Surface-sampled simulations of turbulent flow at high Reynolds number

A new approach to turbulence simulation, based on a combination of large-eddy simulation (LES) for the whole flow and an array of non-space-filling quasi-direct numerical simulations (QDNS), which sample the response of near-wall turbulence to large-scale forcing, is proposed and evaluated. The technique overcomes some of the cost limitations of turbulence simulation, since the main flow is treated with a coarse-grid LES, with the equivalent of wall functions supplied by the near-wall sampled QDNS. Two cases are tested, at friction Reynolds number Re$_\tau$=4200 and 20,000. The total grid node count for the first case is less than half a million and less than two million for the second case, with the calculations only requiring a desktop computer. A good agreement with published DNS is found at Re$_\tau$=4200, both in terms of the mean velocity profile and the streamwise velocity fluctuation statistics, which correctly show a substantial increase in near-wall turbulence levels due to a modulation of near-wall streaks by large-scale structures. The trend continues at Re$_\tau$=20,000, in agreement with experiment, which represents one of the major achievements of the new approach. A number of detailed aspects of the model, including numerical resolution, LES-QDNS coupling strategy and sub-grid model are explored. A low level of grid sensitivity is demonstrated for both the QDNS and LES aspects. Since the method does not assume a law of the wall, it can in principle be applied to flows that are out of equilibrium.Comment: Author accepted version. Accepted for publication in the International Journal for Numerical Methods in Fluids on 26 April 201

Fluctuation symmetries for work and heat

We consider a particle dragged through a medium at constant temperature as described by a Langevin equation with a time-dependent potential. The time-dependence is specified by an external protocol. We give conditions on potential and protocol under which the dissipative work satisfies an exact symmetry in its fluctuations for all times. We also present counter examples to that exact fluctuation symmetry when our conditions are not satisfied. Finally, we consider the dissipated heat which differs from the work by a temporal boundary term. We explain when and why there can be a correction to the standard fluctuation theorem due to the unboundedness of that temporal boundary. However, the corrected fluctuation symmetry has again a general validity.Comment: 10 pages, 4 figures (v2: minor typographic corrections

Improving the Reproducibility of LaTeX Documents by Enriching Figures with Embedded Scripts and Data

The introduction of open-access data policies by research councils, the enforcement of best practices, and the deployment of persistent online repositories have enabled datasets which support results in scientific papers to become more widely accessible. Unfortunately, despite this advancement in the curation/publishing workflow, the data-driven figures within a paper often remain difficult to reproduce. Plotting or analysis scripts rarely accompany the manuscript or any associated software release; and even if they do, it may be unclear exactly which version was used. Furthermore, the precise commands and parameters used to execute the scripts are often not included in a README file or in the paper itself. This paper introduces a new open-source digital curation tool, Pynea, for improving the reproducibility of LaTeX documents. Each figure within a document is enriched by automatically embedding the plotting script and data files required to generate it, such that it can be regenerated by readers of the paper in the future. The command used to execute the plotting script is also added to the figure's metadata, along with details of the specific version of the script used (if the script is tracked with the Git version control system). If the document is to be recompiled with a figure that has since changed, or had its plotting script or data files modified, the figure is regenerated such that the author can be confident that the latest version of the figure and its dependencies are included

Integrating Research Data Management into Geographical Information Systems

Ocean modelling requires the production of high-fidelity computational meshes upon which to solve the equations of motion. The production of such meshes by hand is often infeasible, considering the complexity of the bathymetry and coastlines. The use of Geographical Information Systems (GIS) is therefore a key component to discretising the region of interest and producing a mesh appropriate to resolve the dynamics. However, all data associated with the production of a mesh must be provided in order to contribute to the overall recomputability of the subsequent simulation. This work presents the integration of research data management in QMesh, a tool for generating meshes using GIS. The tool uses the PyRDM library to provide a quick and easy way for scientists to publish meshes, and all data required to regenerate them, to persistent online repositories. These repositories are assigned unique identifiers to enable proper citation of the meshes in journal articles.Comment: Accepted, camera-ready version. To appear in the Proceedings of the 5th International Workshop on Semantic Digital Archives (http://sda2015.dke-research.de/), held in Pozna\'n, Poland on 18 September 2015 as part of the 19th International Conference on Theory and Practice of Digital Libraries (http://tpdl2015.info/