Journal Sciences News
Urologic Oncology: Seminars and Original Investigations
February 2018
Sub-seasonal prediction of significant wave heights over the Western Pacific and Indian Oceans, part II: The impact of ENSO and MJO
Publication date: March 2018
Source:Ocean Modelling, Volume 123 Author(s): Ravi P Shukla, James L. Kinter, Chul-Su Shin This study evaluates the effect of El Ni
February 2018
Editorial Board
Publication date: February 2018
Source:Ocean Modelling, Volume 122

February 2018
Frontal dynamics at the edge of the Columbia River plume
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s):
February 2018
Vertical and horizontal resolution dependency in the model representation of tracer dispersion along the continental slope in the northern Gulf of Mexico
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Annalisa Bracco, Jun Choi, Jaison Kurian, Ping Chang A set of nine regional ocean model simulations at various horizontal (from 1 to 9
February 2018
Idealised modelling of ocean circulation driven by conductive and hydrothermal fluxes at the seabed
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Jowan M. Barnes, Miguel A. Morales Maqueda, Jeff A. Polton, Alex P. Megann Geothermal heating is increasingly recognised as an important factor affecting ocean circulation, with modelling studies suggesting that this heat source could lead to first-order changes in the formation rate of Antarctic Bottom Water, as well as a significant warming effect in the abyssal ocean. Where it has been represented in numerical models, however, the geothermal heat flux into the ocean is generally treated as an entirely conductive flux, despite an estimated one third of the global geothermal flux being introduced to the ocean via hydrothermal sources. A modelling study is presented which investigates the sensitivity of the geothermally forced circulation to the way heat is supplied to the abyssal ocean. An analytical two-dimensional model of the circulation is described, which demonstrates the effects of a volume flux through the ocean bed. A simulation using the NEMO numerical general circulation model in an idealised domain is then used to partition a heat flux between conductive and hydrothermal sources and explicitly test the sensitivity of the circulation to the formulation of the abyssal heat flux. Our simulations suggest that representing the hydrothermal flux as a mass exchange indeed changes the heat distribution in the abyssal ocean, increasing the advective heat transport from the abyss by up to 35% compared to conductive heat sources. Consequently, we suggest that the inclusion of hydrothermal fluxes can be an important addition to course-resolution ocean models.

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February 2018
Impacts of sea-surface salinity in an eddy-resolving semi-global OGCM
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Ryo Furue, Kohei Takatama, Hideharu Sasaki, Niklas Schneider, Masami Nonaka, Bunmei Taguchi To explore the impacts of sea-surface salinity (SSS) on the interannual variability of upper-ocean state, we compare two 10-year runs of an eddy-resolving ocean general circulation model (OGCM): in one, SSS is strongly restored toward a monthly climatology (World Ocean Atlas ’98) and in the other, toward the SSS of a monthly gridded Argo product. The inclusion of the Argo SSS generally improves the interannual variability of the mixed layer depth; particularly so in the western tropical Pacific, where so-called “barrier layers” are reproduced when the Argo SSS is included. The upper-ocean subsurface salinity variability is also improved in the tropics and subtropics even below the mixed layer. To understand the reason for the latter improvement, we separate the salinity difference between the two runs into its “dynamical” and “spiciness” components. The dynamical component is dominated by small-scale noise due to the chaotic nature of mesoscale eddies. The spiciness difference indicates that as expected from the upper-ocean general circulation, SSS variability in the mixed layer is subducted into the thermocline in subtropics; this signal is generally advected downward, equatorward, and westward in the equator-side of the subtropical gyre. The SSS signal subducted in the subtropical North Pacific appears to enter the Indian Ocean through the Indonesian Throughflow, although this signal is weak and probably insignificant in our model.
February 2018
A commentary on the Atlantic meridional overturning circulation stability in climate models
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Peter R. Gent The stability of the Atlantic meridional overturning circulation (AMOC) in ocean models depends quite strongly on the model formulation, especially the vertical mixing, and whether it is coupled to an atmosphere model. A hysteresis loop in AMOC strength with respect to freshwater forcing has been found in several intermediate complexity climate models and in one fully coupled climate model that has very coarse resolution. Over 40% of modern climate models are in a bistable AMOC state according to the very frequently used simple stability criterion which is based solely on the sign of the AMOC freshwater transport across 33°
February 2018
Resolving high-frequency internal waves generated at an isolated coral atoll using an unstructured grid ocean model
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Matthew D. Rayson, Gregory N. Ivey, Nicole L. Jones, Oliver B. Fringer We apply the unstructured grid hydrodynamic model SUNTANS to investigate the internal wave dynamics around Scott Reef, Western Australia, an isolated coral reef atoll located on the edge of the continental shelf in water depths of 500,m and more. The atoll is subject to strong semi-diurnal tidal forcing and consists of two relatively shallow lagoons separated by a 500 m deep, 2 km wide and 15 km long channel. We focus on the dynamics in this channel as the internal tide-driven flow and resulting mixing is thought to be a key mechanism controlling heat and nutrient fluxes into the reef lagoons. We use an unstructured grid to discretise the domain and capture both the complex topography and the range of internal wave length scales in the channel flow. The model internal wave field shows super-tidal frequency lee waves generated by the combination of the steep channel topography and strong tidal flow. We evaluate the model performance using observations of velocity and temperature from two through water-column moorings in the channel separating the two reefs. Three different global ocean state estimate datasets (global HYCOM, CSIRO Bluelink, CSIRO climatology atlas) were used to provide the model initial and boundary conditions, and the model outputs from each were evaluated against the field observations. The scenario incorporating the CSIRO Bluelink data performed best in terms of through-water column Murphy skill scores of water temperature and eastward velocity variability in the channel. The model captures the observed vertical structure of the tidal (M 2) and super-tidal (M 4) frequency temperature and velocity oscillations. The model also predicts the direction and magnitude of the M 2 internal tide energy flux. An energy analysis reveals a net convergence of the M 2 energy flux and a divergence of the M 4 energy flux in the channel, indicating the channel is a region of either energy transfer to higher frequencies or energy loss to dissipation. This conclusion is supported by the mooring observations that reveal high frequency lee waves breaking on the turning phase of the tide.
Available online 3 January 2018
Dynamically adaptive data-driven simulation of extreme hydrological flows
Publication date: February 2018
Source:Ocean Modelling, Volume 122 Author(s): Pushkar Kumar Jain, Kyle Mandli, Ibrahim Hoteit, Omar Knio, Clint Dawson Hydrological hazards such as storm surges, tsunamis, and rainfall-induced flooding are physically complex events that are costly in loss of human life and economic productivity. Many such disasters could be mitigated through improved emergency evacuation in real-time and through the development of resilient infrastructure based on knowledge of how systems respond to extreme events. Data-driven computational modeling is a critical technology underpinning these efforts. This investigation focuses on the novel combination of methodologies in forward simulation and data assimilation. The forward geophysical model utilizes adaptive mesh refinement (AMR), a process by which a computational mesh can adapt in time and space based on the current state of a simulation. The forward solution is combined with ensemble based data assimilation methods, whereby observations from an event are assimilated into the forward simulation to improve the veracity of the solution, or used to invert for uncertain physical parameters. The novelty in our approach is the tight two-way coupling of AMR and ensemble filtering techniques. The technology is tested using actual data from the Chile tsunami event of February 27, 2010. These advances offer the promise of significantly transforming data-driven, real-time modeling of hydrological hazards, with potentially broader applications in other science domains.
January 2018
CMIP5-based global wave climate projections including the entire Arctic Ocean
Publication date: Available online 3 January 2018
Source:Ocean Modelling Author(s): M. Casas-Prat, X.L. Wang, N. Swart This study presents simulations of the global ocean wave climate corresponding to the surface winds and sea ice concentrations as simulated by five CMIP5 (Coupled Model Intercomparison Project Phase 5) climate models for the historical (1979–2005) and RCP8.5 scenario future (2081–2100) periods. To tackle the numerical complexities associated with the inclusion of the North Pole, the WAVEWATCH III (WW3) wave model was used with a customized unstructured Spherical Multi-Cell grid of
January 2018
Editorial Board
Publication date: January 2018
Source:Ocean Modelling, Volume 121

January 2018
Eddy dynamics over continental slopes under retrograde winds: Insights from a model inter-comparison
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Yan Wang, Andrew L. Stewart Mesoscale eddies are ubiquitous in the ocean and play a key role in exchanges across continental slopes. In this study the properties of wind-driven baroclinic turbulence are investigated using eddy-resolving process simulations, focusing on the case of retrograde winds that arises around the margins of the subtropical gyres. In contrast to a flat-bottomed ocean, over steep slopes eddies develop from baroclinic instabilities are confined to the top few hundred meters. Deeper in the water column baroclinic instability and vertical momentum transfer are suppressed, so wind-input momentum is exported toward the open ocean by eddies before traversing down to the ocean bed. Close to the sloping topography, eddy energy sourced from the upper ocean is converted to potential energy, steepening isopycnals and driving bottom-trapped prograde flows. This process is associated with upgradient lateral buoyancy fluxes and downgradient isopycnal potential vorticity fluxes, and cannot be reproduced via linear stability calculations. These properties of wind-driven shelf/slope turbulence are contrasted against simulations with flat bathymetry. The key differences described above hinge on the flow close to the steep topographic slope, which may be sensitive to the model’s vertical coordinate system. The simulations are therefore replicated using models that employ geopotential coordinates, terrain-following coordinates, and isopycnal coordinates. Quantitative inter-model discrepancies in the momentum and energy budgets are much more pronounced in the presence of a steep bottom slope. However, the key findings of this study are consistent across the models, suggesting that they are robust and warrant incorporation into parameterizations of eddy transfer across continental slopes.
January 2018
Estimating the numerical diapycnal mixing in an eddy-permitting ocean model
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Alex Megann Constant-depth (or “z-coordinate”) ocean models such as MOM4 and NEMO have become the de facto workhorse in climate applications, having attained a mature stage in their development and are well understood. A generic shortcoming of this model type, however, is a tendency for the advection scheme to produce unphysical numerical diapycnal mixing, which in some cases may exceed the explicitly parameterised mixing based on observed physical processes, and this is likely to have effects on the long-timescale evolution of the simulated climate system. Despite this, few quantitative estimates have been made of the typical magnitude of the effective diapycnal diffusivity due to numerical mixing in these models. GO5.0 is a recent ocean model configuration developed jointly by the UK Met Office and the National Oceanography Centre. It forms the ocean component of the GC2 climate model, and is closely related to the ocean component of the UKESM1 Earth System Model, the UK's contribution to the CMIP6 model intercomparison. GO5.0 uses version 3.4 of the NEMO model, on the ORCA025 global tripolar grid. An approach to quantifying the numerical diapycnal mixing in this model, based on the isopycnal watermass analysis of Lee et al. (2002), is described, and the estimates thereby obtained of the effective diapycnal diffusivity in GO5.0 are compared with the values of the explicit diffusivity used by the model. It is shown that the effective mixing in this model configuration is up to an order of magnitude higher than the explicit mixing in much of the ocean interior, implying that mixing in the model below the mixed layer is largely dominated by numerical mixing. This is likely to have adverse consequences for the representation of heat uptake in climate models intended for decadal climate projections, and in particular is highly relevant to the interpretation of the CMIP6 class of climate models, many of which use constant-depth ocean models at
January 2018
Parameter estimation for a cohesive sediment transport model by assimilating satellite observations in the Hangzhou Bay: Temporal variations and spatial distributions
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Daosheng Wang, Jicai Zhang, Xianqiang He, Dongdong Chu, Xianqing Lv, Ya Ping Wang, Yang Yang, Daidu Fan, Shu Gao Model parameters in the suspended cohesive sediment transport models are critical for the accurate simulation of suspended sediment concentrations (SSCs). Difficulties in estimating the model parameters still prevent numerical modeling of the sediment transport from achieving a high level of predictability. Based on a three-dimensional cohesive sediment transport model and its adjoint model, the satellite remote sensing data of SSCs during both spring tide and neap tide, retrieved from Geostationary Ocean Color Imager (GOCI), are assimilated to synchronously estimate four spatially and temporally varying parameters in the Hangzhou Bay in China, including settling velocity, resuspension rate, inflow open boundary conditions and initial conditions. After data assimilation, the model performance is significantly improved. Through several sensitivity experiments, the spatial and temporal variation tendencies of the estimated model parameters are verified to be robust and not affected by model settings. The pattern for the variations of the estimated parameters is analyzed and summarized. The temporal variations and spatial distributions of the estimated settling velocity are negatively correlated with current speed, which can be explained using the combination of flocculation process and Stokes’ law. The temporal variations and spatial distributions of the estimated resuspension rate are also negatively correlated with current speed, which are related to the grain size of the seabed sediments under different current velocities. Besides, the estimated inflow open boundary conditions reach the local maximum values near the low water slack conditions and the estimated initial conditions are negatively correlated with water depth, which is consistent with the general understanding. The relationships between the estimated parameters and the hydrodynamic fields can be suggestive for improving the parameterization in cohesive sediment transport models.
January 2018
Lagrangian ocean analysis: Fundamentals and practices
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Erik van Sebille, Stephen M. Griffies, Ryan Abernathey, Thomas P. Adams, Pavel Berloff, Arne Biastoch, Bruno Blanke, Eric P. Chassignet, Yu Cheng, Colin J. Cotter, Eric Deleersnijder, Kristofer D
January 2018
Impact of increasing antarctic glacial freshwater release on regional sea-ice cover in the Southern Ocean
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Nacho Merino, Nicolas C. Jourdain, Julien Le Sommer, Hugues Goosse, Pierre Mathiot, Gael Durand The sensitivity of Antarctic sea-ice to increasing glacial freshwater release into the Southern Ocean is studied in a series of 31-year ocean/sea-ice/iceberg model simulations. Glaciological estimates of ice-shelf melting and iceberg calving are used to better constrain the spatial distribution and magnitude of freshwater forcing around Antarctica. Two scenarios of glacial freshwater forcing have been designed to account for a decadal perturbation in glacial freshwater release to the Southern Ocean. For the first time, this perturbation explicitly takes into consideration the spatial distribution of changes in the volume of Antarctic ice shelves, which is found to be a key component of changes in freshwater release. In addition, glacial freshwater-induced changes in sea ice are compared to typical changes induced by the decadal evolution of atmospheric states. Our results show that, in general, the increase in glacial freshwater release increases Antarctic sea ice extent. But the response is opposite in some regions like the coastal Amundsen Sea, implying that distinct physical mechanisms are involved in the response. We also show that changes in freshwater forcing may induce large changes in sea-ice thickness, explaining about one half of the total change due to the combination of atmospheric and freshwater changes. The regional contrasts in our results suggest a need for improving the representation of freshwater sources and their evolution in climate models.
January 2018
Linear shoaling of free-surface waves in multi-layer non-hydrostatic models
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Yefei Bai, Kwok Fai Cheung The capability to describe shoaling over sloping bottom is fundamental to modeling of coastal wave transformation. The linear shoaling gradient provides a metric to measure this property in non-hydrostatic models with layer-integrated formulations. The governing equations in Boussinesq form facilitate derivation of the linear shoaling gradient, which is in the form of a [ 2 P + 2 , 2 P ] expansion of the water depth parameter kd with P equal to 1 for a one-layer model and ( 4 N
January 2018
A probabilistic method for the estimation of ocean surface currents from short time series of HF radar data
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Charles-Antoine Gu
December 2017
Simulating the Agulhas system in global ocean models – nesting vs. multi-resolution unstructured meshes
Publication date: January 2018
Source:Ocean Modelling, Volume 121 Author(s): Arne Biastoch, Dmitry Sein, Jonathan V. Durgadoo, Qiang Wang, Sergey Danilov Many questions in ocean and climate modelling require the combined use of high resolution, global coverage and multi-decadal integration length. For this combination, even modern resources limit the use of traditional structured-mesh grids. Here we compare two approaches: A high-resolution grid nested into a global model at coarser resolution (NEMO with AGRIF) and an unstructured-mesh grid (FESOM) which allows to variably enhance resolution where desired. The Agulhas system around South Africa is used as a testcase, providing an energetic interplay of a strong western boundary current and mesoscale dynamics. Its open setting into the horizontal and global overturning circulations also requires global coverage. Both model configurations simulate a reasonable large-scale circulation. Distribution and temporal variability of the wind-driven circulation are quite comparable due to the same atmospheric forcing. However, the overturning circulation differs, owing each model's ability to represent formation and spreading of deep water masses. In terms of regional, high-resolution dynamics, all elements of the Agulhas system are well represented. Owing to the strong nonlinearity in the system, Agulhas Current transports of both configurations and in comparison with observations differ in strength and temporal variability. Similar decadal trends in Agulhas Current transport and Agulhas leakage are linked to the trends in wind forcing. Although the number of 3D wet grid points used in FESOM is similar to that in the nested NEMO, FESOM uses about two times the number of CPUs to obtain the same model throughput (in terms of simulated model years per day). This is feasible due to the high scalability of the FESOM code.
December 2017
Inside Front Cover - Editorial Board Page/Cover image legend if applicable
Publication date: December 2017
Source:Ocean Modelling, Volume 120

December 2017
Comparison of in situ microstructure measurements to different turbulence closure schemes in a 3-D numerical ocean circulation model
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Andrea Costa, Andrea M. Doglioli, Patrick Marsaleix, Anne A. Petrenko In situ measurements of kinetic energy dissipation rate
December 2017
Impact of the “Symmetric Instability of the Computational Kind” at mesoscale- and submesoscale-permitting resolutions
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Nicolas Ducousso, J. Le Sommer, J.-M. Molines, M. Bell The energy- and enstrophy-conserving momentum advection scheme (EEN) used over the last 10 years in NEMO is subject to a spurious numerical instability. This instability, referred to as the Symmetric Instability of the Computational Kind (SICK), arises from a discrete imbalance between the two components of the vector-invariant form of momentum advection. The properties and the method for removing this instability have been documented by Hollingsworth et al. (1983), but the extent to which the SICK may interfere with processes of interest at mesoscale- and submesoscale-permitting resolutions is still unkown. In this paper, the impact of the SICK in realistic ocean model simulations is assessed by comparing model integrations with different versions of the EEN momentum advection scheme. Investigations are undertaken with a global mesoscale-permitting resolution (1/4
December 2017
Kinetic energy flux budget across air-sea interface
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Yalin Fan, Paul Hwang The kinetic energy (KE) fluxes into subsurface currents (EFc) is an important boundary condition for ocean circulation models. Traditionally, numerical models assume the KE flux from wind (EFair ) is identical to EFc , that is, no net KE is gained (or lost) by surface waves. This assumption, however, is invalid when the surface wave field is not fully developed, and acquires KE when it grows in space or time. In this study, numerical experiments are performed to investigate the KE flux budget across the air-sea interface under both uniform and idealized tropical cyclone (TC) winds. The wave fields are simulated using the WAVEWATCH III model under different wind forcing. The difference between EFair and EFc is estimated using an air-sea KE budget model. To address the uncertainty of these estimates resides in the variation of source functions, two source function packages are used for this study: the ST4 source package (Ardhuin et al, 2010), and the ST6 source package (Babanin, 2011). The modeled EFc is significantly reduced relative to EFair under growing seas for both the uniform and TC experiments. The reduction can be as large as 20%, and the variation of this ratio is highly dependent on the choice of source function for the wave model. Normalized EFc are found to be consistent with analytical expressions by Hwang and Sletten (2008) and Hwang and Walsh (2016) and field observations by Terray et al. (1996) and Drennan et al. (1996), while the scatters are more widely in the TC cases due to the complexity of the associated wave field. The waves may even give up KE to subsurface currents in the left rear quadrant of fast moving storms. Our results also suggest that the normalized KE fluxes may depend on both wave age and friction velocity (u*).
December 2017
Assessing the performance of wave breaking parameterizations in shallow waters in spectral wave models
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Shangfei Lin, Jinyu Sheng Depth-induced wave breaking is the primary dissipation mechanism for ocean surface waves in shallow waters. Different parametrizations were developed for parameterizing depth-induced wave breaking process in ocean surface wave models. The performance of six commonly-used parameterizations in simulating significant wave heights (SWHs) is assessed in this study. The main differences between these six parameterizations are representations of the breaker index and the fraction of breaking waves. Laboratory and field observations consisting of 882 cases from 14 sources of published observational data are used in the assessment. We demonstrate that the six parameterizations have reasonable performance in parameterizing depth-induced wave breaking in shallow waters, but with their own limitations and drawbacks. The widely-used parameterization suggested by Battjes and Janssen (1978, BJ78) has a drawback of underpredicting the SWHs in the locally-generated wave conditions and overpredicting in the remotely-generated wave conditions over flat bottoms. The drawback of BJ78 was addressed by a parameterization suggested by Salmon et al. (2015, SA15). But SA15 had relatively larger errors in SWHs over sloping bottoms than BJ78. We follow SA15 and propose a new parameterization with a dependence of the breaker index on the normalized water depth in deep waters similar to SA15. In shallow waters, the breaker index of the new parameterization has a nonlinear dependence on the local bottom slope rather than the linear dependence used in SA15. Overall, this new parameterization has the best performance with an average scatter index of
December 2017
Mixed layer depth calculation in deep convection regions in ocean numerical models
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Peggy Courtois, Xianmin Hu, Clark Pennelly, Paul Spence, Paul G. Myers Mixed Layer Depths (MLDs) diagnosed by conventional numerical models are generally based on a density difference with the surface (e.g., 0.01
December 2017
A potential method to accelerate spin up of turbulent ocean models
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Fenwick C. Cooper We demonstrate a simple method to quickly spin up (equilibrate) the temperature field of a turbulent idealised primitive equation ocean gyre model. We make use of the assumption that both velocity fields and non-linear eddy advection terms equilibrate on a shorter timescale than tracer fields.
December 2017
Can we reconstruct mean and eddy fluxes from Argo floats?
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Christopher Chapman, Jean-Baptiste Sall
December 2017
SOMAR-LES: A framework for multi-scale modeling of turbulent stratified oceanic flows
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Vamsi K Chalamalla, Edward Santilli, Alberto Scotti, Masoud Jalali, Sutanu Sarkar A new multi-scale modeling technique, SOMAR-LES, is presented in this paper. Localized grid refinement gives SOMAR (the Stratified Ocean Model with Adaptive Resolution) access to small scales of the flow which are normally inaccessible to general circulation models (GCMs). SOMAR-LES drives a LES (Large Eddy Simulation) on SOMAR’s finest grids, forced with large scale forcing from the coarser grids. Three-dimensional simulations of internal tide generation, propagation and scattering are performed to demonstrate this multi-scale modeling technique. In the case of internal tide generation at a two-dimensional bathymetry, SOMAR-LES is able to balance the baroclinic energy budget and accurately model turbulence losses at only 10% of the computational cost required by a non-adaptive solver running at SOMAR-LES’s fine grid resolution. This relative cost is significantly reduced in situations with intermittent turbulence or where the location of the turbulence is not known a priori because SOMAR-LES does not require persistent, global, high resolution. To illustrate this point, we consider a three-dimensional bathymetry with grids adaptively refined along the tidally generated internal waves to capture remote mixing in regions of wave focusing. The computational cost in this case is found to be nearly 25 times smaller than that of a non-adaptive solver at comparable resolution. In the final test case, we consider the scattering of a mode-1 internal wave at an isolated two-dimensional and three-dimensional topography, and we compare the results with Legg (2014) numerical experiments. We find good agreement with theoretical estimates. SOMAR-LES is less dissipative than the closure scheme employed by Legg (2014) near the bathymetry. Depending on the flow configuration and resolution employed, a reduction of more than an order of magnitude in computational costs is expected, relative to traditional existing solvers.
November 2017
Will high-resolution global ocean models benefit coupled predictions on short-range to climate timescales?
Publication date: December 2017
Source:Ocean Modelling, Volume 120 Author(s): Helene T. Hewitt, Michael J. Bell, Eric P. Chassignet, Arnaud Czaja, David Ferreira, Stephen M. Griffies, Pat Hyder, Julie L. McClean, Adrian L. New, Malcolm J. Roberts As the importance of the ocean in the weather and climate system is increasingly recognised, operational systems are now moving towards coupled prediction not only for seasonal to climate timescales but also for short-range forecasts. A three-way tension exists between the allocation of computing resources to refine model resolution, the expansion of model complexity/capability, and the increase of ensemble size. Here we review evidence for the benefits of increased ocean resolution in global coupled models, where the ocean component explicitly represents transient mesoscale eddies and narrow boundary currents. We consider lessons learned from forced ocean/sea-ice simulations; from studies concerning the SST resolution required to impact atmospheric simulations; and from coupled predictions. Impacts of the mesoscale ocean in western boundary current regions on the large-scale atmospheric state have been identified. Understanding of air-sea feedback in western boundary currents is modifying our view of the dynamics in these key regions. It remains unclear whether variability associated with open ocean mesoscale eddies is equally important to the large-scale atmospheric state. We include a discussion of what processes can presently be parameterised in coupled models with coarse resolution non-eddying ocean models, and where parameterizations may fall short. We discuss the benefits of resolution and identify gaps in the current literature that leave important questions unanswered.
November 2017
Inside Front Cover - Editorial Board Page/Cover image legend if applicable
Publication date: November 2017
Source:Ocean Modelling, Volume 119

November 2017
Climate driven variability of wind-waves in the Red Sea
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): P.R. Shanas, V.M. Aboobacker, Alaa
November 2017
A coupled model of interior balanced and boundary flow
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): B. Deremble, E.R. Johnson, W.K. Dewar Ocean circulation modeling requires parameterizations of sub-grid scale processes, which in turn involves two separate issues. First, the parameterization should mirror the effect of important sub-grid dynamics and second, constants and boundary conditions as required by the parameterization must be determined. In modern ocean circulation modeling, many parameterizations take the form of viscous operators with poorly known coefficients, and the boundary conditions options are free-slip, partial-slip or no-slip, suitably adjusted for the order of the operator. The extent to which viscous operators are dynamically apt is unclear and there is virtually no dynamical guidance on how to choose between the boundary conditions. Often the decision about the suitability of the parameterizations and the boundary conditions is made based on qualitative characteristics of the solution, which is somewhat subjective. Here, a dynamical boundary layer model is developed that explicitly determines the boundary potential vorticity fluxes resulting from the sub-grid scale interactions of the resolved flow with the boundaries. When applied to a quasi-geostrophic model, comparisons of model evolution with high resolution primitive equation simulations are favorable. The recipe outlined here, while far from a complete parameterization of boundary dynamics, represents a step toward resolving the issues currently surrounding sub-grid scale parameterization. The results also argue that boundary dynamics naturally dissipate balanced energy and are likely to represent a principal means by which the oceanic mesoscale energy budget is balanced.
November 2017
The intertidal zones of the South Atlantic Bight and their local and regional influence on astronomical tides
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): Peter Bacopoulos, Scott C. Hagen Astronomical tides in the South Atlantic Bight are simulated with a fine-resolution (down to
November 2017
Application of a fast Newton–Krylov solver for equilibrium simulations of phosphorus and oxygen
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): Weiwei Fu, Fran
November 2017
Attribution of horizontal and vertical contributions to spurious mixing in an Arbitrary Lagrangian–Eulerian ocean model
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): Angus H. Gibson, Andrew McC. Hogg, Andrew E. Kiss, Callum J. Shakespeare, Alistair Adcroft We examine the separate contributions to spurious mixing from horizontal and vertical processes in an ALE ocean model, MOM6, using reference potential energy (RPE). The RPE is a global diagnostic which changes only due to mixing between density classes. We extend this diagnostic to a sub-timestep timescale in order to individually separate contributions to spurious mixing through horizontal (tracer advection) and vertical (regridding/remapping) processes within the model. We both evaluate the overall spurious mixing in MOM6 against previously published output from other models (MOM5, MITGCM and MPAS-O), and investigate impacts on the components of spurious mixing in MOM6 across a suite of test cases: a lock exchange, internal wave propagation, and a baroclinically-unstable eddying channel. The split RPE diagnostic demonstrates that the spurious mixing in a lock exchange test case is dominated by horizontal tracer advection, due to the spatial variability in the velocity field. In contrast, the vertical component of spurious mixing dominates in an internal waves test case. MOM6 performs well in this test case owing to its quasi-Lagrangian implementation of ALE. Finally, the effects of model resolution are examined in a baroclinic eddies test case. In particular, the vertical component of spurious mixing dominates as horizontal resolution increases, an important consideration as global models evolve towards higher horizontal resolutions.
November 2017
The effect of lagoons on Adriatic Sea tidal dynamics
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): Christian Ferrarin, Francesco Maicu, Georg Umgiesser In this study the effects that lagoons exert on the barotropic tidal dynamics of a regional sea, the Adriatic Sea, were numerically explored. This semi-enclosed basin is one of the places with the highest tidal range in the Mediterranean Sea and is characterised by the presence of several lagoons in its northern part. The tidal dynamics of a system comprising the whole Adriatic Sea and the lagoons of Venice, Marano-Grado and Po Delta were investigated using an unstructured hydrodynamic model. Numerical experiments with and without lagoons reveal that even if the considered shallow water bodies represent only the 0.5 and 0.002% of the Adriatic Sea surface and volume, respectively, they significantly affect the entire Northern Adriatic Sea tidal dynamics by enhancing tidal range (by 5%) and currents (by 10%). The inclusion of lagoons in the computation improved the model performance by 25% in reproducing tidal constituents in the Adriatic Sea. The back-effect of the lagoons on the open-sea tide is due to the waves radiating from the co-oscillating lagoons into the adjacent sea. This is the first time these processes are shown to be relevant for the Adriatic Sea, thus enhancing the understanding of the tidal dynamics in this regional sea. These findings may also apply to other coastal seas with connections to lagoons, bays and estuaries.
November 2017
Simulating multi-scale oceanic processes around Taiwan on unstructured grids
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): Hao-Cheng Yu, Yinglong J. Zhang, Jason C.S. Yu, C. Terng, Weiling Sun, Fei Ye, Harry V. Wang, Zhengui Wang, Hai Huang We validate a 3D unstructured-grid (UG) model for simulating multi-scale processes as occurred in Northwestern Pacific around Taiwan using recently developed new techniques (Zhang et al., Ocean Modeling, 102, 64–81, 2016) that require no bathymetry smoothing even for this region with prevalent steep bottom slopes and many islands. The focus is on short-term forecast for several months instead of long-term variability. Compared with satellite products, the errors for the simulated Sea-surface Height (SSH) and Sea-surface Temperature (SST) are similar to a reference data-assimilated global model. In the nearshore region, comparison with 34 tide gauges located around Taiwan indicates an average RMSE of 13
November 2017
Simulation of breaking waves using the high-order spectral method with laboratory experiments: Wave-breaking onset
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): Betsy R. Seiffert, Guillaume Ducrozet, F
November 2017
Rotating 2d point source plume models with application to Deepwater Horizon
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): A. Fabregat, B. Deremble, N. Wienders, A. Stroman, A. Poje, T.M.
October 2017
Corrigendum to ``A positive and multi-element conserving time stepping scheme for biogeochemical processes in marine ecosystem models'' [Ocean Modeling 85 (2015) 32–41]
Publication date: November 2017
Source:Ocean Modelling, Volume 119 Author(s): H. Radtke, H. Burchard
October 2017
Inside Front Cover - Editorial Board Page/Cover image legend if applicable
Publication date: October 2017
Source:Ocean Modelling, Volume 118

October 2017
Internal wave scattering in continental slope canyons, part 1: Theory and development of a ray tracing algorithm
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Robert H. Nazarian, Sonya Legg When internal waves interact with topography, such as continental slopes, they can transfer wave energy to local dissipation and diapycnal mixing. Submarine canyons comprise approximately ten percent of global continental slopes, and can enhance the local dissipation of internal wave energy, yet parameterizations of canyon mixing processes are currently missing from large-scale ocean models. As a first step in the development of such parameterizations, we conduct a parameter space study of M2 tidal-frequency, low-mode internal waves interacting with idealized V-shaped canyon topographies. Specifically, we examine the effects of varying the canyon mouth width, shape and slope of the thalweg (line of lowest elevation). This effort is divided into two parts. In the first part, presented here, we extend the theory of 3-dimensional internal wave reflection to a rotated coordinate system aligned with our idealized V-shaped canyons. Based on the updated linear internal wave reflection solution that we derive, we construct a ray tracing algorithm which traces a large number of rays (the discrete analog of a continuous wave) into the canyon region where they can scatter off topography. Although a ray tracing approach has been employed in other studies, we have, for the first time, used ray tracing to calculate changes in wavenumber and ray density which, in turn, can be used to calculate the Froude number (a measure of the likelihood of instability). We show that for canyons of intermediate aspect ratio, large spatial envelopes of instability can form in the presence of supercritical sidewalls. Additionally, the canyon height and length can modulate the Froude number. The second part of this study, a diagnosis of internal wave scattering in continental slope canyons using both numerical simulations and this ray tracing algorithm, as well as a test of robustness of the ray tracing, is presented in the companion article.
October 2017
Internal wave scattering in continental slope canyons, Part 2: A comparison of ray tracing and numerical simulations
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Robert H. Nazarian, Sonya Legg When internal waves interact with topography, such as continental slopes, they can transfer wave energy to local dissipation and diapycnal mixing. Submarine canyons comprise approximately ten percent of global continental slopes, and can enhance the local dissipation of internal wave energy, yet parameterizations of canyon mixing processes are currently missing from large-scale ocean models. As a first step in the development of such parameterizations, we conduct a parameter space study of M2 tidal-frequency, low-mode internal waves interacting with idealized V-shaped canyon topographies. Specifically, we examine the effect of varying the canyon mouth width, shape and slope of the thalweg (line of lowest elevation) (i.e. flat bottom or near-critical slope). In Part 1 of this study (Nazarian and Legg, 2017a), we developed a ray tracing algorithm and used it to estimate how canyons can increase the wave Froude number, by increasing energy density and increasing vertical wavenumber. Here in Part 2 we examine the internal wave scattering in continental slope canyons using numerical simulations, and compare the results with the linear ray tracing predictions. We find that at intermediate canyon widths, a large fraction of incoming wave energy can be dissipated, which can be explained as a consequence of the increase in ray density and, for near-critical slope canyons, increase in vertical wave number, which leads to lower Richardson number followed by instability. Relative to a steep continental slope without a canyon, we find that V-shaped flat bottom canyons always dissipate more energy and are an effective geometry for wave trapping and subsequent energy loss. When both flat bottom canyons and near-critical slope canyons are made narrower, less wave energy enters the canyon, but a larger fraction of that energy is lost to dissipation due to subsequent reflections and wave trapping. There is agreement between the diagnostics calculated from the numerical model and the linear ray tracing, lending support for the use of linear theory to understand the fundamental dynamics of internal wave scattering in canyons.
October 2017
Analytical approximations to spurious short-wave baroclinic instabilities in ocean models
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Michael J. Bell, Andrew A. White Most community ocean models that use z- or s-coordinates stagger their variables in the vertical using a Lorenz grid. Spurious short-wave baroclinic instabilities have been shown to occur on that grid by Arakawa and Moorthi. As the vertical resolution of the grid is improved, the wavelength of the spurious modes decreases and they become more and more trapped near one of the boundaries but they continue to grow at almost the same rate as the deep Eady/Charney modes. The spurious instabilities in the case of the Eady problem are here shown to be accurately reproduced by an analytical calculation which reduces the stability problem to a quadratic equation for their complex phase speeds. The interpretation of these spurious instabilities as resulting from spurious sheets of potential vorticity is revisited. A new interpretation is presented using a finite difference analogue of the Charney–Stern–Pedlosky integral constraint. This indicates that the spurious instabilities result from a vertical averaging of the advection of the relative vorticity which leads to a spurious interior source term in the finite difference potential vorticity equation.
October 2017
Seasonality of eddy kinetic energy in an eddy permitting global climate model
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Takaya Uchida, Ryan Abernathey, Shafer Smith We examine the seasonal cycle of upper-ocean mesoscale turbulence in a high resolution CESM climate simulation. The ocean model component (POP) has 0.1° resolution, mesoscale resolving at low and middle latitudes. Seasonally and regionally resolved wavenumber power spectra are calculated for sea-surface eddy kinetic energy (EKE). Although the interpretation of the spectral slopes in terms of turbulence theory is complicated by the strong presence of dissipation and the narrow inertial range, the EKE spectra consistently show higher power at small scales during winter throughout the ocean. Potential hypotheses for this seasonality are investigated. Diagnostics of baroclinc energy conversion rates and evidence from linear quasigeostrophic stability analysis indicate that seasonally varying mixed-layer instability is responsible for the seasonality in EKE. The ability of this climate model, which is not considered submesoscale resolving, to produce mixed layer instability although damped by dissipation, demonstrates the ubiquity and robustness of this process for modulating upper ocean EKE.
October 2017
Sea level modelling in the Baltic and the North Sea: The respective role of different parts of the forcing
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Magnus Hieronymus, Jenny Hieronymus, Lars Arneborg The effects of winds, tides, sea level pressure and storm surges on sea levels are quantified in a regional model for the North Sea and The Baltic Sea. The sea level variability in the two different basins have different primary drivers. The variability in the North Sea is mostly tidal, while most of the variability in the Baltic Sea is wind driven. A factorization technique is used to separate the effects of the different forcings, as well as the effects of interactions between different forcings. The interactions are found to have a positive feedback on the sea level variability in the Baltic Sea, and to be mostly damping in the North Sea. How sea level signals are transmitted through the domain is also studied using transfer function, and the transmission between the basins is found to be strongly damped for high frequency variability. Lastly, the effects of the different forcings on the sea level distributions in the model are also quantified, and large differences are found between the two basins.
October 2017
Numerical simulations of ocean surface waves under hurricane conditions: Assessment of existing model performance
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Qingxiang Liu, Alexander Babanin, Yalin Fan, Stefan Zieger, Changlong Guan, Il-Ju Moon Using the well-observed hurricane case Ivan (2004) as an example, we investigate and intercompare the performance of two wave models under hurricane conditions. One is the WAVEWATCH III model (WW3) and the other is the University of Miami Wave Model (UMWM). Within WW3, four different source term packages (ST2/3/4/6) of wind input, wave breaking dissipation and swell decay are chosen for comparison purposes. Based on the comparisons between model results and measurements from various platforms, we concluded that UMWM shows less accuracy than WW3 in specification of bulk wave parameters. This is possibly because (i) UMWM-estimated drag coefficient does not clearly show a saturation trend when wind speeds are beyond
October 2017
Computing eddy-driven effective diffusivity using Lagrangian particles
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Phillip J. Wolfram, Todd D. Ringler A novel method to derive effective diffusivity from Lagrangian particle trajectory data sets is developed and then analyzed relative to particle-derived meridional diffusivity for eddy-driven mixing in an idealized circumpolar current. Quantitative standard dispersion- and transport-based mixing diagnostics are defined, compared and contrasted to motivate the computation and use of effective diffusivity derived from Lagrangian particles. The effective diffusivity is computed by first performing scalar transport on Lagrangian control areas using stored trajectories computed from online Lagrangian In-situ Global High-performance particle Tracking (LIGHT) using the Model for Prediction Across Scales Ocean (MPAS-O). The Lagrangian scalar transport scheme is compared against an Eulerian scalar transport scheme. Spatially-variable effective diffusivities are computed from resulting time-varying cumulative concentrations that vary as a function of cumulative area. The transport-based Eulerian and Lagrangian effective diffusivity diagnostics are found to be qualitatively consistent with the dispersion-based diffusivity. All diffusivity estimates show a region of increased subsurface diffusivity within the core of an idealized circumpolar current and results are within a factor of two of each other. The Eulerian and Lagrangian effective diffusivities are most similar; smaller and more spatially diffused values are obtained with the dispersion-based diffusivity computed with particle clusters.
October 2017
Compact symmetric Poisson equation discretization for non-hydrostatic sigma coordinates ocean model
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Roullet Guillaume, Molemaker M. Jeroen, Ducousso Nicolas, Dubos Thomas In anticipation of relaxing the hydrostatic assumption in a sigma coordinates primitive equations ocean model, we show how a projection method can be designed with the use of a compact symmetric 15-point stencil for the Poisson equation. This is achieved by recognizing that, owing the non-orthogonality of the grid, the velocity has a contravariant and covariant set of components. The two sets play a different role in the primitive equations: the contravariant components enter the definition of the model fluxes, whereas the covariant components experience the forces and in particular the pressure gradient. By treating these two sets separately, the discretized gradient and divergence operators are simple finite differences. The two sets of components are related via a linear transformation, the metric tensor, which is entirely determined by the kinetic energy. We show how the spatial discretization of the kinetic energy fully controls the Poisson equation discretization, including its boundary conditions. The discretization of the Poisson equation is shown to converge at second order and to behave as well or better than alternative methods. This approach is a prerequisite to implement later an efficient Poisson solver, such as a multigrid algorithm.

Sensitivity of the Antarctic Circumpolar Current transport to surface buoyancy conditions in the North Atlantic
Publication date: October 2017
Source:Ocean Modelling, Volume 118 Author(s): Shantong Sun, Jinliang Liu The sensitivity of the Antarctic Circumpolar Current (ACC) transport to surface buoyancy conditions in the North Atlantic is investigated using a sector configuration of an ocean general circulation model. We find that the sensitivity of the ACC transport is significantly weaker than previous studies. We attribute this difference to the different depth of the simulated Atlantic Meridional Overturning Circulation. Because a fast restoring buoyancy boundary condition is used that strongly constrains the surface buoyancy structure at the Southern Ocean surface, the ACC transport is determined by the isopycnal slope that is coupled to the overturning circulation in the Southern Ocean. By changing the surface buoyancy in the North Atlantic, the shared buoyancy contour between the North Atlantic and the Southern Ocean is varied, and consequently the strength of the overturning circulation is modified. For different depth of the simulated overturning circulation, the response of the ACC transport to changes in the strength of the overturning circulation varies substantially. This is illustrated in two conceptual models based on the residual-mean theory of overturning circulation. Our results imply that the sensitivity of the ACC transport to surface forcing in the North Atlantic could vary substantially in different models depending on the simulated vertical structure of the overturning circulation.
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