the tokamak Scrape-Off Layer (SOL). SOL-KiT (Scrape-Off Layer Kinetic Transport) is a fully implicit 1D code with kinetic (or fluid) electrons, fluid (or stationary) ions, and diffusive neutrals. The code is designed for fundamental exploration of non-local physics in the SOL and utilizes an arbitrary degree Legendre polynomial decomposition

Single-file diffusion is a paradigm for strongly correlated classical stochastic many-body dynamics and has widespread applications in soft condensed matter and biophysics. However, exact results for single-file systems are sparse and limited to the simplest scenarios. We present an algorithm for computing the non-Markovian time-dependent conditional probability density function of a tagged-particle

Computational physics problems often have a common set of aspects to them that any particular numerical code will have to address. Because these aspects are common to many problems, having a framework already designed and ready to use will not only speed the development of new codes, but also enhance compatibility between codes. Some of the most common aspects of computational physics problems are:

We introduce a new Python package (pyHMA) that interfaces with VASP to compute (classical) anharmonic properties of crystalline systems by post-processing data from NVT Born–Oppenheimer ab initio molecular dynamics (AIMD) simulation. It is based on the recently developed harmonically mapped averaging (HMA) method, which leverages the analytically known harmonic behavior to reformulate the direct/conventional

The nuclear mean-field model based on Skyrme forces can predict a variety of properties of nuclear ground states. We present the Code SkyAx solving the Hartree–Fock equations in two spatial dimensions assuming axial symmetry. Pairing can be included in the BCS approximation. The code is implemented with a view on computational speed. Program summary Program title: SkyAx CPC Library link to program

Potential energy is important ingredient in static and dynamical investigations of a nuclear fission process. The calculation of surface, nuclear, Coulomb, rotational, curvature, congruence, and Wigner energy functionals is presented for large variety of nuclear shapes generated by a {c,h,α} parametrization. Using these functionals one can calculate the potential energy in several macroscopic models

The iS3D particlization module simulates the emission of hadrons from heavy-ion collisions via Monte-Carlo sampling of the Cooper–Frye formula which converts fluid dynamical information into local phase-space distributions for hadrons. The code package includes multiple choices for the non-equilibrium correction to these distribution functions: the 14-moment approximation, first-order Chapman–Enskog

This work presents novel discrete event-based simulation algorithms based on the Quantized State System (QSS) numerical methods. QSS provides attractive features for particle transportation processes, in particular a very efficient handling of discontinuities in the simulation of continuous systems. We focus on High Energy Physics (HEP) particle tracking applications that typically rely on discrete

A customized finite-difference field solver for the particle-in-cell (PIC) algorithm that provides higher fidelity for wave-particle interactions in intense electromagnetic waves is presented. In many problems of interest, particles with relativistic energies interact with intense electromagnetic fields that have phase velocities near the speed of light. Numerical errors can arise due to (1) dispersion

Monte Carlo ray-tracing method has become a promising technique for solving radiative transfer. However, large memory footprint or long CPU time hamper its further utilization. In this work, a Monte Carlo ray-tracing method radiation solver called mcrtFOAM is developed in the framework of open source CFD toolbox OpenFOAM. The radiative source term is calculated based on the radiation distribution factor

Spectral analysis systems using gamma radiation to determine the percentage fraction of several compounds in a sample need several stages. The conditioning number of covariance matrices associated with the least-squares system needs to be very close to one so that the determined values are as close as possible to the actual values. Scientific evidence gives us reason to believe that these matrices

Accurate evaluation of the thermal conductivity of a material can be a challenging task from both experimental and theoretical points of view. In particular for the nanostructured materials, the experimental measurement of thermal conductivity is associated with diverse sources of uncertainty. As a viable alternative to experiment, the combination of density functional theory (DFT) simulations and

We focus here on a class of fourth-order parabolic equations that can be written as a system of second-order equations by introducing an auxiliary variable. We design a novel second-order fully discrete mixed finite element method to approximate these equations. In our approach, we propose new techniques using the second-order backward differentiation formula for the time derivative and a special technique

Finite-grid (or aliasing) instabilities are pervasive in particle-in-cell (PIC) plasma simulation algorithms, and force the modeler to resolve the smallest (Debye) length scale in the problem regardless of dynamical relevance. These instabilities originate in the aliasing of interpolation errors between mesh quantities and particles (which live in the space–time continuum). Recently, strictly energy-conserving

Fluid flow simulation is a highly active area with applications in a wide range of engineering problems and interactive systems. Meshless methods like the Moving Particle Semi-implicit (MPS) are a great alternative to deal efficiently with large deformations and free-surface flow. However, mesh-based approaches can achieve higher numerical precision than particle-based techniques with a performance

We present high-performance and high-accuracy numerical simulations of quantum turbulence modelled by the Gross–Pitaevskii equation for the time-evolution of the macroscopic wave function of the system. The hydrodynamic analogue of this model is a flow in which the viscosity is absent and all rotational flow is carried by quantized vortices with identical topological line-structure and circulation

A novel inline data compression method is presented for single-precision vectors in three dimensions. The primary application of the method is for accelerating computational physics calculations where the throughput is bound by memory bandwidth. The scheme employs spherical polar coordinates, angle quantisation, and a bespoke floating-point representation of the magnitude to achieve a fixed compression

Every computer model depends on numerical input parameters that are chosen according to mostly conservative but rigorous numerical or empirical estimates. These parameters could for example be the step size for time integrators, a seed for pseudo-random number generators, a threshold or the number of grid points to discretize a computational domain. In case a numerical model is enhanced with new algorithms

The Finite Element Gaussian Belief Propagation (FGaBP) method is an iterative algorithm with abundant parallelism making it an alternative for the traditional Finite Element Method (FEM), especially for large multi-physics problems. In this paper, we extend the FGaBP method to solve the coupled electrical-thermal problem that emerges in the modeling of radiofrequency ablation (RFA) of hepatic tumors

We present SimpleBounce, a C++ package for finding the bounce solution for the false vacuum decay. This package is based on a flow equation which is proposed by the author R. Sato (2020) and solves Coleman–Glaser–Martin’s reduced problem (S. R. Coleman et al. 1978): the minimization problem of the kinetic energy while fixing the potential energy. The bounce configuration is obtained by a scale transformation

In this paper, we present the basic routines of the C++-program Matslise 3.0, an updated but yet restricted version of the matlab package Matslise 2.0. Matslise 3.0 currently allows the accurate, but in comparison to Matslise 2.0, faster computation of eigenvalues and eigenfunctions of one dimensional time-independent Schrödinger problems. The numerical examples show that speed up factors up to 20

A general program to fit global adiabatic potential energy surfaces of up to tetratomic molecules to ab initio points and available spectroscopic data for simple diatomics is reported. It is based on the Combined-Hyperbolic-Inverse-Power-Representation (CHIPR) method. The final form describes all dissociating fragments and long-range/valence interactions, while obeying the system permutational symmetry

In Grossu et al., (2019) we proposed a Chaos Many-Body Engine (CMBE) quark toy-model for the Compressed Baryonic Matter (CBM) energies. We started from the following assumptions: (1) the system can be decomposed into a set of two or three-body quark “elementary systems”, i.e. “white” color charged, mesonic or baryonic systems; (2) the bi-particle force is limited to the domain of each elementary system;

When computing electric conductivity based on the Kubo formula, vertex corrections describe such effects as anisotropic scattering and quantum interference and are important in determining quantum transport properties. These vertex corrections are obtained by solving the Bethe–Salpeter equation, which can become numerically intractable when a large number of k-points and multiple bands are involved

For Euler equations defined in a domain Ω with boundary conditions specified on a curved boundary Γ, we consider a discontinuous Galerkin (DG) method with high order polynomial basis functions on a geometry fitting triangular and tetrahedral grids. We derive a modification to the DG scheme defined on a boundary triangle and tetrahedron based on the general curvilinear element DG method. In the modified

We develop a conservative configuration- and velocity-space (i.e., phase-space) moving-grid strategy for the Vlasov–Fokker–Planck (VFP) equation in a planar geometry. The velocity-space grid is normalized and shifted in terms of the thermal speed and the bulk-fluid velocity, respectively. The configuration-space grid is moved according to a mesh-motion-partial-differential equation (MMPDE), which equidistributes

Inclusive Monte-Carlo samples are indispensable for signal selection and background suppression in many high energy physics experiments. A clear knowledge of the physics processes involved in the samples, including the types of processes and the number of processes in each type, is a great help to investigating signals and backgrounds. To help analysts obtain the physics process information from the

I present a Mathematica package designed for manipulations and evaluations of triple-K integrals and conformal correlation functions in momentum space. Additionally, the program provides tools for evaluation of a large class of 2- and 3-point massless multi-loop Feynman integrals with generalized propagators. The package is accompanied by five Mathematica notebooks containing detailed calculations

We present an open-source software package, NIC-CAGE (Novel Implementation of Constrained Calculations for Automated Generation of Excitations), for predicting quantum optimal control fields in photo-excited chemical systems. Our approach utilizes newly derived analytic gradients for maximizing the transition probability (based on a norm-conserving Crank–Nicolson propagation scheme) for driving a system

The calculation of overlaps between many-electron wave functions at different nuclear geometries during nonadiabatic dynamics simulations requires the evaluation of a large number of determinants of matrices that differ only in a few rows/columns. While this calculation is fast for small systems, its cost grows faster than the alternative electronic structure calculation used to obtain the wave functions

We have developed a flexible toolkit, named qvasp (quickly use vienna ab-initio simulation package), to assist users to prepare input files and process output files for Vienna Ab-initio Simulation Package (VASP) during materials simulations. Here, we systematically introduced its design architecture and techniques, as well as how to use qvasp to save time and energy during the materials calculations

In the world of computational fluid dynamics (CFD), solving the governing equations of incompressible, turbulent, single-phase fluid flow still represents the basis of many industrial and academic applications. The implicitly coupled (monolithic) solution approach is still being developed and investigated for industrial-size applications. A parallel selection algebraic multigrid algorithm (AMG) based

A new code to simulate special relativistic hydrodynamic flows on supercomputer architectures with distributed memory is described. The code is based on a combination of Godunov’s method and a piecewise parabolic method with a local stencil. This approach has good conservation properties, correctly reproduces shock waves, and ensures high accuracy on smooth solutions and low dissipation on discontinuities

We develop Kω, an open-source linear algebra library for the shifted Krylov subspace methods. The methods solve a set of shifted linear equations (zkI−H)x(k)=b(k=0,1,2,…) for a given matrix H and a vector b, simultaneously. The leading order of the operational cost is the same as that for a single equation. The shift invariance of the Krylov subspace is the mathematical foundation of the shifted Krylov

Restricted Boltzmann machines (RBM) provide a general framework for modeling physical systems, but their behavior is dependent on hyperparameters such as the learning rate, the number of hidden nodes and the form of the threshold function. This article accordingly examines in detail the influence of these parameters on Ising spin system calculations. A tradeoff is identified between the accuracy of

A method to derive the convenient representations for many two-photon amplitudes is suggested. It is based on the use of the gauge in which the photon propagator has only space components. The amplitudes obtained have no any strong numerical cancellations and, therefore, are very convenient for numerical evaluations. Our approach is illustrated by the consideration of the processes e+e−→e+e−e+e−, e+e−→e+e−μ+μ−

The solution to Maxwell–Bloch systems using an integral-equation-based framework has proven effective at capturing collective features of laser-driven and radiation-coupled quantum dots, such as light localization and modifications of Rabi oscillations. Importantly, it enables observation of the dynamics of each quantum dot in large ensembles in a rigorous, error-controlled, and self-consistent way

We present a framework to solve non-linear eigenvalue problems suitable for a Finite Element discretization. The implementation is based on the open-source finite element software GetDP and the open-source library SLEPc. As template examples, we propose and compare in detail different ways to address the numerical computation of the electromagnetic modes of frequency-dispersive objects. This is a non-linear

A radiating electric dipole is located near the interface with a layer of material. The electric and magnetic fields reflect off the interface and transmit through the material. The exact solution of Maxwell’s equations can be found in terms of Sommerfeld-type integrals. These integrals have in general a singularity on the integration axis, and the integrands are extremely complicated functions of

MITNS (Multiple-Ion Transport Numerical Solver) is a new numerical tool designed to perform 1D simulations of classical cross-field transport in magnetized plasmas. Its detailed treatment of multi-species effects makes it a unique tool in the field. We describe the physical model it simulates, as well as its numerical implementation and performance. Program summary Program Title: MITNS (Multiple-Ion

Nonequispaced discrete Fourier transformation (NDFT) is widely applied in all aspects of computational science and engineering. The computational efficiency and accuracy of NDFT has always been a critical issue in hindering its comprehensive applications both in intensive and in extensive aspects of scientific computing. In our previous work Yang et al. (2018), a CUNFFT method was proposed and it shown

We present the concept of H-COUP_ver 2, which evaluates the decay rates (including higher order corrections) for the Higgs boson with a mass of 125GeV in various extended Higgs models. In the previous version (H-COUP_1.0), only a full set of the Higgs boson vertices are evaluated at one-loop level in a gauge invariant manner in these models. H-COUP_ver 2 contains all the functions of H-COUP_1.0. After

An efficient implementation of the self-consistent GW method in the FlapwMBPT code https://www.bnl.gov/cmpmsd/flapwmbpt/ is presented. It features the evaluation of polarizability and self-energy which scales linearly with respect to the system size. Altogether the computational time scaling was measured to be between linear and quadratic in the applications to silicon supercells with up to 72 atoms

A program, ARTEMIS, has been developed for the study of interface structures. This software allows for the generation of interfaces by identifying lattice matches between two parent crystal structures. To allow for further exploration of the energetic space of the interface, multiple surface terminations parallel to the Miller plane, interface alignments and intermixings are used to generate sets of

The construction of perfectly-matched-layer (PML) boundary conditions is extended to wave equations with non-trivial energy–momentum dispersion relation. Complex coordinate extension is based upon the relative sign between the surface-normal component of group velocity and the k-vector. This ensures selective damping of propagating and counter-propagating modes at the simulation boundaries. Moreover

The governing equations of the flow of an oldroyd-B fluid are discretized using the finite element method. To overcome the convective nature of the momentum equation, the Galerkin/Least-Squares Finite Element Method (GLS/FEM) is used while the Discrete Elastic–Viscous Stress-Splitting (DEVSS) method is used to overcome the instability due to the absence of diffusion in the constitutive equations. The

Numerical modeling is an essential approach to understanding the behavior of thermal plasmas in various industrial applications. We propose a deep learning method for solving the partial differential equations in thermal plasma models. In this method a deep feed-forward neural network is constructed to surrogate the solution of the model. A loss function is designed to measure the discrepancy between

We present LieART 2.0 which contains substantial extensions to the Mathematica application LieART (Lie Algebras and Representation Theory) for computations frequently encountered in Lie algebras and representation theory, such as tensor product decomposition and subalgebra branching of irreducible representations. The basic procedure is unchanged—it computes root systems of Lie algebras, weight systems

We present and distribute a FreeFem++ Toolbox for the parallel computing of two- or three-dimensional liquid–solid phase-change systems involving natural convection. FreeFem++ (www.freefem.org) is a free finite-element software available for all existing operating systems. We use the recent library ffddm that makes available in FreeFem++ state-of-the-art scalable Schwarz domain decomposition methods

stgf is a community code employed for outer-region R-matrix calculations, describing electron-impact collisional processes. It is widely recognised that the original version of stgf was written by M.J. Seaton in 1983, but through constant refinement over the next decades by worldwide contributors has evolved into its current form that more reflects modern coding practice and current computer architectures

The rapid development of the high-throughput calculations and materials genome approaches in recent years has improved researchers’ ability to design advanced materials. Crystal structure prediction techniques play an important role in high-throughput calculations and materials genome approaches. However, the huge computational cost of the widely used crystal structure prediction techniques based on

We present a Fourier Continuation-based parallel pseudospectral method for incompressible fluids in cuboid non-periodic domains. The method produces dispersionless and dissipationless derivatives with fast spectral convergence inside the domain, and with very high order convergence at the boundaries. Incompressibility is imposed by solving a Poisson equation for the pressure. Being Fourier-based, the

A java-based graphical tool for drawing Feynman diagrams is presented. It differs from similar existing tools in various respects. For example, it is based on models, consisting of particles (lines) and (optionally) vertices, each of which can be given their individual properties (line style, color, arrows, label, etc.). The diagrams can be exported in any standard image format, or as PDF. Aside from