Article
Computer Science, Interdisciplinary Applications
Carolina M. Jauregui, Jaeyub Hyun, Andreas Neofytou, Justin S. Gray, Hyunsun Alicia Kim
Summary: The aim of this work is to introduce a unified description of topology optimization (TO) methods, which modularizes and generalizes all TO methods, both density based and boundary based. This unified description allows for the implementation of a reusable modular TO software, ParaLeSTO, which specializes in level set TO (LSTO). In addition, we use this software as a means to propose a guideline for research software metadata in the TO community. The proposed guideline for the research software metadata is based on the FAIR principles for research software, which focuses on improving the findability, accessibility, interoperability, and reusability of research software and its metadata. The modularized TO framework separates the analysis, which solves the state equations and does the sensitivity analysis, and the design modification, which represents and modifies the design. Mapping is then used to interface between the two. We demonstrate the interoperability and reusability of this framework through numerical examples.
STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION
(2023)
Article
Mathematics, Applied
David Kamensky
Summary: This paper introduces the open-source libraries tIGAr and CouDALFISh, demonstrating the utility of tIGAr in complex problems and the use of the DAL method in CouDALFISh for fluid-shell coupling. The automation of numerical routines brings transparency and reproducibility to immersogeometric FSI analysis, while also emphasizing the usefulness of frameworks like FEniCS in non-standard workflows.
COMPUTERS & MATHEMATICS WITH APPLICATIONS
(2021)
Article
Computer Science, Interdisciplinary Applications
Grant E. Neighbor, Han Zhao, Mehdi Saraeian, Ming-Chen Hsu, David Kamensky
Summary: Code generation technology has a transformative impact on the field of numerical PDEs, allowing for automatic compilation of high-performance solver routines from abstract mathematical descriptions. This paper demonstrates the integration of FEniCS into a custom implementation of IMGA, for handling complex domain geometries. The results show that code generation enables rapid implementation of different material models and provides robustness and flexibility.
ENGINEERING WITH COMPUTERS
(2023)
Article
Physics, Fluids & Plasmas
Aleksandar P. Jovanovic, Detlef Loffhagen, Markus M. Becker
Summary: This paper introduces the finite element discharge modelling (FEDM) code, developed using the open-source computing platform FEniCS. The code extends FEniCS by allowing the automated implementation and numerical solution of fully coupled fluid-Poisson models with particle balance equations. It is verified using exact solutions and benchmarking, and its performance is compared to COMSOL Multiphysics, showing comparable parallel speed-up and good performance on high-performance compute clusters.
PLASMA SOURCES SCIENCE & TECHNOLOGY
(2023)
Article
Environmental Sciences
Stavroula Biri, Richard C. Cornes, David I. Berry, Elizabeth C. Kent, Margaret J. Yelland
Summary: The turbulent exchanges of heat, moisture and momentum between the atmosphere and the ocean are crucial for the Earth's climate system. Direct measurements of turbulent fluxes are challenging and limited, leading to uncertainties in empirical parameterizations. This paper presents AirSeaFluxCode, an open-source software package for flux computation, providing a variety of parameterizations to explore uncertainty. Height adjustment and consideration of exchange processes also impact flux estimates. Rating: 10/10.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Mathematics, Applied
Han Zhao, Xiangbei Liu, Andrew H. Fletcher, Ru Xiang, John T. Hwang, David Kamensky
Summary: This paper introduces an open-source framework for analyzing aerospace structures represented as collections of untrimmed NURBS patches. The framework utilizes mechanical modeling and isogeometric discretization for computational analysis.
COMPUTERS & MATHEMATICS WITH APPLICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Mamdouh Alenezi
Summary: The evolution of software systems and understanding their internal quality is crucial in software engineering. This study analyzed the evolution of object-oriented open-source software systems in terms of size, internal quality metrics, showing significant differences among systems in LOC, significant correlations between internal quality metrics, and positive effects of complexity and inheritance on LOC. Coupling and Cohesion did not show significant effects on LOC.
APPLIED SCIENCES-BASEL
(2021)
Article
Computer Science, Software Engineering
Damian A. Tamburri, Fabio Palomba, Rick Kazman
Summary: Software engineering success relies on balancing distance, culture, global engineering practices and more. This paper introduces an automated approach, CodeFace4Smells, to identify four community smell types. A large-scale empirical study on 60 open-source communities reveals that community smells are highly diffused in open-source and perceived by developers as significant issues for software community evolution.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Computer Science, Software Engineering
Georgia M. Kapitsaki, Georgia Charalambous
Summary: This paper introduces findOSSLicense, a license recommender that helps users choose the appropriate open source license for their software under creation. The recommendation process is based on a hybrid recommender that considers user needs and system flexibility, and involves analysis of existing open source licenses.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Computer Science, Information Systems
Marc Oriol, Carlos Mueller, Jordi Marco, Pablo Fernandez, Xavier Franch, Antonio Ruiz-Cortes
Summary: Recent surveys show that the use of Open Source Software (OSS) is increasingly important for organizations. However, choosing the right OSS or contributing to its development is a complex task. There is a lack of useful OSSECO analysis tools for potential adopters or contributors.
INTERNET OF THINGS
(2023)
Article
Computer Science, Artificial Intelligence
Linda Erlenhov, Francisco Gomes de Oliveira Neto, Philipp Leitner
Summary: This paper presents an empirical study on bot activity, using both quantitative and qualitative analysis. The study highlights the differences in definitions of bot activity in open-source software and identifies tools that comply with the characteristics of Devbots. The analysis also reveals that most projects experiment with multiple bots before making a decision on adoption or switching. Factors such as generated noise and required adaptation in development practices are found to drive discussions about the adoption or removal of Devbots.
PEERJ COMPUTER SCIENCE
(2022)
Article
Computer Science, Information Systems
Di Cui, Lingling Fan, Sen Chen, Yuanfang Cai, Qinghua Zheng, Yang Liu, Ting Liu
Summary: This paper presents the first attempt to understand bug fixes from the perspective of dependencies. A systematic study on bug fixes collected from 157 Apache open source projects is conducted, revealing a relatively high proportion of bug fixes introducing dependency-level changes. These fixes are strongly correlated with high priority, large fixing churn, long fixing time, frequent bug reopening, and bug inducing. In addition, patched files with dependency-level changes consume much more maintenance costs compared to those without these changes.
SCIENCE CHINA-INFORMATION SCIENCES
(2022)
Article
Engineering, Manufacturing
Zach Zhizhong Zhou, Vidyanand Choudhary
Summary: The impact of competition from open source software on proprietary software providers is complex, sometimes leading to improvements in software quality and pricing by proprietary providers, but also potentially causing a decrease in social welfare.
PRODUCTION AND OPERATIONS MANAGEMENT
(2022)
Article
Computer Science, Software Engineering
Xiao Ling, Rishabh Agrawal, Tim Menzies
Summary: Different types of projects require tuning of prioritization approaches for effective detection and fixing of software faults.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Mathematics, Applied
James McDonagh, Nunzio Palumbo, Neeraj Cherukunnath, Nikolay Dimov, Nada Yousif
Summary: This research introduces a three-dimensional permanent magnet synchronous motor model developed using FEniCSx, which shows comparable results to the verification model. This method provides the accuracy needed to make electric propulsion systems feasible for large vehicles.
FINITE ELEMENTS IN ANALYSIS AND DESIGN
(2022)
Article
Biochemical Research Methods
Van-Dang Nguyen, Johan Jansson, Hoang Trong An Tran, Johan Hoffman, Jing-Rebecca Li
JOURNAL OF MAGNETIC RESONANCE
(2019)
Article
Computer Science, Interdisciplinary Applications
Rahul Bale, Neelesh A. Patankar, Niclas Jansson, Keiji Onishi, Makoto Tsubokura
COMPUTERS & FLUIDS
(2020)
Article
Biochemistry & Molecular Biology
Cornelia Bratengeier, Aneta Liszka, Johan Hoffman, Astrid D. Bakker, Anna Fahlgren
Article
Engineering, Multidisciplinary
Maximilian Balmus, Andre Massing, Johan Hoffman, Reza Razavi, David A. Nordsletten
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2020)
Article
Engineering, Multidisciplinary
Jeannette Hiromi Spuhler, Johan Hoffman
Summary: An interface tracking finite element methodology is proposed for 3D turbulent flow fluid-structure interaction, with a specific focus on heart valve simulations. This methodology is based on a unified continuum fluid-structure interaction model and utilizes standard finite element methods to solve partial differential equations. Contact is modeled using local phase changes in the unified continuum, and computational results demonstrate the potential of this approach.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING
(2021)
Article
Computer Science, Hardware & Architecture
Marco Atzori, Wiebke Kopp, Steven W. D. Chien, Daniele Massaro, Fermin Mallor, Adam Peplinski, Mohamad Rezaei, Niclas Jansson, Stefano Markidis, Ricardo Vinuesa, Erwin Laure, Philipp Schlatter, Tino Weinkauf
Summary: The study reveals that in situ visualization on high-performance computing systems significantly impairs the parallel efficiency of the code, with bottlenecks in the image composition phase due to MPI communication and an imbalance in in situ processing time among different ranks. Improving parallel image composition and load balancing can greatly enhance the performance of the code with in situ capabilities.
JOURNAL OF SUPERCOMPUTING
(2022)
Letter
Mechanics
Johan Hoffman
Summary: The triple decomposition of the velocity gradient proposed by Kolar in 2007 has implications for energy stability analysis of the Navier-Stokes equations and the mathematical analysis of turbulent flow. It suggests a scenario where unstable irrotational straining flow structures rapidly evolve into linearly unstable shear flow and stable rigid body rotational flow at macroscopic scales. Viscous dissipation stabilizes unstable flow structures near the Kolmogorov microscales.
Review
Physiology
Jussi T. Koivumaki, Johan Hoffman, Mary M. Maleckar, Gaute T. Einevoll, Joakim Sundnes
Summary: Mathematical models have greatly advanced cardiovascular physiology research, but barriers between experimental and computational approaches remain, calling for closer integration.
Article
Computer Science, Hardware & Architecture
Martin Karp, Daniele Massaro, Niclas Jansson, Alistair Hart, Jacob Wahlgren, Philipp Schlatter, Stefano Markidis
Summary: In this paper, we propose an approach to simulate turbulence in sustainable shipping using direct numerical simulations. We leverage modern Fortran and the spectral element method on supercomputers powered by Nvidia A100 and AMD Instinct MI250X GPUs, providing support for user software developed in Fortran. We demonstrate the efficiency of our approach by successfully simulating the flow around a Flettner rotor and its interaction with a turbulent boundary layer at Re = 30,000. We also compare the performance of AMD Instinct MI250X and Nvidia A100 GPUs for scalable computational fluid dynamics, showing that one MI250X performs as well as two A100 GPUs with similar power efficiency based on on-chip energy sensors.
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
(2023)
Article
Mechanics
Joel Kronborg, Johan Hoffman
Summary: The triple decomposition of a velocity gradient tensor splits the flow into irrotational straining flow, shear flow, and rigid body rotational flow. We show that the standardized real Schur form is a solution to the optimization problem posed by Kolar and demonstrate that using the standardized variant of the real Schur form makes computation of the triple decomposition more efficient. Additionally, we illustrate how different structures of the real Schur form correspond to different alignments of the coordinate system with the fluid flow and propose a new algorithm for computing the triple decomposition that guarantees consistent results.
Article
Entomology
Serdar Goktepe, Mustafa Avci, Nicklas Jansson
Summary: This research investigated the saproxylic Coleoptera fauna in oak trees of different ages in Mersin/Gulnar in the Eastern Mediterranean Region in 2017. Window traps were used to sample beetles on the oak trees, and a total of 13,217 individuals from the order Coleoptera were collected. The study identified 242 saproxylic beetle species belonging to 44 families, including 33 species that were new records for the Turkish fauna. Notably, three species found are listed as Vulnerable on the IUCN European and Mediterranean red list.
TURKIYE ENTOMOLOJI DERGISI-TURKISH JOURNAL OF ENTOMOLOGY
(2023)
Proceedings Paper
Computer Science, Hardware & Architecture
Tim Dykes, Clement Foyer, Harvey Richardson, Martin Svedin, Artur Podobas, Niclas Jansson, Stefano Markidis, Adrian Tate, Simon McIntosh-Smith
Summary: In recent times, high performance computing architectures have become increasingly heterogeneous, posing a multi-faceted portability issue for applications, libraries, programming models, and languages. Approaches for performance portability often focus on efficient usage of parallel compute architectures, but neglect data locality abstractions and complex memory systems. The introduction of a library named Mamba aims to assist high performance application/library developers in using heterogeneous memory systems more easily through high level array-based abstractions for memory management.
PROCEEDINGS OF 2021 INTERNATIONAL WORKSHOP ON PERFORMANCE, PORTABILITY & PRODUCTIVITY IN HPC (P3HPC 2021)
(2021)
Proceedings Paper
Computer Science, Hardware & Architecture
Felix Liu, Niclas Jansson, Artur Podobas, Albin Fredriksson, Stefano Markidis
Summary: Radiation Treatment Planning (RTP) is a complex and compute-intensive process for planning external beam radiotherapy for cancer patients. This study explores the use of accelerators, specifically GPUs, to reduce calculating time, achieving faster implementation with higher operational intensity than existing libraries.
2021 IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS (IPDPSW)
(2021)
Proceedings Paper
Computer Science, Hardware & Architecture
Niclas Jansson
2020 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER 2020)
(2020)
Proceedings Paper
Computer Science, Hardware & Architecture
Niclas Jansson
PROCEEDINGS OF INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING IN ASIA-PACIFIC REGION (HPC ASIA 2021)
(2020)
Article
Computer Science, Interdisciplinary Applications
Jin Bao, Zhaoli Guo
Summary: At the equilibrium state of a two-phase fluid system, the chemical potential is constant and the velocity is zero. However, it is challenging to capture this equilibrium state accurately in numerical simulations, resulting in inconsistent thermodynamic interfacial properties and spurious velocities. Therefore, numerical schemes with well-balanced properties are preferred for simulating two-phase flows.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Brian C. Vermeire
Summary: This study presents a framework for implicit large eddy simulation (ILES) of incompressible flows by combining the entropically damped artificial compressibility (EDAC) method with the flux reconstruction (FR) approach. Experimental results demonstrate that the method is accurate and stable for low-order solutions, while higher-order solutions exhibit significantly higher accuracy and lower divergence error compared to reference direct numerical simulation.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Mijian Li, Rui Wang, Xinyu Guo, Xinyu Liu, Lianzhou Wang
Summary: In this study, the flow mechanisms around wall-mounted structures were investigated using Large Eddy Simulation (LES). The impact of inflow turbulence on the flow physics, dynamic response, and hydrodynamic performance was explored. The results revealed strong interference between velocity fluctuations and the wake past the cylinder, as well as significant convection effects in the far wake region.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Donatella Passiatore, Luca Sciacovelli, Paola Cinnella, Giuseppe Pascazio
Summary: A high-order shock-capturing central finite-difference scheme is evaluated for numerical simulations of hyper-sonic high-enthalpy flows out of thermochemical equilibrium. The scheme utilizes a tenth-order accurate central-difference approximation of inviscid fluxes, along with high-order artificial dissipation and shock-capturing terms. The proposed approach demonstrates accuracy and robustness for a variety of thermochemical non-equilibrium configurations.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Philipp Bahavar, Claus Wagner
Summary: Condensation is an important aspect in flow applications, and simulating the gas phase and tracking the deposition rates of condensate droplets can capture the effects of surface droplets on the flow while reducing computational costs.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Andras Szabo, Gyorgy Paal
Summary: This paper introduces an efficient calculation method, the parabolized stability equations (PSE), for solving stability equations. By calculating LU factorization once in each marching step, the time spent on solving linear systems of equations can be significantly reduced. Numerical experiments demonstrate the effectiveness of this method in reducing the solution time for linear equations, and its applicability to similar problems.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
A. Khalifa, M. Breuer
Summary: This study evaluates a recently developed data-driven model for collision-induced agglomerate breakup in high mass loading flows. The model uses artificial neural networks to predict the post-collision behavior of agglomerates, reducing computational costs compared to coupled CFD-DEM simulations.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Chunmei Du, Maojun Li
Summary: This paper considers the bilayer shallow water wave equations in one-dimensional space and presents an invariant domain preserving DG method to avoid Kelvin-Helmholtz instability.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Jean-Michel Tucny, Mihir Durve, Andrea Montessori, Sauro Succi
Summary: The prediction of non-equilibrium transport phenomena in disordered media is a challenging problem for conventional numerical methods. Physics-informed neural networks (PINNs) show potential for solving this inverse problem. In this study, PINNs were used to successfully predict the velocity field of rarefied gas flow, and AdamW was found to be the best optimizer.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Min Gao, Pascal Mossier, Claus-Dieter Munz
Summary: In recent decades, the arbitrary Lagrangian-Eulerian (ALE) approach has gained popularity in dealing with fluid flows with moving boundaries. This paper presents a novel algorithm that combines the ALE finite volume (FV) and ALE discontinuous Galerkin (DG) methods into a stable and efficient hybrid approach. The main challenge of this mixed ALE FV and ALE DG method is reducing the inconsistency between the two discretizations. The proposed algorithm is implemented into a loosely-coupled fluid-structure interaction (FSI) framework and is demonstrated through various benchmark test cases and complex scenarios.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Dawid Strzelczyk, Maciej Matyka
Summary: In this study, the numerical convergence of the Meshless Lattice Boltzmann Method (MLBM) is investigated through three benchmark tests. The results are compared to the standard Lattice Boltzmann Method (LBM) and the analytical solution of the Navier-Stokes equation. It is found that MLBM outperforms LBM in terms of error value for the same number of nodes discretizing the domain.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Kanishka Bhattacharya, Tapan Jana, Amit Shaw, L. S. Ramachandra, Vishal Mehra
Summary: In this work, an adaptive algorithm is developed to address the issue of tensile instability in Smoothed Particle Hydrodynamics (SPH) by adjusting the shape of the kernel function to satisfy stability conditions. The effectiveness of the algorithm is demonstrated through dispersion analysis and fluid dynamics simulations.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Luis Laguarda, Stefan Hickel
Summary: We propose several enhancements to improve the accuracy and performance of the digital filter turbulent inflow generation technique, such as introducing a more realistic correlation function and varying target length scales. Additionally, we suggest generating inflow data in parallel at a prescribed time interval to improve computational performance. Based on the results of large-eddy simulations, these enhancements have shown to be beneficial. Suppressing streamwise velocity fluctuations at the inflow leads to the fastest relaxation of pressure fluctuations. However, this approach increases the adaptation length, which can be shortened by artificially increasing the wall-normal Reynolds stresses.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Constantin Zenz, Michele Buttazzoni, Tobias Florian, Katherine Elizabeth Crespo Armijos, Rodrigo Gomez Vazquez, Gerhard Liedl, Andreas Otto
Summary: A new model for compressible multiphase flows involving sharp interfaces and phase change is presented, with a focus on the treatment of compressibility and phase change in the multiphase fluid flow model. The model's accuracy and suitability are demonstrated through comparisons with experimental observations.
COMPUTERS & FLUIDS
(2024)
Article
Computer Science, Interdisciplinary Applications
Joseph O'Connor, Sylvain Laizet, Andrew Wynn, Wouter Edeling, Peter V. Coveney
Summary: This article aims to apply uncertainty quantification and sensitivity analysis to the direct numerical simulation (DNS) of low Reynolds number wall-bounded turbulent channel flow. By using a highly scalable DNS framework and UQ techniques, the study evaluates the influence of different numerical parameters on the simulation results without explicitly modifying the code. The findings provide guidance for numerical simulations of wall-bounded turbulent flows.
COMPUTERS & FLUIDS
(2024)
