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In a companion study \cite{patterson2020computing2D}, we present a numerical method for simulating 2D viscous flow through an open compliant closed channel, drive by pressure gradient. We consider the highly viscous regime, where fluid…
Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science…
The Hiperwalk package is designed to facilitate the simulation of quantum walks using heterogeneous high-performance computing, taking advantage of the parallel processing power of diverse processors such as CPUs, GPUs, and acceleration…
The applications and impact of high fidelity simulation of fluid flows are far-reaching. They include settling some long-standing and fundamental questions in turbulence. However, the computational resources required for such efforts are…
Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…
This paper presents SPLASH, a publicly available interactive visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations. Visualisation of SPH data is more complicated than for grid-based codes because the data is defined on a…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
We present Paicos, a new object-oriented Python package for analyzing simulations performed with Arepo. Paicos strives to reduce the learning curve for students and researchers getting started with Arepo simulations. As such, Paicos…
Fuzzy logic is an accepted and well-developed approach for constructing verbal models. Fuzzy based methods are getting more popular, while the engineers deal with more daily life tasks. This paper presents a new Python toolkit for Interval…
In this paper, we present a new Python library called mPyPl, which is intended to simplify complex data processing tasks using functional approach. This library defines operations on lazy data streams of named dictionaries represented as…
Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales, however, the utility of these simulations is often limited by our ability to directly compare them with the…
We are interested in the computational study of shock hydrodynamics, i.e. problems involving compressible solids, liquids, and gases that undergo large deformation. These problems are dynamic and nonlinear and can exhibit complex…
In this work, we report on strategies and results of our initial approach for modernization of Titan2D code. Titan2D is a geophysical mass flow simulation code designed for modeling of volcanic flows, debris avalanches and landslides over a…
Normalizing flows model probability distributions through an expressive tractable density. They transform a simple base distribution, such as a Gaussian, through a sequence of invertible functions, which are referred to as layers. These…
This paper describes a novel Python package, named causalgraph, for modeling and saving causal graphs embedded in knowledge graphs. The package has been designed to provide an interface between causal disciplines such as causal discovery…
During the last two years the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational grids. Since smoothly working production grids are not yet available, we have been able to…
Dissipation can be represented in Hamiltonian mechanics in an extended phase space as a symplectic process. The method uses an auxiliary variable which represents the excitation of unresolved dynamics and a Hamiltonian for the interaction…
VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large numbers of particles. VPIC's…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
The paper presents the results of computation of some simple internal flows of incompressible fluid with the software package CFX-5. In the previous paper of the author, the same flows were used for testing of another CFD software tool,…