New Studies and Replication Studies in Aerodynamics of Animal Flyers with Fully Reproducible Computational Fluid Dynamics
Open Access DepositedThe present work highlights tools and workflows adopted to conduct reproducible Computational Fluid Dynamics (CFD) research. Our main application concerns the aerodynamic performance of the gliding snake species Chrysopelea paradisi. In 2014, our research laboratory published a study on the lift-enhancement mechanism using two-dimensional direct numerical simulations of the flow past an anatomically accurate cross-section of the glider. The flattened cross-section, immersed in a freestream flow at a 35-degree angle of attack, experiences a noticeable gain in lift force at Reynolds numbers 2000 and above. In this work, we first achieved a full-replication study of our results with four CFD software packages (including the code used in the original study) to confirm the lift-enhancement mechanism of the glider. The replication study highlights various obstacles one can face to reproduce and replicate scientific findings. Parallel to that, the need for scaling and more physical three-dimensional simulations led to the development of PetIBM, a toolbox to solve the incompressible Navier-Stokes equations with an immersed-boundary method (IBM) with regularized-delta transfer kernels. The software is open-source (3-Clause BSD License) and runs on distributed-memory architectures with the capability to solve sparse linear systems on multiple GPU devices. In a new effort to make our research transparent and reproducible by others, we developed a workflow to run and share computational studies on the public cloud Microsoft Azure. It uses Docker containers to create an image of the application software stack and Batch Shipyard to create pools of nodes and submit jobs to them. We ran benchmarks and small-scale examples to show that Azure offerings are adequate to complete CFD studies with in-house research software that uses parallel computing with GPUs. We used the workflow to run two-dimensional direct numerical simulations with PetIBM and three-dimensional large-eddy simulations with OpenFOAM, and quantify the effect of the ventrally-oriented lateral lips of the gliding snake section. The trailing-edge lip increases the camber and surface area of the profile to enhance lift. The leading-edge lip re-directs the flow to delay the separation point so that the lifting bluff body can operate effectively at higher angles of attack. Finally, we adapted the reproducible workflow to our university-managed high-performance-computing (HPC) cluster to fully replicate the scientific findings from another research laboratory. We ran PetIBM in Singularity containers to replicate the trends in aerodynamic performance and wake topology of low-aspect-ratio pitching-rolling wings published by other researchers.
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