The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The design and operation of such devices can benefit from simulations that resolve flow-structure interactions at sub-micron resolution. We present a computational tool for large scale, efficient and high throughput mesoscale

The numerical approximations for the coupled Cahn–Hilliard system describing the phase separation of the copolymer and homopolymer mixtures are considered in this paper. To develop easy to implement time marching schemes with unconditional energy stabilities, we use the Scalar Auxiliary Variable (SAV) approach for achieving two efficient, decoupled, and linear numerical schemes, where a new scalar

NLOX is a computer program for calculations in high-energy particle physics. It provides fully renormalized scattering matrix elements in the Standard Model of particle physics, up to one-loop accuracy for all possible coupling-power combinations in the strong and electroweak couplings, and for processes with up to six external particles. Program summary Program Title: NLOX Program Files doi: http://dx

We develop a FORTRAN code to compute fluctuations in atomic condensates (FACt) by solving the Bogoliubov-de Gennes (BdG) equations for two component Bose–Einstein condensate (TBEC) in quasi-two dimensions. The BdG equations are recast as matrix equations and solved self consistently. The code is suitable for handling quantum fluctuations as well as thermal fluctuations at temperatures below the critical

Amphiphile-based aggregates are extensively used in numerous applications for encapsulation, storage, transport and delivery of toxic, active molecules due to the structural properties of the aggregates. The properties of the aggregates in turn are dictated by the molecular architecture of the amphiphiles. A complete understanding of the multiscale architecture-structure-function relationship for amphiphile-based

In this paper a simple, robust, and general purpose approach to implement the Incompressible Smoothed Particle Hydrodynamics (ISPH) method is proposed. This approach is well suited for implementation on CPUs and GPUs. The method is matrix-free and uses an iterative formulation to setup and solve the pressure-Poisson equation. A novel approach is used to ensure homogeneous particle distributions and

The freud Python package is a library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on laptops, workstations, and supercomputing clusters. The package provides the core tools for finding particle neighbors in periodic systems, and offers a uniform API to a wide

A program to calculate the three–particle hyperspherical brackets is presented. Test results are listed and it is seen that the program is well applicable up to very high values of the hypermomentum and orbital momenta. The listed runs show that it is also very fast. Applications of the brackets to calculating interaction matrix elements and constructing hyperspherical bases for identical particles

We have refactored the Breit–Pauli R-Matrix integral package within the RMatrxI package to employ a B-Spline basis to allow for level-resolved time-dependent R-Matrix calculations involving a laser pulse. The B-Spline approach independently verifies the accuracy of the current integral package pstg1r.f, but requires greater flexibility at the R-Matrix boundary when describing the continuum wavefunctions

In this study, the open-source Hypersonics Task-based Research (HTR) solver for hypersonic aerothermodynamics is described. The physical formulation of the code includes thermochemical effects induced by high temperatures (vibrational excitation and chemical dissociation). The HTR solver uses high-order TENO-based spatial discretization on structured grids and efficient time integrators for stiff systems

We present a parallel implementation of a direct solver for Poisson’s equation on extreme-scale supercomputers with accelerators. We introduce a chunked-pencil decomposition as the domain-decomposition strategy to distribute work among processing elements to achieve improved scalability at high counts of accelerators. Chunked-pencil decomposition enables overlapping MPI communication and data transfer

The radiation shielding design for advanced nuclear facilities is a typical complicated multi-objective and multi-parameter optimization problem in the nuclear engineering. To obtain an optimal solution of the shielding design is of significance in developing high-performance advanced nuclear facilities, especially for compact and mobile devices. The classical method of shielding design is a brute

A new 3D unpslit Godunov scheme for solving Maxwell’s equations with polarization is presented. The numerical scheme avoids the use of limiters by interpolating the field components that are continuous at cell boundaries, making the algorithm simpler and faster. The algorithm allows the use of metals and a wide variety of polarization models: Lorentz, non-linear as Kerr type or Havriliak-Negami dielectric

The Grad-Shafranov equation is solved using spectral elements for tokamak equilibrium with toroidal rotation. The Grad-Shafranov solver builds upon and extends the NIMEQ code (Howell and Sovinec, 2014) previously developed for static tokamak equilibria. Both geometric and algebraic convergence are achieved as the polynomial degree of the spectral-element basis increases. A new analytical solution to

This work presents a comprehensive analysis of key elements determining the efficiency of Simulated Tempering implementations for lattice models. Important aspects like the proper choice of the replicas temperature set ϒR, their quantity R and adequate estimation of the weight factors (establishing the probabilities of jumps between the replicas) are considered. A number of tests to validate distinct

An isothermal implementation of Smoothed Dissipative Particle Dynamics (SDPD) for LAMMPS is presented. SDPD is useful for hydrodynamics simulations at mesoscale where the effect of thermal fluctuations are important, but a molecular dynamics simulation is prohibitively expensive. We have used this package to simulate diffusion of spherical colloids. The results (particularly the long-time behaviour

Recently a non-empirical stochastic walker algorithm has been developed to search for the minimum-energy escape paths from the minima of the potential surface (Akashi and Nagornov, 2018; Nagornov and Akashi, 2019). This method is based on the Master equation for the distribution function of the atomic configuration which has a nature to seek the reaction path up along the valley of the potential surface

We extend to three dimensions a new projection method for simulating hypo-elastoplastic solids in the quasi-static limit. The method is based on a mathematical correspondence to the incompressible Navier–Stokes equations, where the projection method of Chorin (1968) is an established numerical technique. We first review the method and present its extension to three dimensions. We discuss the development

diaphane is a portable, scalable, and extensible library for modeling the transport of energy by radiation or relativistic particles (in particular neutrinos). Energy transport modelling is crucial for the hydrodynamic modelling of a wide range of astrophysical phenomena such as planet and galaxy formation, supernova explosions, and cosmic structure evolution. The diaphane library provides a computational

Ab initio many-body perturbation theory within the GW approximation is a Green’s function formalism widely used in the calculation of quasiparticle excitation energies of solids. In what has become an increasingly standard approach, Kohn–Sham eigenenergies, generated from a DFT calculation with a strategically-chosen exchange correlation functional “starting point”, are used to construct G and W, and

ExaHyPE (“An Exascale Hyperbolic PDE Engine”) is a software engine for solving systems of first-order hyperbolic partial differential equations (PDEs). Hyperbolic PDEs are typically derived from the conservation laws of physics and are useful in a wide range of application areas. Applications powered by ExaHyPE can be run on a student’s laptop, but are also able to exploit thousands of processor cores

We propose a high-order adaptive numerical solver for the semilinear elliptic boundary value problem modelling magnetic plasma equilibrium in axisymmetric confinement devices. In the fixed boundary case, the equation is posed on curved domains with piecewise smooth curved boundaries that may present corners. The solution method we present is based on the hybridizable discontinuous Galerkin method and

The recently published set of programs H_FUN for calculation of the Chandrasekhar function [Comput. Phys. Commun. 235 (2019) 489-501] is replaced with a new set H_FUN_v2 which has the following improvements: (i) increased accuracy from 14 decimals to 15-16 decimals, (ii) the upper limit of albedo values increased from ω=0.85 to ω=1, (iii) a reasonably short execution time, and (iv) brevity and simplicity

In manufacturing industries, predicting the work of adhesion between complex solid and liquid surfaces has become essential. FE-CLIP offers a routine for evaluating the work of adhesion between solid and liquid surfaces by calling a subroutine from a molecular dynamics simulation code. When FE-CLIP is applied to the solid–liquid interface, liquid molecules are separated from the solid surface according

A numerical method to implement a linearized Coulomb collision operator in the two-weight δf Monte Carlo method for multi-ion-species neoclassical transport simulation is developed. The conservation properties and the self-adjoint property of the operator in the collisions between two particle species with different temperatures are verified. The linearized operator in a δf Monte Carlo code is benchmarked

Pair potentials or kernels, ψ(|r|), play a critical role in a number of areas; these include biophysics, electrical engineering, fluid dynamics, diffusion physics, solid state physics, and many more. The need to evaluate these potentials rapidly for N particles gives rise to the classical N-body problem. In this paper, we present scalable parallel algorithms for evaluation of these potentials for highly

We consider the application of three performance-portable programming models in the context of a high-order spectral element, implicit time-stepping solver for the Navier–Stokes equations. We aim to evaluate whether the use of these models allows code developers to deliver high-performance solvers for computational fluid dynamics simulations that are capable of effectively utilising both many-core

We present a computer framework to store and evaluate likelihoods coming from High Energy Physics experiments. Due to its flexibility it can be interfaced with existing fitting codes and allows to uniform the interpretation of the experimental results among users. The code is provided with large open database, which contains the experimental measurements. The code is of use for users who perform phenomenological

In this updated version of ZMCintegral, we have added the functionality of parameter scan for integrations with a large parameter space (up to 1010 points to be scanned). The Python API is kept the same as the previous ones and users have full flexibility to define their own integrands. The performance of the new functionality is tested for multi-nodes conditions. Program summary Program Title: ZMCintegral

Particle tracking, that is, the repeated localization of particles within a grid by means of tracking the particles’ trajectories, is routinely applied in particle-based schemes where the domain is described by an unstructured polyhedral grid. A range of tracking algorithms are available in the literature, which are inherently similar to algorithmic approaches common both in event-driven particle dynamics

In a recent publication (Eghtesad et al., 2018), we have reported a message passing interface (MPI)-based domain decomposition parallel implementation of an elasto-viscoplastic fast Fourier transform-based (EVPFFT) micromechanical solver to facilitate computationally efficient crystal plasticity modeling of polycrystalline materials. In this paper, we present major extensions to the previously reported

In several burnup and activation problems there is a recurrent issue related to the singularities in the Bateman’s solution due to its inability to solve linear transmutation schemes where there are repeated isotopes, or where there are two different isotopes with the same removal coefficients. Most of these types of transmutation schemes are called cyclic chains. In these cases, the Bateman’s solution

A nonlinear wave model is constructed in the current work to examine the nonlinear dynamics of extremely oblique whistler waves in radiation belts. For this purpose, numerical simulation technique has been employed. The coupled normalized equations of highly oblique whistler wave and low frequency slow Alfvén wave have been developed. The ponderomotive force of high frequency whistler wave creates

The suggested package FUMILIM, based on the famous FUMILI minimization package, has the following advantages: multi-optional user interface; speed advantage when the number of parameters is high enough; there are options to ignore wrong experimental points and correct experimental errors. The preliminary scan is envisaged for complicated tasks. The next version of FUMILIM is capable of working efficiently

Gyrokinetic codes in plasma physics need outstanding computational resources to solve increasingly complex problems, requiring the effective exploitation of cutting-edge HPC architectures. This paper focuses on the enabling of ORB5, a state-of-the-art, first-principles-based gyrokinetic code, on modern parallel hybrid multi-core, multi-GPU systems. ORB5 is a Lagrangian, Particle-In-Cell (PIC), finite

This work presents a dynamic parallel distribution scheme for the Hartree–Fock exchange (HFX) calculations based on the real-space NAO2GTO framework. The most time-consuming electron repulsion integrals (ERIs) calculation is perfectly load-balanced with 2-level master-worker dynamic parallel scheme, the density matrix and the HFX matrix are both stored in the sparse format, the network communication

Beam Delivery Simulation (BDSIM) is a program that simulates the passage of particles in a particle accelerator. It uses a suite of standard high energy physics codes (Geant4, ROOT and CLHEP) to create a computational model of a particle accelerator that combines accurate accelerator tracking routines with all of the physics processes of particles in Geant4. This unique combination permits radiation

We explain the construction of Forcer, a Form program for the reduction of four-loop massless propagator-type integrals to master integrals. The resulting program performs parametric IBP reductions similar to the three-loop Mincer program. We show how one can solve many systems of IBP identities parametrically in a computer-assisted manner. Next, we discuss the structure of the Forcer program, which

The computation of Feynman integrals often involves square roots. One way to obtain a solution in terms of multiple polylogarithms is to rationalize these square roots by a suitable variable change. We present a program that can be used to find such transformations. After an introduction to the theoretical background, we explain in detail how to use the program in practice. Program summary Program

Future experiments in high-energy physics will pose stringent requirements to computing, in particular to real-time data processing. As an example, the CBM experiment at FAIR Germany intends to perform online data selection exclusively in software, without using any hardware trigger, at extreme interaction rates of up to 10 MHz. In this article, we describe how heterogeneous computing platforms, Graphical

We develop Hybrid Monte Carlo (HMC) algorithms for constrained Hamiltonian systems of gauge-Higgs models and introduce a new observable for the constraint effective Higgs potential. We use an extension of the so-called Rattle algorithm to general Hamiltonians for constrained systems, which we adapt to the 4D Abelian-Higgs model and the 5D SU(2) gauge theory on the torus and on the orbifold. The derivative

In this work we present ZEFR, a GPU accelerated flow solver based around the high-order accurate flux reconstruction (FR) approach. Written in a combination of C++ and CUDA, ZEFR is designed to perform scale resolving simulations within the vicinity of complex geometrical configurations. A unique feature of ZEFR is its support for overset grids; a feature which greatly expands the addressable problem

The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been validated by comparison with the analytic theory describing ion trap dynamics. Notable features include GPU-accelerated force calculations, and treating collections

SPHERA v.9.0.0 (RSE SpA) is a FOSS CFD-SPH research code validated on the following application fields: floods with transport of solid bodies and bed-load transport; fast landslides and their interactions with water reservoirs; sediment removal from water bodies; fuel sloshing tanks; hydrodynamic lubrication for energy efficiency actions in the industrial sector. SPHERA is featured by several numerical

The DIRQFAM code calculates the multipole response of even-even axially symmetric deformed nuclei using the framework of relativistic self-consistent mean-field models. The response is calculated by implementing the finite amplitude method for relativistic quasiparticle random phase approximation. Program summary Program Title: DIRQFAM Program Files doi: http://dx.doi.org/10.17632/6gv8nxg4ns.1 Licensing

We present and distribute a new numerical system using classical finite elements with mesh adaptivity for computing two-dimensional liquid–solid phase-change systems involving natural convection. The programs are written as a toolbox for FreeFem++ (www3.freefem.org), a free finite-element software available for all existing operating systems. The code implements a single domain approach. The same set

A numerical method to build an orthonormal basis of properly symmetrized hyperspherical harmonic functions is developed. As a part of it, refined algorithms for calculating the transformation coefficients between hyperspherical harmonics constructed from different sets of Jacobi vectors are derived and discussed. Moreover, an algorithm to directly determine the numbers of independent symmetric hyperspherical

The study of photon-induced reactions in collisions of heavy nuclei at RHIC and the LHC has become an important direction of the research program of these facilities in recent years. In particular, the production of vector mesons in ultra-peripheral collisions (UPC) has been intensively studied. Owing to the intense photon fluxes, the two nuclei participating in such processes undergo electromagnetic

In electronic structure and quantum transport calculations, many physical quantities are integrations over the electron energy, weighted by the Fermi-Dirac distribution function. Green’s function based approaches commonly circumvent the numerically difficult real energy integration by extending the integrand analytically into the complex energy plane, and using a Gaussian quadrature integration over

Accurate simulations of metal under heavy shocks, leading to fragmentation and ejection of particles, can not be achieved by simply hydrodynamic models and require to be performed at atomic scale using molecular dynamics methods. In order to cope with billions of particles exposed to short range interactions, such molecular dynamics methods need to be highly optimized over massively parallel supercomputers

A multi-GPGPU development for Mesoscale Simulations using the Dissipative Particle Dynamics method is presented. This distributed GPU acceleration development is an extension of the DL_MESO package to MPI+CUDA in order to exploit the computational power of the latest NVIDIA cards on hybrid CPU–GPU architectures. Details about the extensively applicable algorithm implementation and memory coalescing

We present a code for the large-scale data analysis of electron cyclotron emission (ECE) measurements from magnetized plasmas called ECRad – the Electron Cyclotron Radiation transport model for Advanced Data analysis. Its key features are low computational cost, high robustness and the capability to predict ECE spectra of plasmas with non-thermal electron populations. This is accomplished by combining

Generalised polylogarithms naturally appear in higher-order calculations of quantum field theories. We present handyG, a Fortran 90 library for the evaluation of such functions, by implementing the algorithm proposed by Vollinga and Weinzierl. This allows fast numerical evaluation of generalised polylogarithms with currently relevant weights, suitable for Monte Carlo integration. Program summary Program

In this paper, we construct a novel linearized finite difference/spectral-Galerkin scheme for three-dimensional distributed-order time-space fractional nonlinear reaction–diffusion-wave equation. By using Gauss–Legendre quadrature rule to discretize the distributed integral terms in both the spatial and temporal directions, we first approximate the original distributed-order fractional problem by the

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of

In this paper, a linearly-implicit Fourier pseudo-spectral method which preserves discrete mass and energy is developed for the time-dependent 3D Gross–Pitaevskii equation with additional angular momentum rotation. By establishing several discrete semi-norm equivalences between the Fourier pseudo-spectral method and the finite difference method, we establish an optimal H1-error estimate for the proposed