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/

Efficient unstructured mesh generation for marine renewable energy applications

Renewable energy is the cornerstone of preventing dangerous climate change whilst maintaining a robust energy supply. Tidal energy will arguably play a critical role in the renewable energy portfolio as it is both predictable and reliable, and can be put in place across the globe. However, installation may impact the local and regional ecology via changes in tidal dynamics, sediment transport pathways or bathymetric changes. In order to mitigate these effects, tidal energy devices need to be modelled in order to predict hydrodynamic changes. Robust mesh generation is a fundamental component required for developing simulations with high accuracy. However, mesh generation for coastal domains can be an elaborate procedure. Here, we describe an approach combining mesh generators with Geographical Information Systems. We demonstrate robustness and efficiency by constructing a mesh with which to examine the potential environmental impact of a tidal turbine farm installation in the Orkney Islands. The mesh is then used with two well-validated ocean models, to compare their flow predictions with and without a turbine array. The results demonstrate that it is possible to create an easy-to-use tool to generate high-quality meshes for combined coastal engineering, here tidal turbines, and coastal ocean simulations

OceanMesh2D 1.0: MATLAB-based software for two-dimensional unstructured mesh generation in coastal ocean modeling

OceanMesh2D is a set of MATLAB functions with preprocessing and post-processing utilities to generate two-dimensional (2-D) unstructured meshes for coastal ocean circulation models. Mesh resolution is controlled according to a variety of feature-driven geometric and topo-bathymetric functions. Mesh generation is achieved through a force balance algorithm to locate vertices and a number of topological improvement strategies aimed at improving the worst-case triangle quality. The placement of vertices along the mesh boundary is adapted automatically according to the mesh size function, eliminating the need for contour simplification algorithms. The software expresses the mesh design and generation process via an objected-oriented framework that facilitates efficient workflows that are flexible and automatic. This paper illustrates the various capabilities of the software and demonstrates its utility in realistic applications by producing high-quality, multiscale, unstructured meshes.</p

Subgrid scale modelling of transport processes.

Consideration of stabilisation techniques is essential in the development of physical models if they are to faithfully represent processes over a wide range of scales. Careful application of these techniques can significantly increase flexibility of models, allowing the computational meshes used to discretise the underlying partial differential equations to become highly nonuniform and anisotropic, for example. This exibility enables a model to capture a wider range of phenomena and thus reduce the number of parameterisations required, bringing a physically more realistic solution. The next generation of fluid flow and radiation transport models employ unstructured meshes and anisotropic adaptive methods to gain a greater degree of flexibility. However these can introduce erroneous artefacts into the solution when, for example, a process becomes unresolvable due to an adaptive mesh change or advection into a coarser region of mesh in the domain. The suppression of these effects, caused by spatial and temporal variations in mesh size, is one of the key roles stabilisation can play. This thesis introduces new explicit and implicit stabilisation methods that have been developed for application in fluid and radiation transport modelling. With a focus on a consistent residual-free approach, two new frameworks for the development of implicit methods are presented. The first generates a family of higher-order Petrov-Galerkin methods, and the example developed is compared to standard schemes such as streamline upwind Petrov-Galerkin and Galerkin least squares in accurate modelling of tracer transport. The dissipation generated by this method forms the basis for a new explicit fourth-order subfilter scale eddy viscosity model for large eddy simulation. Dissipation focused more sharply on unresolved scales is shown to give improved results over standard turbulence models. The second, the inner element method, is derived from subgrid scale modelling concepts and, like the variational multiscale method and bubble enrichment techniques, explicitly aims to capture the important under-resolved fine scale information. It brings key advantages to the solution of the Navier-Stokes equations including the use of usually unstable velocity-pressure element pairs, a fully consistent mass matrix without the increase in degrees of freedom associated with discontinuous Galerkin methods and also avoids pressure filtering. All of which act to increase the flexibility and accuracy of a model. Supporting results are presented from an application of the methods to a wide range of problems, from simple one-dimensional examples to tracer and momentum transport in simulations such as the idealised Stommel gyre, the lid-driven cavity, lock-exchange, gravity current and backward-facing step. Significant accuracy improvements are demonstrated in challenging radiation transport benchmarks, such as advection across void regions, the scattering Maynard problem and demanding source-absorption cases. Evolution of a free surface is also investigated in the sloshing tank, transport of an equatorial Rossby soliton, wave propagation on an aquaplanet and tidal simulation of the Mediterranean Sea and global ocean. In combination with adaptive methods, stabilising techniques are key to the development of next generation models. In particular these ideas are critical in achieving the aim of extending models, such as the Imperial College Ocean Model, to the global scale

Modelling of intertidal floodplains for enhanced estuarine transport and decay of faecal indicator organisms from a diffuse source

The noncompliance of microbiological quality to the standards of the EU Water Framework Directive at shellfish harvesting waters in the UK has become a serious threat to human health. The infected filter-feeding shellfish by enteric bacteria or viruses from these waters is major to the spreading of foodborne diseases as humans consumed them raw or undercooked. Although the quality of effluents from the wastewater treatment works has been improved significantly, diffuse source of pathogens from urban and agricultural settings remained as the reason to the microbiological noncompliance. The exploitation of natural wetlands along with poor management practices at catchments delivered the overloading of faecal contaminants from sources into the receiving water. In this study, a developed hydro-environmental model is novel in contributing to the understanding of the microbial behaviour on the implicit response to the complex estuarine environment from the perspective of their morphological characteristics. Besides, the extended modelling domain at intertidal floodplains is novel in contributing to the representation of the tidal creek connectivity with the sub-mesh scale design based on the hydrological characteristic of the complex floodplain topography. Furthermore, the modelled of FIO transport and decay from intertidal marshlands is novel in contributing to the inclusion of the diffuse source with the integration to the release-kinetic model and based on an active source at the wetting and drying boundary. The hydrodynamic calibration at several sites resulted in an optimum Manning’s n of 0.025. The successful integration between the bathymetric and topographic data at intertidal floodplains resulted in a significant improvement for the tidal circulation within the study area. The sensitivity analysis on the diffusive transport has suggested the decrease in the tracer diffusivity with the increase in the mesh resolution, with the concentration gradient has increased with the decrease of the former parameter. The sensitivity analysis on the bottom roughness has suggested the increase in the tracer retention at floodplains with the increase in the roughness during low tides, with the concentration in subtidal channels was less sensitive to the roughness changes during high tides. The sensitivity analysis on the microbial kinetic has suggested that MS2 coliphage experienced the biphasic decay in the estuarine environment, with the T90 value ranged at 1 hour and from 50 to 125 hours for the first and second components decay respectively. The sensitivity analysis on the FIOs transport from the diffuse ii source has suggested the increase in the spreading area and the flush-out mass with the decrease i

IX Simposio Nacional sobre Taludes y Laderas Inestables

Presentamos una nueva edición, la novena, del Simposio Nacional sobre Taludes y Laderas Inestables. Este Simposio se ha consolidado como un foro independiente, abierto y pluridisciplinar, con el objetivo de difundir los conocimientos, presentar los avances recientes y fomentar la discusión entre expertos que trabajan en este apasionante campo. La edición de 2017 pone de manifiesto la notable evolución experimentada en los últimos años de las herramientas de caracterización y análisis así como de las medidas estabilización y protección. Las técnicas de captura remota de datos como el láser escáner, la interferometría radar, la fotogrametría y videometría digital, con el apoyo de los vehículos aéreos no tripulados, han cambiado la forma de analizar y monitorizar las laderas. No sólo permiten salvar los problemas de accesibilidad en las paredes rocosas de gran desarrollo sino que proporcionan productos de una gran resolución. Como resultado de todo ello, aparece un nuevo reto como es el almacenamiento, tratamiento y gestión de las ingentes cantidades de datos generadas.Postprint (published version

Dipterocarps protected by Jering local wisdom in Jering Menduyung Nature Recreational Park, Bangka Island, Indonesia

Apart of the oil palm plantation expansion, the Jering Menduyung Nature Recreational Park has relatively diverse plants. The 3,538 ha park is located at the north west of Bangka Island, Indonesia. The minimum species-area curve was 0.82 ha which is just below Dalil conservation forest that is 1.2 ha, but it is much higher than measurements of several secondary forests in the Island that are 0.2 ha. The plot is inhabited by more than 50 plant species. Of 22 tree species, there are 40 individual poles with the average diameter of 15.3 cm, and 64 individual trees with the average diameter of 48.9 cm. The density of Dipterocarpus grandiflorus (Blanco) Blanco or kruing, is 20.7 individual/ha with the diameter ranges of 12.1 – 212.7 cm or with the average diameter of 69.0 cm. The relatively intact park is supported by the local wisdom of Jering tribe, one of indigenous tribes in the island. People has regulated in cutting trees especially in the cape. The conservation agency designates the park as one of the kruing propagules sources in the province. The growing oil palm plantation and the less adoption of local wisdom among the youth is a challenge to forest conservation in the province where tin mining activities have been the economic driver for decades. More socialization from the conservation agency and the involvement of university students in raising environmental awareness is important to be done