An implicit wetting and drying approach for non-hydrostatic baroclinic flows in high aspect ratio domains

A new approach to modelling free surface flows is developed that enables, for the first time, 3D consistent non-hydrostatic baroclinic physics that wets and drys in the large aspect ratio spatial domains that characterise geophysical systems. This is key in the integration of physical models to permit seamless simulation in a single consistent arbitrarily unstructured multiscale and multi-physics dynamical model. A high order continuum representation is achieved through a general Galerkin finite element formulation that guarantees local and global mass conservation, and consistent tracer advection. A flexible spatial discretisation permits conforming domain bounds and a variable spatial resolution, whilst atypical use of fully implicit time integration ensures computational efficiency. Notably this brings the natural inclusion of non-hydrostatic baroclinic physics and a consideration of vertical inertia to flood modelling in the full 3D domain. This has application in improving modelling of inundation processes in geophysical domains, where dynamics proceeds over a large range of horizontal extents relative to vertical resolution, such as in the evolution of a tsunami, or in urban environments containing complex geometric structures at a range of scales.Environmental Fluid Mechanic

Shingle 2.0: Generalising self-consistent and automated domain discretisation for multi-scale geophysical models

The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model- or application-specific, and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, to ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions that enable full accounts of provenance, sharing, and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed that is automated, robust and repeatable, quick-to-draft, rigorously verified, and consistent with the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics. Library code, verification tests, and examples available in the repository at https://github.com/shingleproject/Shingle</a. Further details of the project presented at http://shingleproject.org.Environmental Fluid Mechanic

Kralendijk Declaration, recommendations from Coastal Dynamics and Ecosystem Change: Caribbean, Quo Vadis?: Bonaire, October 18-21, 2016

The Kralendijk Declaration is the outcome of the conference on "Coastal Dynamics and Ecosystem Change: Caribbean, Quo Vadis?" that was held on Bonaire, October 18-21 2016.Environmental Fluid Mechanic

A multiscale analysis of the stability of Caribbean coastal ecosystems through the biogeomorphic modelling of its complex bays and inlets

The Dutch Caribbean consists of two island groups, the Leeward Antilles off the Venezuelan coast separated from the Windward Islands east of Puerto Rico over distances of the scale of the Caribbean Sea itself. Climate change in the Caribbean Sea is predicted to lead to rising sea levels, warming waters and changing eddy fields. Warming waters lead to an increase in the intensity and occurrence of tropical storms and hurricanes, and are linked to an increased risk of surge flooding. Changing eddy fields are likely to affect the path of storm tracks. All of which further influence the environment of the Caribbean, and hence the stability of its ecosystems.Environmental Fluid Mechanic

The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model.Environmental Fluid Mechanic

Maintaining Tropical Beaches with Seagrass and Algae: A Promising Alternative to Engineering Solutions

Tropical beaches provide coastal flood protection, income from tourism, and habitat for flagship species. They urgently need protection from erosion, which is being exacerbated by changing climate and coastal development. Traditional coastal engineering solutions are expensive, provide unstable temporary solutions, and often disrupt natural sediment transport. Instead, natural foreshore stabilization and nourishment may provide a sustainable and resilient long-term solution. Field flume and ecosystem process measurements, along with data from the literature, show that sediment stabilization by seagrass in combination with sediment-producing calcifying algae in the foreshore form an effective mechanism for maintaining tropical beaches worldwide. The long-term efficacy of this type of nature-based beach management is shown at a large scale by comparing vegetated and unvegetated coastal profiles. We argue that preserving and restoring vegetated beach foreshore ecosystems offers a viable, self-sustaining alternative to traditional engineering solutions, increasing the resilience of coastal areas to climate change.Environmental Fluid MechanicsPhysical and Space Geodes

Water motion and vegetation control the pH dynamics in seagrass-dominated bays

Global oceanic pH is lowering, which is causing great concern for the natural functioning of marine ecosystems. Current pH predictions are based on open ocean models; however, coastal zones are dynamic systems with seawater pH fluctuating temporally and spatially. To understand how coastal ecosystems will respond in the future, we first need to quantify the extent that local processes influence the pH of coastal zones. With this study, we show that over a single diurnal cycle, the total pH can fluctuate up to 0.2 units in a shallow seagrass-dominated bay, driven by the photosynthesis and respiration of the vegetation. However, these biologically controlled pH fluctuations vary significantly over small distances. Monitoring conducted at neighboring sites with contrasting hydrodynamic regimes highlights how water motion controls the extent that the local pH is altered by the metabolism of vegetation. The interactive effects of hydrodynamics and vegetation were further investigated with an in situ experiment, where the hydrodynamics were constrained and thus the local water residence time was increased, displaying the counteractive effect of hydrodynamics on the pH change caused by vegetation. With this research, we provide detailed in situ evidence of the spatial variation of pH within marine ecosystems, highlighting the need to include hydrodynamic conditions when assessing the pH-effects of vegetation, and identifying potential high-pH refuges in a future low pH ocean.Environmental Fluid MechanicsPhysical and Space Geodes

Mechanisms of the 40–70 Day Variability in the Yucatan Channel Volume Transport

The Yucatan Channel connects the Caribbean Sea with the Gulf of Mexico and is the main outflow region of the Caribbean Sea. Moorings in the Yucatan Channel show high-frequent variability in kinetic energy (50–100 days) and transport (20–40 days), but the physical mechanisms controlling this variability are poorly understood. In this study, we show that the short-term variability in the Yucatan Channel transport has an upstream origin and arises from processes in the North Brazil Current. To establish this connection, we use data from altimetry and model output from several high resolution global models. A significant 40–70 day variability is found in the sea surface height in the North Brazil Current retroflection region with a propagation toward the Lesser Antilles. The frequency of variability is generated by intrinsic processes associated with the shedding of eddies, rather than by atmospheric forcing. This sea surface height variability is able to pass the Lesser Antilles, it propagates westward with the background ocean flow in the Caribbean Sea and finally affects the variability in the Yucatan Channel volume transport.Physical and Space GeodesyEnvironmental Fluid Mechanic