Advanced Methods for Numerical Modelling of Regional Seas

Chapter 3 has been published as Bruciaferri, D., Shapiro, G.I. and Wobus, F. (2018) A multi-envelope vertical coordinate system for numerical ocean modelling. Ocean Dynamics, Volume 68(10), Pages 1239-1258, doi:10.1007/s10236-018-1189-x. Chapter 4 has been published as Bruciaferri, D., Shapiro, G., Stanichny, S., Zatsepin, A., Ezer, T., Wobus, F., Francis, X., Hilton, D. The development of a 3D computational mesh to improve the representation of dynamic processes: the Black Sea test case, Ocean Modelling, 146 (2020), 101534, doi:10.1016/j.ocemod.2019.101534.Regional seas are of paramount importance for human life. They play a key role in the planetary Earth system dynamics while they also represent a fundamental component of the global economy, making the overuse of ocean resources and the consequent degradation of local marine ecosystems a major concern of our society. Regional ocean modelling represents a powerful and efficacious tools to understand, manage and preserve the changing oceans and seas. This PhD research focuses on improving some of the techniques used for the numerical modelling of regional seas. This is done by developing a novel vertical discretisation scheme for numerical ocean modelling and conducting numerical experiments in an idealized domain as well as in two complex and contrasting real marine environments, the Black Sea and the Dead Sea. In Chapter 3 a Multi-Envelope generalised coordinate system for numerical ocean modelling is introduced. In this system, computational levels are curved and adjusted to multiple `virtual bottoms' (aka envelopes) rather than following geopotential levels or the actual bathymetry. This allows defining computational levels which are optimised to best represent different physical processes in different sub-domains of the model. In particular, we show how it can be used to improve the representation of tracer advection in the ocean interior. The new vertical system is compared with a widely used z-partial step scheme. The modelling skill of the models is assessed by comparison with the analytical solutions or results produced by a model with a very high resolution z-level grid. Three idealised process-oriented numerical experiments are carried out. Experiments show that numerical errors produced by the new scheme are much smaller than those produced by the standard z-partial step scheme at a comparable vertical resolution. In particular, the new scheme shows superiority in simulating the formation of a cold intermediate layer in the ocean interior and in representing dense water cascading down a steep topography. Chapter 4 deals with the numerical modelling of the Black Sea hydrodynamics. The Black Sea is one of the largest land-locked basin in the world. Due to the vulnerability of its unique marine ecosystem, accurate long-term modelling of its hydrodynamics is needed. Any ocean model contains inaccuracies which deviate simulations from reality and data assimilation (DA) is a widely used method to improve model results. Whilst there is abundance of sea surface data, measurements of water column profiles to be used for DA are much scarcer. Therefore, a model which generates smaller errors in free-run (without DA) is needed. In this Chapter we first compare the skills of four NEMO based Black Sea models in free-run which use different discretization schemes. We conclude that the best results are obtained with the model (named CUR-MEs) which uses Multi-Envelope curved vertical s-levels and a curvilinear horizontal grid. It has increased horizontal resolution (≈ 950m) over the shelf-break and lower resolution (≈ 6km) in areas where the scale of relevant processes is larger (about 20 km). The Multi-Envelope system is designed to optimize the representation of the Cold Intermediate Layer (CIL). Second, we compare CUR-MEs in free-run with the CMEMS operational Black Sea model using DA (CMEMS reanalysis). We conclude that in many aspects the skills of the two models are similar, and CUR-MEs is slightly better for representing independently obtained profiles. Finally, we investigate the variability of the Mean Kinetic Energy of geostrophic currents and the CIL simulated by our CUR-MEs model and CMEMS reanalysis. In Chapter 5 we tackle the numerical modelling of the Dead Sea. From 1980s−1990s the Dead Sea water level is constantly decreasing, and currently it has an unprecedented rate of approximately 1.1 m/year. Since 2000, double-diffusive thermohaline staircases have been regularly observed during summer periods. Despite the increasing role of anthropogenic pressures, the evaporation−precipitation balance is still a significant factor which contributes to the recess of the sea level. In this Chapter we study the effect of different vertical mixing regimes on the features of Dead Sea water column and their potential impacts on its rate of evaporation. The methodology is based on simulating the evolution of the Dead Sea water column presenting thermohaline staircases with two contrasting numerical models. One is named SPP and it uses a standard vertical mixing scheme which does not take into account the presence of thermohaline staircases. The second is named MPP and it uses a vertical mixing parameterization compatible with the presence of step-like structures in the water column. Sensitivity experiments show that numerical horizontal pressure gradients errors, though small in both models, are higher in the MPP model, due to its ability to preserve the step-like structures of the initial condition which conversely are smoothed out in the SPP model. Realistic experiments indicate that, under the same atmospheric conditions, a vertical mixing regime typical of a water column presenting step-like structures might be able to reduce the heat transport to greater depths in comparison to a more diffusive diapycnal mixing, contributing to an increase of the Dead Sea water level recession by up to 0.1 m/year during the modelling period of August 2016

The effect of vertical coordinates on the accuracy of a shelf sea model

The vertical coordinates (VC) are one of the most important set of configuration options of an ocean model. Optimisation is, however, a non-trivial exercise. We compare nine configurations to investigate different VC options and contrast the Vanishing Quasi-Sigma (VQS), partial step z-level, s-z hybrid and Multi-Envelope (MEs) approaches. Using NEMO model simulations, a hierarchy of experiments are conducted, including: unforced simulations, multi-year climatological simulations with comparisons against tracer profile observations, and tide-only simulations. Hydrostatic pressure gradient errors on the continental slope in the VQS coordinates are found to be consistent with reduced domain-averaged accuracy in both unforced and realistic simulations. Reduced accuracy on the continental shelf is associated with larger advective tracer transports at the shelfbreak. Accuracy is improved by using separate definitions of the computational surfaces on the shelf and slope using the MEs and s-z hybridisation approaches. MEs configurations employing VQS on the continental slope with a computational slope steepness parameter, , of 0.04–0.07, perform comparably with s-z hybrid configurations. Restrictions on the tilt of computational surfaces on the shelf and upper slope appear less important. In contrast, tide-only experiments without stratification show that tidal simulation quality is linked with accurately representing the shelf bathymetry, which favours terrain-following systems. The experiments support transitioning the vertical coordinates across the shelfbreak using either a MEs or hybrid s-z approach as a flexible route to improving accuracy in regional and global models

Localized general vertical coordinates for quasi‐Eulerian ocean models: The Nordic overflows test‐case

A generalized methodology to deploy different types of vertical coordinate system in arbitrarily defined time-invariant local areas of quasi-Eulerian numerical ocean models is presented. After detailing its characteristics, we show how the general localization method can be used to improve the representation of the Nordic Seas overflows in the UK Met Office NEMO-based eddy-permitting global ocean configuration. Three z*-levels with partial steps configurations localizing different types of hybrid geopotential/terrain-following vertical coordinates in the proximity of the Greenland-Scotland ridge are implemented and compared against a control configuration. Experiments include a series of idealized and realistic numerical simulations where the skill of the models in computing pressure forces, reducing spurious diapycnal mixing and reproducing observed properties of the Nordic Seas overflows are assessed. Numerical results prove that the localization approach proposed here can be successfully used to embed terrain-following levels in a global geopotential levels-based configuration, provided that the localized vertical coordinate chosen is flexible enough to allow a smooth transition between the two. In addition, our experiments show that deploying localized terrain-following levels via the multi-envelope method allows the crucial reduction of spurious cross-isopycnal mixing when modeling bottom intensified buoyancy driven currents, significantly improving the realism of the Nordic Seas overflows simulations in comparison to the other configurations. Important hydrographic biases are found to similarly affect all the realistic experiments and a discussion on how their interaction with the type of localized vertical coordinate affects the realism of the simulated overflows is provided

Reproducible and relocatable regional ocean modelling: Fundamentals and practices

In response to an increasing demand for bespoke or tailored regional ocean modelling configurations, we outline fundamental principles and practices that can expedite the process to generate new configurations. The paper develops the principle of Reproducibility and advocates adherence by presenting benefits to the community and user. The elements to this principle are reproducible workflows and standardised assessment, with additional effort over existing working practices being balanced against the added value generated. The paper then decomposes the complex build process, for a new regional ocean configuration, into stages and presents guidance, advice and insight on each component. This advice is compiled from across the user community, is presented in the context of NEMOv4, though aims to transcend NEMO version. Detail and region specific worked examples are linked in companion repositories and DOIs. The aim is to broaden the user community skill base, and to accelerate development of new configurations in order to increase available time exploiting the configurations

A Structured and Unstructured grid Relocatable ocean platform for Forecasting (SURF)

AbstractWe present a numerical platform named Structured and Unstructured grid Relocatable ocean platform for Forecasting (SURF). The platform is developed for short-time forecasts and is designed to be embedded in any region of the large-scale Mediterranean Forecasting System (MFS) via downscaling. We employ CTD data collected during a campaign around the Elba island to calibrate and validate SURF. The model requires an initial spin up period of a few days in order to adapt the initial interpolated fields and the subsequent solutions to the higher-resolution nested grids adopted by SURF. Through a comparison with the CTD data, we quantify the improvement obtained by SURF model compared to the coarse-resolution MFS model

Study of a wind-wave numerical model and its integration with ocean and oil-spill numerical models

The ability to represent the transport and fate of an oil slick at the sea surface is a formidable task. By using an accurate numerical representation of oil evolution and movement in seawater, the possibility to asses and reduce the oil-spill pollution risk can be greatly improved. The blowing of the wind on the sea surface generates ocean waves, which give rise to transport of pollutants by wave-induced velocities that are known as Stokes’ Drift velocities. The Stokes’ Drift transport associated to a random gravity wave field is a function of the wave Energy Spectra that statistically fully describe it and that can be provided by a wave numerical model. Therefore, in order to perform an accurate numerical simulation of the oil motion in seawater, a coupling of the oil-spill model with a wave forecasting model is needed. In this Thesis work, the coupling of the MEDSLIK-II oil-spill numerical model with the SWAN wind-wave numerical model has been performed and tested. In order to improve the knowledge of the wind-wave model and its numerical performances, a preliminary sensitivity study to different SWAN model configuration has been carried out. The SWAN model results have been compared with the ISPRA directional buoys located at Venezia, Ancona and Monopoli and the best model settings have been detected. Then, high resolution currents provided by a relocatable model (SURF) have been used to force both the wave and the oil-spill models and its coupling with the SWAN model has been tested. The trajectories of four drifters have been simulated by using JONSWAP parametric spectra or SWAN directional-frequency energy output spectra and results have been compared with the real paths traveled by the drifters

The impact of the vertical discretization scheme on the accuracy of a model of the European north-west shelf

The choice of the vertical coordinate system is the single most important factor affecting the quality of ocean model simulations (e.g. Griffies et al. 2000). This is especially true in regions such as the European North-West Shelf (NWS), where complex ocean dynamics result from the combination of a variety of multi-scale physical processes. As part of the Copernicus Marine Environment Monitoring Service, the Met Office runs an operational coupled ocean-wave forecasting system of the NWS. The ocean model employed is a regional implementation of NEMO hydrodynamic code (Madec 2017), further developed by both the Met Office and the National Oceanography Centre under the umbrella of the Joint Marine Modelling Programme (JMMP). Here we describe the work of the JMMP group in assessing the impact of different vertical coordinate systems on the accuracy of the solution of the free-running NWS ocean model. Five different vertical discretization schemes are compared: i) geopotential z-levels with partial steps, ii) s-levels following a smooth version of the bottom topography using either the Song & Haidvogel (1994) or iii) the Siddorn & Furner (2013) stretching functions, iv) the hybrid Harle et al. (2013) s-z with partial step scheme, and v) the multi-envelope s-coordinate system of Bruciaferri et al. (2018). Three different type of numerical experiments with increasing level of complexity are conducted: i) an idealised test for horizontal pressure gradient errors (HPGE), ii) a barotropic simulation forced only by the astronomical tides (TIDE) and iii) a fully baroclinic simulation using realistic initial condition and external forcing (REAL). Numerical results of the HPGE test show that s-levels models develop the highest spurious currents (order of cm/s), the multi-enveloping method allows relatively reduction of the error of pure s-levels grids while z-levels with partial steps or the hybrid s-z scheme are affected by the smallest error (order of mm/s). The TIDE experiment reveals some differences between the models for amplitude and phase of the major tidal components. Preliminary results of the REAL experiment show that models differing only in the vertical discretization schemes broadly represent the same general ocean dynamics, although presenting non-trivial differences in the active tracers and flow fields especially in the proximity of the shelf-break

The impact of wave model source terms and coupling strategies to rapidly developing waves across the north-west European shelf during extreme events

Prediction of severe natural hazards requires accurate forecasting systems. Recently, there has been a tendency towards more integrated solutions, where different components of the Earth system are coupled to explicitly represent the physical feedbacks between them. This study focuses on rapidly developing waves under extratropical storms to understand the impact of different wave source term parameterisations in the WAVEWATCH III (WWIII) model (ST4 and ST6) and coupling strategies (surface roughness closure versus surface stress closure) on the accuracy of the Met Office regional atmosphere‑ocean‑wave coupled research system for the north‑west (NW) European shelf (UKC4). Results of a study focused on simulations during winter 2013/14 demonstrate that ST6 allows for a faster wave growth than the ST4 parameterisation but might degrade low to mid energy wave states. The difference between ST6 and ST4 in wave growth is larger for higher wind speeds and short fetches. The experiment with ST4 and roughness closure consistently under‑predicts the wave growth in those locations where fetch dependence is an important factor (i.e., seas at the East (E) of Ireland and the UK for storms coming from the NW‑WNW). The implementation in the wave model of ST6 physics with the stress closure coupling strategy appears to improve growth of young wind‑seas, reducing bias in those locations where the storms are underestimated. The slower wave growth when using surface roughness closure seems to be related to an underestimation of the momentum transfer computed by the wave model when coupling the wind speeds. For very young to young wind seas, this can be overcome when the surface stress is computed by the atmospheric model and directly passed to the ocean

Challenges simulating the AMOC in climate models

The latest assessment report from the Intergovernmental Panel on Climate Change concluded that the Atlantic Meridional Overturning Circulation (AMOC) was very likely to decline over the twenty-first century under all emissions scenarios; however, there was low confidence in the magnitude of the decline. Recent research has highlighted that model biases in the mean climate state can affect the AMOC in its mean state, variability and its response to climate change. Hence, understanding and reducing these model biases is critical for reducing uncertainty in the future changes of the AMOC and in its impacts on the wider climate. We discuss how model biases, in particular salinity biases, influence the AMOC and deep convection. We then focus on biases in the UK HadGEM3-GC3-1 climate model and how these biases change with resolution. We also discuss ongoing model development activities that affect these biases, and highlight priorities for improved representation of processes, such as the position of the North Atlantic Current, transports in narrow boundary current, resolution (or improved parameterization) of eddies and spurious numerical mixing in overflows. This article is part of a discussion meeting issue ‘Atlantic overturning: new observations and challenges’