We study the parallelization of a flexible order Cartesian treecode algorithm for evaluating electrostatic potentials of charged particle systems in which N particles are located on the molecular surfaces of biomolecules such as proteins. When the well-separated condition is satisfied, the treecode algorithm uses a far-field Taylor expansion to compute O(NlogN) particle-cluster interactions to replace

The present article complements the earlier ones in this series. The first part contains various results on the constituent system Cκ(M) of a graph model M, and on its feasibility system Iη(M) (which comprises a number of identities that define the number conservation rules). Those results include the general form of the (particle) number conservation rules in models without explicit propagator mixing

As the characteristic lengths of advanced electronic devices are approaching the atomic scale, ab initio simulation method, with full consideration of quantum mechanical effects, becomes essential to study the quantum transport phenomenon in them. The widely used non-equilibrium Green’s function (NEGF) combined with the density functional theory (DFT) approach prefers a localized basis set. As many

Since the KKMC program was published for the first time over 20 years ago, it has gained popularity and was exploited in a broad spectrum of applications. The core part of the program itself did not change much. In contrast, some of the libraries have evolved substantially. The aim of this publication is to archive four versions, alternative to the one published 20 years ago versions of the electroweak

The simulation of the transport problem on the sphere is crucial in the numerical modelling of the transport of trace constituents in atmospheric models. One major issue in the numerical simulation is the ability of the solver to obtain accurate constraint-preserving solutions, i.e., ensuring the predicted solution to stay within the physical range. In this paper, we develop and study a variational

This paper is a presentation of a Finite Element Modeling Software named FEMS that integrates mesh generation and adaption features in order to alleviate significantly the difficulty of designing a Finite Element (FE) mesh for a particular problem. FEMS is targeted at engineers and scientists addressing localization problems in mechanics, although it should be suited to many other applications. FEMS

QSW_MPI is a Python package developed for time-series simulation of continuous-time quantum stochastic walks. This model allows for the study of Markovian open quantum systems in the Lindblad formalism, including a generalisation of the continuous-time random walk and continuous-time quantum walk. Consisting of a Python interface accessing parallelised Fortran libraries utilising sparse data structures

We demonstrate how to compute the low energy spectrum for small (N≤50), but otherwise arbitrary, spin–glass instances using modern Graphics Processing Units or similar heterogeneous architecture. Our algorithm performs an exhaustive (i.e., brute–force) search of all possible configurations to select S≪2N lowest ones together with their corresponding energies. We mainly focus on the Ising model defined

The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their interactions with protein targets. In this work, we present PARCE, an open source Protocol for Amino acid Refinement through Computational Evolution that implements an advanced

We present UNDI, an open-source program to analyse the time dependent spin polarization of an isolated muon interacting with the surrounding nuclear magnetic dipoles in the context of standard muon spin rotation and relaxation spectroscopy experiments. The code can perform both exact and approximated estimates of the muon polarization function in presence of external fields and electric field gradients

We present an updated version of the open-source Hypersonics Task-based Research (HTR) solver for hypersonic aerothermodynamics. The solver, whose first version was presented in Di Renzo et al. (Comput. Phys. Commun. 255, 2020), is designed for direct numerical simulation (DNS) of canonical hypersonic flows at high Reynolds numbers in which thermo-chemical effects induced by high temperatures are relevant

The aim of this study is to devise an efficient and scalable computational procedure to solve the many tridiagonal systems in multi-dimensional partial differential equations. The modified Thomas algorithm and a newly designed communication scheme were used to reduce the communication overhead encountered while solving the many tridiagonal systems. Benchmark test results reveal an advantage of the

In this paper we present a simple, easily implemented and effective approach for explicitly-filtered Large Eddy Simulation with a Discontinuous Galerkin (DG) discretision for velocity. DG formulations are often desirable due to their stability and increased accuracy, however this can come at greater computational expense due to the additional degrees of freedom in the velocity field. Additionally,

A degenerate perturbation k⋅p approach for effective mass calculations is implemented in the all-electron density functional theory (DFT) package WIEN2k. The accuracy is tested on major group IVA, IIIA-VA, and IIB-VIA semiconductor materials. Then, the effective mass in graphene and CuI with defects is presented as illustrative applications. For states with significant Cu-d character additional local

We present a module to calculate the mobility and conductivity of semiconducting materials using Rode’s algorithm. This module uses a variety of electronic structure inputs derived from the Density Functional Theory (DFT). We have demonstrated good agreement with experimental results for the case of Cadmium Sulfide (CdS). We also provide a comparison with the widely used method, the so-called relaxation

We describe the Hybrid seeding, a stand-alone pattern recognition algorithm aiming at finding charged particle trajectories for the LHCb upgrade. A significant improvement to the charged particle reconstruction efficiency is accomplished by exploiting the knowledge of the LHCb magnetic field and the position of energy deposits in the scintillating fibre tracker detector. Moreover, we achieve a low

This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated bubbles, bubble dynamics and coalescence, surface tension, the stabilizing disjoining pressure between bubbles, and Newtonian and non-Newtonian rheological models. The

Particle-In-Cell codes are widely used for plasma physics simulations. It is often the case that particles within a computational cell need to be split to improve the statistics or, in the case of non-uniform meshes, to avoid the development of fictitious self-forces. Existing particle splitting methods are largely empirical and their accuracy in preserving the distribution function has not been evaluated

This is a new version of the DFMSPH (DFMSPH14, DFMSPH19) code published earlier. The new version is designed to obtain the nucleus–nucleus potential between two spherical nuclei using the double folding model (DFM). In particular, the code enables one to find the Coulomb barrier. Using the new version, one can employ three types of effective nucleon–nucleon interaction: the M3Y, Migdal, and relativistic

This paper presents a novel open-source discrete element code, SudoDEM, for efficient modeling of both 2D and 3D non-spherical particles under a GPL v3 or later license. Built upon a popular open-source code YADE, our code inherits the core of a classic DEM framework empowered by OpenMP acceleration, and further offers unique features of a rich library of prime particle shapes, including poly-superellipsoids

The computational modeling of high-speed flows (e.g. hypersonic) and space plasmas is characterized by plethora of complex physical phenomena, in particular involving strong bow shocks and/or shock waves boundary layer interactions. The characterization of those flows requires accurate, robust, advanced numerical techniques and well tailored computational meshes for resolving all features of interest

We present a multithreaded event-chain Monte Carlo algorithm (ECMC) for hard spheres. Threads synchronize at infrequent breakpoints and otherwise scan for local horizon violations. Using a mapping onto absorbing Markov chains, we rigorously prove the correctness of a sequential-consistency implementation for small test suites. On x86 and ARM processors, a C++ (OpenMP) implementation that uses compare-and-swap

Radiation symmetry evaluation is critical to the laser driven Inertial Confinement Fusion (ICF), which is usually obtained through a view-factor equation model. The model is nonlinear, and its equation number can be very large when the size of discrete mesh element is very small to achieve a prescribed accuracy, which may lead to an intensive equation solving process. In this paper, an efficient radiation

This paper presents an automatic method for data classification in nuclear physics experiments based on evolutionary computing and vector quantization. The major novelties of our approach are the fully automatic mechanism and the use of analytical models to provide physics constraints, yielding to a fast and physically reliable classification with nearly-zero human supervision. Our method is successfully

In this paper, a fast multipole method (FMM) is proposed for 3-D Laplace equations in layered media. The potential due to charges embedded in layered media is decomposed into a free space component and four types of reaction field components, and the latter can be associated with the potential of a polarization source defined for each type. New multipole expansions (MEs) and local expansions (LEs)

This study focuses on finding high-performance numerical solutions to fluid–structure coupling problems encountered in biomechanical engineering. A numerical framework for simulating fluid–structure interaction (FSI) is proposed by strongly coupling the finite element and lattice Boltzmann methods. The lattice Boltzmann method is efficient for solving weakly compressible fluid flows. The explicit finite

Here, we present simple and efficient numerical scheme to study static and dynamic properties of spin-1 Bose–Einstein condensates (BECs) with spin–orbit (SO) coupling by solving three coupled Gross–Pitaevskii equations (CGPEs) in three-, quasi-two and quasi-one dimensional systems. We provide a set of three codes developed in FORTRAN 90/95 programming language with user defined ‘option’ of imaginary

We present a novel open-source Python framework called NanoNET (Nanoscale Non-equilibrium Electron Transport) for modeling electronic structure and transport. Our method is based on the tight-binding method and non-equilibrium Green’s function theory. The core functionality of the framework is providing facilities for efficient construction of tight-binding Hamiltonian matrices from a list of atomic

Module for ab initio structure evolution (MAISE) is an open-source package for materials modeling and prediction. The code’s main feature is an automated generation of neural network (NN) interatomic potentials for use in global structure searches. The systematic construction of Behler–Parrinello-type NN models approximating ab initio energy and forces relies on two approaches introduced in our recent

A new version of the Fortran program elsepa, which calculates differential and integrated cross sections for elastic scattering of electrons and positrons, is presented. Details of the program and its applications are given in the original paper [Comput. Phys. Commun. 165 (2005) 157–190]. Dirac phase shifts are now calculated by using the recently published subroutine package radial (Salvat and Fernández-Varea

We report a simulation program which facilitates the calculation of changes in the intensity of specular reflection of electron beams in RHEED experiments for thin epitaxial films deposited on crystalline surfaces. It has been shown that the amplitude of the RHEED intensity oscillations greatly depends on the glancing angle of the incident electron beam, the coverages of the growing layers and the

We present a spectral element algorithm and open-source code for computing the fractional Laplacian defined by the eigenfunction expansion on finite 2D/3D complex domains with both homogeneous and nonhomogeneous boundaries. We demonstrate the scalability of the spectral element algorithm on large clusters by constructing the fractional Laplacian based on computed eigenvalues and eigenfunctions using

We present two approaches for computing rational approximations to multivariate functions, motivated by their effectiveness as surrogate models for high-energy physics (HEP) applications. Our first approach builds on the Stieltjes process to efficiently and robustly compute the coefficients of the rational approximation. Our second approach is based on an optimization formulation that allows us to

We describe the second version (v2.0.0) of the code ADG that automatically (1) generates all valid off-diagonal Bogoliubov many-body perturbation theory diagrams at play in particle-number projected Bogoliubov many-body perturbation theory (PNP-BMBPT) and (2) evaluates their algebraic expression to be implemented for numerical applications. This is achieved at any perturbative order p for a Hamiltonian

This paper describes the track-finding algorithm that is used for event reconstruction in the Belle II experiment operating at the SuperKEKB B-factory in Tsukuba, Japan. The algorithm is designed to balance the requirements of a high efficiency to find charged particles with a good track parameter resolution, a low rate of spurious tracks, and a reasonable demand on CPU resources. The software is implemented

Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite generic family of partial differential equations. These equations can be discretized using: (i) standard finite-difference for systems with derivatives up to any order

We present OpenMP versions of FORTRAN programs for solving the Gross–Pitaevskii equation for a harmonically trapped three-component spin-1 spinor Bose–Einstein condensate (BEC) in one (1D) and two (2D) spatial dimensions with or without spin–orbit (SO) and Rabi couplings. Several different forms of SO coupling are included in the programs. We use the split-step Crank–Nicolson discretization for imaginary-

We have developed a software MagGene to predict magnetic structures by using genetic algorithm. Starting from an atom structure, MagGene repeatedly generates new magnetic structures and calls first-principles calculation engine to get the most stable magnetic structure. This software is applicable to both collinear and noncollinear systems. It is particularly convenient for predicting the magnetic

We introduce the package SWANLOP to calculate scattering waves and corresponding observables for nucleon elastic collisions off spin-zero nuclei. The code is capable of handling local and nonlocal optical potentials superposed to long-range Coulomb interaction. Solutions to the implied Schrödinger integro-differential equation are obtained by solving an integral equation of Lippmann–Schwinger type

Small displacement methods have been successfully used to calculate the lattice dynamical properties of crystals. It involves displacing atoms by a small amount in order to calculate the induced forces on all atoms in a supercell for the computation of force constants. Even though these methods are widely in use, to our knowledge, there is no systematic discussion of optimal displacement directions

Experiments in high energy physics (HEP) operate at the forefront of detector technology, electronics, data acquisition (DAQ), data analysis, and computing. With the advent of high-energy accelerators running at large beam intensities, there is a great demand for radiation-hard high speed protocol for data transmission. Along with the detector data, communication signals like trigger, timing and control

Furthering our understanding of many of today’s interesting problems in plasma physics – including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects – requires large-scale kinetic simulations using particle-in-cell (PIC) codes. However, these simulations are extremely demanding, requiring that contemporary PIC codes be designed to efficiently

Positive geometries provide a modern approach for computing scattering amplitudes in a variety of physical models. In order to facilitate the exploration of these new geometric methods, we introduce a Mathematica package called “amplituhedronBoundaries” for calculating the boundary structures of three positive geometries: the amplituhedron, the momentum amplituhedron and the hypersimplex. The first

The natural orbital functional theory (NOFT) has emerged as an alternative formalism to both density functional (DF) and wavefunction methods. In NOFT, the electronic structure is described in terms of the natural orbitals (NOs) and their occupation numbers (ONs). The approximate NOFs have proven to be more accurate than those of the density for systems with a significant multiconfigurational character

We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that for a water system of 12,582,912 atoms, the GPU version can be 7 times faster than the CPU version under the same power consumption. The code can scale up to the entire Summit

This paper develops a two-dimensional implicit particle-in-cell model, which considers algorithms without and with magnetic field, based on the anisotropic immersed-finite-element method. The direct implicit particle-in-cell (DIPIC) algorithm is utilized to track the movement of electrons and ions, while the anisotropic immersed-finite-element method is developed to compute the electric field. Compared

The wide application of ion sources requires the optimization of the ion optics to achieve a balance between the performance, life cycle and size. A 2D hybrid model is represented to simulate the ion optics for positive ion extraction where adaptive particle management and parallel computing are considered. Then, misunderstandings and inconsistencies in the previous numerical models of positive ion

Experimental thermodynamic measurements in multicomponent systems exhibit high complexity. Theoretical calculations by extrapolation of constitutive binary systems are an excellent tool to estimate the thermodynamic properties in ternary or quaternary systems. In this context, the Miedema and Bakker semi-empirical models are good to estimate the enthalpy of mixing or formation. This work presents a

A novel kinetic-fluid hybrid model is developed for electromagnetic plasma turbulence in tokamak geometry. In this model, by combining kinetic and fluid approaches, ions are treated with the conventional gyrokinetic particle-in-cell method, while the bounce averaged drift-kinetic method is used for trapped electrons, and passing electrons are modeled as a massless fluid to avoid numerical instabilities

We have developed an automated and efficient scheme for the fitting of data using Curvature Constrained Splines (CCS), to construct accurate two-body potentials. The approach enabled the construction of an oscillation-free, yet flexible, potential. We show that the optimization problem is convex and that it can be reduced to a standard Quadratic Programming (QP) problem. The improvements are demonstrated

An exact momentum update useful for particle codes was previously given. The expressions involved were unwieldy. By treating the momentum as a representation of SU(2)⊗SU(2) instead of SO(3,1), a more compact expression for the exact momentum update is obtained. An expansion in powers of the timestep can be formulated such that invariance properties are exactly preserved, and push rates comparable to

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

Monte Carlo ray-tracing method has become a promising technique for solving radiative transfer. However, large memory footprint or long CPU time hampers 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

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

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

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

Monte Carlo generation of high energy particle collisions is a critical tool for both theoretical and experimental particle physics, connecting perturbative calculations to phenomenological models, and theory predictions to full detector simulation. The generation of minimum bias events can be particularly computationally expensive, where non-perturbative effects play an important role and specific

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