Alexandros Avdis

PyRDM: A Python-based library for automating the management and online publication of scientific software and data

The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key findings published in journal articles, thereby making it difficult or impossible for the wider scientific community to verify the correctness of a result or to build further research on it. This paper presents a new Python-based library, PyRDM, whose functionality aims to automate the process of sharing the software and data via online, citable repositories such as Figshare. The library is integrated into the workflow of an open-source computational fluid dynamics package, Fluidity, to demonstrate an example of its usage.

Tidal dynamics and mangrove carbon sequestration during the Oligo–Miocene in the South China Sea

Modern mangroves are among the most carbon-rich biomes on Earth, but their long-term (≥106 years) impact on the global carbon cycle is unknown. The extent, productivity and preservation of mangroves are controlled by the interplay of tectonics, global sea level and sedimentation, including tide, wave and fluvial processes. The impact of these processes on mangrove-bearing successions in the Oligo–Miocene of the South China Sea (SCS) is evaluated herein. Palaeogeographic reconstructions, palaeotidal modelling and facies analysis suggest that elevated tidal range and bed shear stress optimized mangrove development along tide-influenced tropical coastlines. Preservation of mangrove organic carbon (OC) was promoted by high tectonic subsidence and fluvial sediment supply. Lithospheric storage of OC in peripheral SCS basins potentially exceeded 4,000 Gt (equivalent to 2,000 p.p.m. of atmospheric CO2). These results highlight the crucial impact of tectonic and oceanographic processes on mangrove OC sequestration within the global carbon cycle on geological timescales.

Meshing ocean domains for coastal engineering applications

As we continue to exploit and alter the coastal environment, the quantification of the potential impacts from planned coastal engineering projects, as well as the minimisation of any detrimental effects through design optimisation, are receiving increasing attention. Geophysical fluid dynamics simulations can provide valuable insight towards the mitigation and prevention of negative outcomes, and as such are routinely used for planning, operational and regulatory reasons. The ability to readily create high-quality computational meshes is critical to such modelling studies as it impacts on the accuracy, efficiency and reproducibility of the numerical results. To that end, most (coastal) ocean modelling packages offer tailored mesh generation utilities. Geographical Information Systems (GIS) offer an ideal framework within which to process data for use in the meshing of coastal regions. GIS have been designed specifically for the processing and analysis of geophysical data and are a popular tool in both the academic and industrial sectors. On the other hand Computer Aided Design (CAD) is the most appropriate tool for designing coastal structures and is usually the user interface to generic three–dimensional mesh generation frameworks. In this paper we combine GIS and CAD with a view towards mesh generation for an impact study of the proposed Swansea Bay Tidal Lagoon project within the Bristol Channel and Severn Estuary. We demonstrate in this work that GIS and CAD can be used in a complementary way to deliver unstructured mesh generation capabilities for coastal engineering applications.