We show how a Monte Carlo method for generating self-avoiding walks on lattice geometries which employs a binary-tree data-structure can be adapted for hard-sphere polymers with continuous degrees of freedom. Data suggests that the time per Monte Carlo move scales logarithmically with polymer size. Next we generalize the method to Lennard-Jones polymers with untruncated monomer–monomer interaction

We present FeynCalc 9.3, a new stable version of a powerful and versatile Mathematica package for symbolic quantum field theory (QFT) calculations. Some interesting new features such as highly improved interoperability with other packages, automatic extraction of the ultraviolet divergent parts of 1-loop integrals, support for amplitudes with Majorana fermions and γ-matrices with explicit Dirac indices

We are launching FindBounce, a Mathematica package for the evaluation of the Euclidean bounce action that enters the decay rate of metastable states in quantum and thermal field theories. It is based on the idea of polygonal bounces, which is a semi-analytical approach to solving the bounce equation by discretizing the potential into piecewise linear segments. This allows for a fast and robust evaluation

In this paper, we develop and analyze a new divergence-free kernel approximation method for the time-dependent incompressible Stokes equations on surfaces. The novelty of our proposed method comes from the surface Helmholtz decomposition, which can convert the surface Stokes equations into a coupled equations in which the velocity is deadly divergence-free so that no inf–sup conditions have to be satisfied

We present LBsoft, an open-source software developed mainly to simulate the hydro-dynamics of colloidal systems based on the concurrent coupling between lattice Boltzmann methods for the fluid and discrete particle dynamics for the colloids. Such coupling has been developed before, but, to the best of our knowledge, no detailed discussion of the programming issues to be faced in order to attain efficient

Ab initio calculations based on the density functional theory (DFT) become a vital tool in material science for understanding and predicting material properties. However, DFT calculations involve several parameters and procedures that call for deep understanding on underlying theories and preceding knowledge on certain properties of target materials. Such technicalities cost a significant amount of

varRhoTurbVOF contains a set of OpenFOAM volume of fluid (VOF) solvers for turbulent isothermal multiphase flows, which are variable-density incompressible. Unlike their official counterparts, where Favre-averaged and Reynolds-averaged velocities coexist in different equations, new solvers use Favre-averaged velocities consistently in all equations. This major update introduces three main improvements

A new tool, PyHoLo software, was developed to help automate the process of determining magnetic field B from a series of holograms, registered at different environmental conditions (e.g. for upside and downside orientations of a sample in a specimen holder). This procedure involves translating single holograms into phase shift of electron wave, but also alignment of holograms (i.e. shift, rotation

We show that the visible sector probability density function of the Riemann-Theta Boltzmann machine corresponds to a Gaussian mixture model consisting of an infinite number of component multi-variate Gaussians. The weights of the mixture are given by a discrete multi-variate Gaussian over the hidden state space. This allows us to sample the visible sector density function in a straight-forward manner

We present and make available novel implementations of the two-dimensional Ising model that is used as a benchmark to show the computational capabilities of modern Graphic Processing Units (GPUs). The rich programming environment now available on GPUs and flexible hardware capabilities allowed us to quickly experiment with several implementation ideas: a simple stencil-based algorithm, recasting the

We have developed a highly efficient and portable fluid–structure interaction (FSI) simulation package, so-called OpenFSI. Within this package, the structure dynamics is accounted by a lattice model (LM) implemented in the framework of Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), demonstrating the same accuracy as finite element analysis. The fluid flow is resolved by Palabos

A new version of PETOOL (Parabolic Equation Toolbox) is introduced with various additional capabilities. PETOOL is an open-source and MATLAB-based software tool with a user-friendly graphical user interface (GUI) for the analysis and visualization of electromagnetic wave propagation over variable terrain and through arbitrary atmosphere. Four novel features of the second version are as follows: (i)

Recently, a continuous-time, deterministic analog solver based on ordinary differential equations (CTDS) was introduced, to solve Boolean satisfiability (SAT), a family of discrete constraint satisfaction problems. Since SAT is NP-complete, efficient algorithms would benefit solving a large number of decision type problems, both within industry and the sciences. Here we present a graphics processing

Solid particles can adhere to fluid interfaces, modifying interfacial properties such as the surface tension and the surface elasticity. We here describe a new simulation method, the Fast Interface Particle Interaction (FIPI) method, capable of simulating on commodity hardware up to 100k particles interacting with fluid interfaces of complex morphology. The method is based on resolving interfacial

In this paper we present a new Monte Carlo event generator ReneSANCe for simulation of processes at electron–positron colliders. In the current release of the generator the Bhabha scattering (e+e−→e−e+) and Higgs-strahlung (e+e−→ZH) process are implemented. Based on the SANC (Support for Analytic and Numeric Calculations for experiments at colliders) modules, the new generator takes into account complete

Many catalyst devices employ flow through porous structures, which leads to a complex macroscopic mass and heat transport. To unravel the detailed dynamics of the reactive gas flow, we present an all-encompassing model, consisting of thermal lattice Boltzmann model by Kang et al., used to solve the heat and mass transport in the gas domain, coupled to a finite differences solver for the heat equation

We present an implicit numerical method to solve the time-dependent equations of radiation hydrodynamics (RHD) in axial symmetry assuming hydrostatic equilibrium perpendicular to the equatorial plane (1+1D) of a gaseous disk. The equations are formulated in conservative form on an adaptive grid and the corresponding fluxes are calculated by a spacial second order advection scheme. Self-gravity of the

We present a program to compute polarizabilities of nominal one-electron systems using the Lagrange-mesh method (LMM) (Mitroy et al., 2010), that was used by Filippin et al., (2018). A semiempirical-core-potential approach is implemented, ultimately solving a Dirac-like equation by diagonalising the corresponding Hamiltonian matrix. In order to build the core potential, the core orbitals are obtained

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the

Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries (finite non-periodic vs. infinite

We describe the implementation of PWDFT.jl, a package for electronic structure calculations written in Julia programming language using plane wave basis set and pseudopotentials. In this package, a typical Kohn–Sham density functional theory (KSDFT) is divided into three steps: initializing the molecular or crystalline structure, constructing the Kohn–Sham Hamiltonian, and solving the Kohn–Sham problem

The KM3NeT Collaboration runs a multi-site neutrino observatory in the Mediterranean Sea. Water Cherenkov particle detectors, deep in the sea and far off the coasts of France and Italy, are already taking data while incremental construction progresses. Data Acquisition Control software is operating off-shore detectors as well as testing and qualification stations for their components. The software

In this work, we first propose a new hydrodynamically-coupled phase-field model for the diblock copolymer melt that is derived based on the Allen-Cahn dynamics where the volume fraction of two composing monomers is conserved by using a nonlocal Lagrange multiplier. Formally, the system is a highly nonlinear system that consists of the incompressible Navier–Stokes equations and a nonlocal-type Allen-Cahn

In this paper, we present a time-explicit sparse grid discontinuous Galerkin method for solving the three-dimensional time-domain Maxwell equations. The conservation properties and convergence rates are established for different choices of numerical fluxes. The convergence rates are proved theoretically and then verified by several numerical examples. Even though our scheme does not preserve the divergence

FLAME is a software package to perform a wide range of atomistic simulations for exploring the potential energy surfaces (PES) of complex condensed matter systems. The available methods include molecular dynamics simulations to sample free energy landscapes, saddle point searches to identify transition states, and gradient relaxations to find dynamically stable geometries. In addition to such common

Simple Quantum Integro-Differential Solver (SQuIDS) is a C++ code designed to solve semi-analytically the evolution of a set of density matrices and scalar functions. This is done efficiently by expressing all operators in an SU(N) basis. SQuIDS provides a base class from which users can derive new classes to include new non-trivial terms from the right hand sides of density matrix equations. The code

Prediction of material properties from first principles is often a computationally expensive task. Recently, artificial neural networks and other machine learning approaches have been successfully employed to obtain accurate models at a low computational cost by leveraging existing example data. Here, we present a software package “Properties from Artificial Neural Network Architectures” (PANNA) that

As the era of microscale technologies becomes increasingly overcome by that of the nanoscale, an ever-increasing emphasis on the accurate modelling of such scaled systems is apparent. This work explores the combination of the finite element method with a new set of statistical algorithms to model the optical properties of disordered nanoscale morphologies. A silicon surface textured with a random distribution

The numerical simulation of the time-dependent Schrödinger equation for quantum systems is a very active research topic. Yet, resolving the solution sufficiently in space and time is challenging and mandates the use of modern high-performance computing systems. While classical parallelization techniques in space can reduce the runtime per time step, novel parallel-in-time integrators expose parallelism

In this paper, the discrete unified gas kinetic scheme (DUGKS), which is a novel direct kinetic method, is developed for a reformulated BGK–Vlasov–Poisson system in all electrostatic plasma regimes characterized by a wide range of Knudsen number and normalized Debye length. The current scheme is constructed for multiscale plasma simulation, while the temporal and spatial step sizes of the method are

MFC is an open-source tool for solving multi-component, multi-phase, and bubbly compressible flows. It is capable of efficiently solving a wide range of flows, including droplet atomization, shock–bubble interaction, and bubble dynamics. We present the 5- and 6-equation thermodynamically-consistent diffuse-interface models we use to handle such flows, which are coupled to high-order interface-capturing

We introduce a method for calculating the divided differences of the exponential function by means of addition and removal of items from the input list to the function. Our technique exploits a new identity related to divided differences recently derived by Zivcovich (2019). We show that upon adding an item to or removing an item from the input list of an already evaluated exponential, the re-evaluation

A recently discovered universal rank-based matrix method to extract trends from noisy time series is described in Ierley and Kostinski (2019) but the formula for the output matrix elements, implemented there as an open-access supplement MATLAB computer code, is O(N4), with N the matrix dimension. This can become prohibitively large for time series with hundreds of sample points or more. Based on recurrence

We present a new code for energy minimization, structure relaxation and evaluation of bulk parameters in the framework of orbital-free density functional theory (OF-DFT). The implementation is based on solving the Euler–Lagrange equation on an equidistant real space grid on which density dependent variables and derivatives are computed. Some potential components are computed in Fourier space. The code

Understanding electron drift and diffusion in gases and gas mixtures is a topic of central importance for the development of modern particle detection instrumentation. The industry-standard MagBoltz code has become an invaluable tool during its 20 years of development, providing capability to solve for electron transport (‘swarm’) properties based on a growing encyclopedia of built-in collision cross

Fractal dimension (FD) has become a very useful tool in neuroscience with a wide range of applications in characterizing several neurodegenerative diseases. The most commonly used method for computing the FD of brain tissues is box-counting. This technique performs very well on 2D images and 3D volumes; however, it presents several drawbacks when processing cortical surfaces in 3D. In this study, we

It is well known that the simulation of fractional systems is a difficult task from all points of view. In particular, the computer implementation of numerical algorithms to simulate fractional systems of partial differential equations in three dimensions is a hard task which has no been solved satisfactorily. In this work, we propose a numerical method to solve systems of hyperbolic (fractional o

We present the Tight-Binding Studio (TB Studio) software package that calculates the different parameters of a tight-binding Hamiltonian from a set of Bloch energy bands obtained from first principle theories such as density functional theory, Hartree–Fock calculations or semi-empirical band-structure theory. This will be helpful for scientists who are interested in studying electronic and optical

In master-field simulations of lattice QCD, the expectation values of interest are obtained from a single or at most a few representative gauge-field configurations on very large lattices. If the light quarks are included, the generation of these fields using standard techniques is however challenging in view of various algorithmic instabilities and precision issues. Ways to overcome these problems

In this paper we present the algorithm and implementation of an open-source immersed boundary code sdfibm, which is based on OpenFOAM v6 and written in C++. The immersed boundary method (“ibm” of the name) treats the velocity field as the volume average of fluid and solid velocities, and applies the volume-average discrete forcing to account for the fluid–solid interaction. The signed distance field

In this work we present a hybrid discontinuous Galerkin scheme for the solution of extremely anisotropic diffusion problems arising in magnetized plasmas for fusion applications. Unstructured meshes, non-aligned with respect to the dominant diffusion direction, allow an unequalled flexibility in discretizing geometries of any shape, but may lead to spurious numerical diffusion. Curved triangles or

Fluid driven fractures propagate in the upper earth crust either naturally or in response to engineered fluid injections. The quantitative prediction of their evolution is critical in order to better understand their dynamics as well as to optimize their creation. We present an open-source Python implementation of a hydraulic fracture growth simulator based on the implicit level set algorithm originally

We present VegasFlow, a new software for fast evaluation of high dimensional integrals based on Monte Carlo integration techniques designed for platforms with hardware accelerators. The growing complexity of calculations and simulations in many areas of science have been accompanied by advances in the computational tools which have helped their developments. VegasFlow enables developers to delegate

A multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius

Upon application of a sufficiently strong electric field, electrons break away from thermal equilibrium and approach relativistic speeds. These highly energetic ‘runaway’ electrons (∼ MeV) play a significant role in tokamak disruption physics, and therefore their accurate understanding is essential to develop reliable mitigation strategies. For this purpose, we have developed a fully implicit solver

This paper presents the vector-based discrete element method applied to two-dimensional elastic bodies, including details of formulation, its implementation on graphics processing units (GPUs) for accelerating simulations and validation cases. Simulation of elastic bodies has traditionally been realised through continuum-mechanics based methods such as finite elements while using discrete element methods

The Monte Carlo generator Prophecy4f provides a PROPer description of the Higgs dECaY into 4 Fermions within the Standard Model, the Standard Model with a fourth fermion generation, a simple Higgs-singlet extension of the Standard Model, and the Two-Higgs-Doublet Model. The fully differential predictions include the full QCD and electroweak next-to-leading-order corrections, all interference contributions

In this paper, our goal is to efficiently solve the Vlasov equation on GPUs. A semi-Lagrangian discontinuous Galerkin scheme is used for the discretization. Such kinetic computations are extremely expensive due to the high-dimensional phase space. The SLDG code, which is publicly available under the MIT license, abstracts the number of dimensions and uses a shared codebase for both GPU and CPU based

A new three-dimensional (3D) transport analysis method is developed and implemented in the light water reactor (LWR) whole-core analysis code STREAM. The method is named as 3D method of characteristics/Diamond-difference (MOC/DD). In this method, 3D variables such as flux and source are expressed as a combination of the two-dimensional (2D) radial component and the one-dimensional (1D) axial component

Fuel depletion analysis is important for the evolutionary behavior of nuclear materials in the reactor. For the accelerator-driven sub-critical system (ADS), the main research focuses on the transmutation of minor actinides (MA) and long-lived fission products(LLFP). To perform nuclide inventory calculation of ADS, a new nuclide point-depletion code IMPC-Depletion has been developed by utilizing Chebyshev

We introduce the package SIDES (Schrödinger Integro-Differential Equation Solver) that solves the integro-differential Schrödinger equation for elastic scattering of a nonlocal optical potential in coordinate space. The code is capable of treating the Coulomb interaction without restrictions. The method is based on previous developments by Jacques Raynal in the DWBA07 code. Elastic scattering observables

We present a program for solving exactly the general pairing Hamiltonian based on diagonalization. The program generates the seniority-zero shell-model-like basis vectors via the ‘01’ inversion algorithm. The Hamiltonian matrix is constructed in this seniority-zero space. The program evaluates all non-zero elements of the Hamiltonian matrix “on the fly” using the scattering operator and a search algorithm

Predictive Molecular Dynamics simulations of thermal transport require forcefields that can simultaneously reproduce several structural, thermodynamic and vibrational properties of materials like lattice constants, phonon density of states, and specific heat. This requires a multi-objective optimization approach for forcefield parameterization. Existing methodologies for forcefield parameterization

We present an efficient implementation of polynomial filtering methods in PARSEC, a real-space pseudopotential based Kohn–Sham density functional theory solver. The implementation described here improves upon a Chebyshev-filtered subspace iteration algorithm used in the previous version of PARSEC. We present a hybrid polynomial filtering scheme that combines Chebyshev-filtered subspace iteration and

Electron radiation belts are regions surrounding Earth, filled with highly energetic electrons and overlapping the majority of satellite orbits. Their multi-scale and rapidly evolving dynamics are modelled by the mean of a diffusion equation involving a highly anisotropic and inhomogeneous diffusion tensor. Finite difference based methods have been the preferred method of discretization in physical

The simulation of unsteady incompressible fluid flow and heat transfer problems is a huge time-consuming task and has been becoming one of the hottest topics in the fields of computational fluid dynamics and numerical heat transfer. Pure spatial parallelization has been so far the most widely used parallel strategy to speed up unsteady simulations but suffers from the problem of speedup saturation

Inverse Ising inference is a method for inferring the coupling parameters of a Potts/Ising model based on observed site-covariation, which has found important applications in protein physics for detecting interactions between residues in protein families. We introduce Mi3-GPU (“mee-three”, for MCMC Inverse Ising Inference) software for solving the inverse Ising problem for protein-sequence datasets

Field ion microscopy (FIM) was the first technique to image individual atoms on the surface of a material. By a careful control of the field evaporation of surface atoms, the bulk of the material is exposed, and, through digital processing of a sequence of micrographs, an atomically-resolved three-dimensional reconstruction can be achieved. 3DFIM is particularly suited to the direct observation of

In high-energy physics, Monte Carlo event generators (MCEGs) are used to simulate the interactions of high energy particles. MCEG event records store the information on the simulated particles and their relationships, and thus reflect the simulated evolution of physics phenomena in each collision event. We present the HepMC3 library, a next-generation framework for MCEG event record encoding and manipulation

Adherent biological cells generate traction forces on a substrate that play a central role for migration, mechanosensing, differentiation, and collective behavior. The established method for quantifying this cell–substrate interaction is traction force microscopy (TFM). In spite of recent advancements, inference of the traction forces from measurements remains very sensitive to noise. However, suppression