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

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

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

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

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 kind of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts

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

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.

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

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

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 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

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

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

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

Equation of motion method has proven efficient for electronic structure calculations of very large systems, i.e. containing several millions of 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

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

Characterization of structural information at the atomistic level in molecular dynamics (MD) simulations is a necessary task for researchers in the fields of materials modeling and simulation. Visualization of the density distribution is typically one of the most important properties in structural characterization. Visual Molecular Dynamics (VMD) is a widely used molecular visualization package that

In this paper a pseudo-spectral incompressible smoothed particle hydrodynamics (FFT-ISPH) solver is presented. While the solution of the linear system arising from the pressure Poisson equation in physical space using iterative solvers in incompressible SPH is a viable solution, it is widely accepted that the computational cost of solving the pressure Poisson equation by iterative solvers is excessive

Circular dichroism spectroscopy is a structural biology technique frequently applied to determine the secondary structure composition of soluble proteins. Our recently introduced computational analysis package SESCA aids the interpretation of protein circular dichroism spectra and enables the validation of proposed corresponding structural models. To further these aims, we present the implementation

Calculating the transport properties, such as electrical conductivity, has been a great challenge in materials modeling fields because of its complexity. We have implemented an algorithm to calculate the electronic transport properties using the generalized Kane band model and perturbation theory in the framework of the relaxation time approximation. Three scattering mechanisms affect the total relaxation

Significant progress in many classes of materials could be made with the availability of experimentally-derived large datasets composed of atomic identities and three-dimensional coordinates. Methods for visualizing the local atomic structure, such as atom probe tomography (APT), which routinely generate datasets comprised of millions of atoms, are an important step in realizing this goal. However

We present the new version 2.0 of the Feynman integral reduction program Kira and describe the new features. The primary new feature is the reconstruction of the final coefficients in integration-by-parts reductions by means of finite field methods with the help of FireFly. This procedure can be parallelized on computer clusters with MPI. Furthermore, the support for user-provided systems of equations

We present an alternative implementation of the Kalman filter employed for track fitting within the LHCb experiment. It uses simple parametrizations for the extrapolation of particle trajectories in the field of the LHCb dipole magnet and for the effects of multiple scattering in the detector material. A speedup of more than a factor of four is achieved while maintaining the quality of the estimated

Surface and volume imperfections can significantly affect the performance of nanoscale or microscale devices used in photonics, optoelectronics or scientific instrumentation. In this article we present an open source software package for Finite-Difference Time-Domain electromagnetic field calculations suitable for calculations on graphics cards. Its special features include handling realistic models

We present the initial release of ARGES, a toolkit for obtaining renormalisation group equations in perturbation theory. As such, ARGES can handle any perturbatively renormalisable four-dimensional quantum field theory. Notable further features include a symbolic rather than numeric computation, input of unconventional scalar and Yukawa sectors, an interactive evaluation and disentanglement as well

We report on an implementation within GiNaC to evaluate iterated integrals related to elliptic Feynman integrals numerically to arbitrary precision within the region of convergence of the series expansion of the integrand. The implementation includes iterated integrals of modular forms as well as iterated integrals involving the Kronecker coefficient functions g(k)(z,τ). For the Kronecker coefficient

We present a GPU-accelerated fast multipole method (FMM) called BLDTT, which uses barycentric Lagrange interpolation for the near-field and far-field approximations, and dual tree traversal to construct the interaction lists. The scheme replaces well-separated particle-particle interactions by adaptively chosen particle-cluster, cluster-particle, and cluster-cluster approximations given by barycentric

In this work we present a FORTRAN code for the calculation of the matrix of the orbital fractional parentage coefficients for five particles (5HOB) in a translationally invariant basis. Our code calculates the 5HOB eigenvector matrix M and the diagonal eigenvalue matrix F. The full 5HOB matrix is obtained from these matrices. Program summary Program title: 5hob_serial CPC Library link to program files:

We present BEC2HPC which is a parallel HPC spectral solver for computing the ground states of the nonlinear Schrödinger equation and the Gross-Pitaevskii equation (GPE) modeling rotating Bose-Einstein condensates (BEC). Considering a standard pseudo-spectral discretization based on Fast Fourier Transforms (FFTs), the method consists in finding the numerical solution of the energy functional minimization

We develop the third-order adaptive Adams-Bashforth time integration and the second-order finite difference equation for variable time steps. We incorporate these schemes in the Celeris Advent software to discretize and solve the 2D extended Boussinesq equations. This software uses a hybrid finite volume – finite difference scheme and leverages the GPU to solve the equations faster than real-time while

Electromagnetic full waveform inversion in Debye dispersive medium (EFWI-D) is a promising technique to reconstruct the inner structure and electrical properties of the medium such as soil, rock and biological tissues. Same as conventional full waveform inversion, EFWI-D requires high computational cost, especially in the 3D case. To reduce the long computation time, we design and implement the EFWI-D

X-ray absorption spectroscopy (XAS) is a powerful method for obtaining electronic and structural information around a well-defined absorbing atom site of different types of matter, from biological systems to condensed materials in almost all possible thermodynamics conditions. The low energy part of the XAS spectrum, from the rising edge up to few hundreds eV, the so called XANES (X-ray absorption

Simulating the long-term evolution of temperature and magnetic fields in neutron stars is a major effort in astrophysics, having significant impact in several topics. A detailed evolutionary model requires, at the same time, the numerical solution of the heat diffusion equation, the use of appropriate numerical methods to control non-linear terms in the induction equation, and the local calculation

Accurate mesh-free simulation of fluid flows involving complex boundaries requires that the boundaries be captured accurately in terms of particles. In the context of incompressible/weakly-compressible fluid flow, the SPH method is more accurate when the particle distribution is uniform. Hence, for time-accurate simulation of flow in the presence of complex boundaries one must have both an accurate

We present a software to simulate the propagation of positive streamers in dielectric liquids. Such liquids are commonly used for electric insulation of high-power equipment. We simulate electrical breakdown in a needle–plane geometry, where the needle and the extremities of the streamer are modeled by hyperboloids, which are used to calculate the electric field in the liquid. If the field is sufficiently

We present a Volume Integral formulation for the solution of large scale eddy-current problems coupled with low-rank approximation techniques. Two alternative approaches are introduced to map the problem unknowns into a subset of grid elements forming a base of global or mixed (global and local) cycles, respectively, and guarantee the well-posedness of the problem both in simply and multiply connected

BESLE is the first available parallel open-source code to analyse the mechanical behaviour of heterogeneous materials using the boundary element method (BEM) in 3D and in both an elastostatic and elastodynamic setting. Unlike all the other codes that are presently available, the software presented here is capable of simulating both isotropic and anisotropic materials comprised of single or multiple

A program to calculate the oscillator brackets, or Talmi–Moshinsky–Smirnov coefficients, is presented. The recursion with respect to radial quantum numbers is employed. The listed runs show that the program is very fast and it produces accurate results up to very high oscillator excitations. The amount of computations per bracket does not increase with the increase of quantum numbers. In one of the

Since variational symplectic integrators for the guiding center was proposed [1], [2], structure-preserving geometric algorithms have become an active research field in plasma physics. We found that the slow manifolds of the classical Pauli particle enable a family of structure-preserving geometric algorithms for guiding center dynamics with long-term stability and accuracy. This discovery overcomes

The robust estimation of chemical kinetic parameters and their associated uncertainty is essential in the field of chemistry and catalysis. The Chemical Kinetics Bayesian Inference Toolbox (CKBIT) is a Python software library introduced to enable users to implement advanced Bayesian inference techniques for kinetic parameter estimation and uncertainty quantification. Leveraging functionalities of other

How best to model systems of interacting electrons in an accurate and computationally efficient manner is an outstanding problem in theoretical and computational materials science. For materials where strong electronic interactions are primarily of a localized character and act within a subspace of localized quantum states on separate atomic sites (e.g., in transition metal and rare-earth compounds)

The Cluster-Cluster Aggregation model (CCA) was often used to simulate the aggregation of colloids, in which the rapid and slow aggregation processes of colloids can be well characterized. In practical system, the movement of particles or clusters occurs in parallel. In the CCA model, in order to facilitate computer simulation, the movement of particles or clusters is processed serially by the method

Coupled-cluster Green's function (GFCC) calculation has drawn much attention in the recent years for targeting the molecular and material electronic structure problems from a many-body perspective in a systematically improvable way. However, GFCC calculations on scientific computing clusters usually suffer from expensive higher dimensional tensor contractions in the complex space, expensive inter-process