A. Adcroft, R. Hallberg, and M. Harrison, A finite volume discretization of the pressure gradient force using analytic integration. Ocean Modell, pp.106-113, 2008.

A. Adcroft, C. Hill, and J. Marshall, Representation of Topography by Shaved Cells in a Height Coordinate Ocean Model, Monthly Weather Review, vol.125, issue.9, pp.2293-2315, 1997.
DOI : 10.1175/1520-0493(1997)125<2293:ROTBSC>2.0.CO;2

A. J. Adcroft and J. M. Campin, Rescaled height coordinates for accurate representation of free-surface flows in ocean circulation models. Ocean Modell, pp.269-284, 2004.

A. J. Adcroft and R. W. Hallberg, On methods for solving the oceanic equations of motion in generalized vertical coordinates. Ocean Modell, pp.224-233, 2006.

A. Arakawa and V. R. Lamb, Computational Design of the Basic Dynamical Processes of the UCLA General Circulation Model, Meth. Comput. Phys, vol.17, pp.174-267, 1977.
DOI : 10.1016/B978-0-12-460817-7.50009-4

F. Auclair, L. Bordois, Y. Dossmann, T. Duhaut, A. Paci et al., A nonhydrostatic non-Boussinesq algorithm for free-surface ocean modelling. Ocean Modell, 2016.
DOI : 10.1016/j.ocemod.2010.09.006

F. Auclair, C. Estournel, J. W. Floor, M. J. Herrmann, C. Nguyen et al., A non-hydrostatic algorithm for free-surface ocean modelling, Ocean Modelling, vol.36, issue.1-2, pp.49-70, 2011.
DOI : 10.1016/j.ocemod.2010.09.006

URL : https://hal.archives-ouvertes.fr/hal-00560340

S. D. Bachmann, B. Fox-kemper, and B. Pearson, A scale-aware subgrid model for quasi-geostrophic turbulence, Journal of Geophysical Research: Oceans, vol.42, issue.5, pp.1529-1554, 2017.
DOI : 10.1175/JPO-D-11-0102.1

J. O. Backhaus, Un mod??le num??rique pour l'hydrodynamique de la zone des petits fonds, Deutsche Hydrographische Zeitschrift, vol.10, issue.6, pp.222-238, 1976.
DOI : 10.1007/BF02226256

J. O. Backhaus, Un mod??le tridimensionnel pour simuler la dynamique oc??anique sur le plateau continental, Deutsche Hydrographische Zeitschrift, vol.310, issue.No. 50, pp.165-187, 1985.
DOI : 10.1007/978-3-642-68838-6_23

B. Barnier, P. Marchesiello, A. P. Miranda, J. M. Molines, and M. Coulibaly, A sigma-coordinate primitive equation model for studying the circulation in the South Atlantic. Part I: Model configuration with error estimates, Deep Sea Research Part I: Oceanographic Research Papers, vol.45, issue.4-5, pp.543-572, 1998.
DOI : 10.1016/S0967-0637(97)00086-1

J. M. Beckers, H. Burchard, J. M. Campin, E. Deleersnijder, and P. P. Mathieu, -Coordinate Ocean Model???, Journal of Physical Oceanography, vol.28, issue.7, pp.1552-1559, 1998.
DOI : 10.1175/1520-0485(1998)028<1552:ARWSDO>2.0.CO;2

J. M. Beckers, H. Burchard, E. Deleersnijder, and P. P. Mathieu, Numerical Discretization of Rotated Diffusion Operators in Ocean Models, Monthly Weather Review, vol.128, issue.8, pp.2711-2733, 2000.
DOI : 10.1175/1520-0493(2000)128<2711:NDORDO>2.0.CO;2

J. M. Beckers and E. Deleersnijder, Stability of a FBTCS Scheme Applied to the Propagation of Shallow-Water Inertia-Gravity Waves on Various Space Grids, Journal of Computational Physics, vol.108, issue.1, pp.95-104, 1993.
DOI : 10.1006/jcph.1993.1166

A. Beckmann and R. Döscher, A Method for Improved Representation of Dense Water Spreading over Topography in Geopotential-Coordinate Models, Journal of Physical Oceanography, vol.27, issue.4, pp.581-591, 1997.
DOI : 10.1175/1520-0485(1997)027<0581:AMFIRO>2.0.CO;2

J. Berntsen, A perfectly balanced method for estimating the internal pressure gradients in ?coordinate ocean models. Ocean Modell, pp.85-95, 2011.

J. Berntsen and G. Furnes, Internal pressure errors in sigma-coordinate ocean models???sensitivity of the growth of the flow to the time stepping method and possible non-hydrostatic effects, Continental Shelf Research, vol.25, issue.7-8, pp.829-848, 2005.
DOI : 10.1016/j.csr.2004.09.025

F. Beron-vera, J. Ochoa, and P. Ripa, A note on boundary conditions for salt and freshwater balances. Ocean Modell, pp.111-118, 1999.

M. Blaas, C. Dong, P. Marchesiello, J. C. Mcwilliams, and K. D. Stolzenbach, Sediment-transport modeling on Southern Californian shelves: A ROMS case study, Continental Shelf Research, vol.27, issue.6, pp.832-853, 2007.
DOI : 10.1016/j.csr.2006.12.003

URL : https://hal.archives-ouvertes.fr/hal-00409280

E. Blayo, Compact Finite Difference Schemes for Ocean Models, Journal of Computational Physics, vol.164, issue.2, pp.241-257, 2000.
DOI : 10.1006/jcph.2000.6565

E. Blayo and L. Debreu, Revisiting open boundary conditions from the point of view of characteristic variables. Ocean Modell, pp.231-252, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00134856

R. Bleck, An oceanic general circulation model framed in hybrid isopycnic-Cartesian coordinates. Ocean Modell, pp.55-88, 2002.

R. Bleck and L. T. Smith, A wind-driven isopycnic coordinate model of the north and equatorial Atlantic Ocean: 1. Model development and supporting experiments, Journal of Geophysical Research, vol.31, issue.C3, pp.3273-3285, 1990.
DOI : 10.1016/0021-9991(79)90051-2

A. F. Blumberg, A Primer for ECOM-si, 1992.

A. F. Blumberg and G. L. Mellor, A coastal ocean numerical model, Mathematical Modelling of Estuarine Physics, pp.203-214, 1978.
DOI : 10.1029/ln001p0203

A. F. Blumberg and G. L. Mellor, A description of a coastal ocean circulation model, Three dimensional ocean models, pp.1-16, 1987.

K. Bolding, H. Burchard, T. Pohlmann, and A. Stips, Turbulent mixing in the Northern North Sea: a numerical model study, Continental Shelf Research, vol.22, issue.18-19, pp.2707-2724, 2002.
DOI : 10.1016/S0278-4343(02)00122-X

A. Bott, Improving the time-splitting errors of one-dimensional advection schemes in multidimensional applications, Atmospheric Research, vol.97, issue.4, pp.619-631, 2010.
DOI : 10.1016/j.atmosres.2010.05.001

N. Botta, R. Klein, S. Langenberg, and S. Lützenkirchen, Well balanced finite volume methods for nearly hydrostatic flows, Journal of Computational Physics, vol.196, issue.2, pp.539-565, 2004.
DOI : 10.1016/j.jcp.2003.11.008

J. A. Brown and K. A. Campana, An Economical Time???Differencing System for Numerical Weather Prediction, Monthly Weather Review, vol.106, issue.8, pp.1125-1136, 1978.
DOI : 10.1175/1520-0493(1978)106<1125:AETSFN>2.0.CO;2

URL : http://journals.ametsoc.org/doi/pdf/10.1175/1520-0493%281978%29106%3C1125%3AAETSFN%3E2.0.CO%3B2

J. Bruggeman and K. Bolding, A general framework for aquatic biogeochemical models, Environmental Modelling & Software, vol.61, pp.249-265, 2014.
DOI : 10.1016/j.envsoft.2014.04.002

URL : http://plymsea.ac.uk/6404/1/BrugBold2014.pdf

H. Burchard, Simulating the Wave-Enhanced Layer under Breaking Surface Waves with Two-Equation Turbulence Models, Journal of Physical Oceanography, vol.31, issue.11, pp.3133-3145, 2001.
DOI : 10.1175/1520-0485(2001)031<3133:STWELU>2.0.CO;2

H. Burchard, Applied turbulence modelling in marine waters, Lecture Notes in Earth Sciences, vol.100, 2002.

H. Burchard, Energy-conserving discretisation of turbulent shear and buoyancy production. Ocean Modell, pp.347-361, 2002.

H. Burchard and T. H. Badewien, Thermohaline residual circulation of the Wadden Sea. Ocean Dyn, pp.1717-1730, 2015.

H. Burchard and H. Baumert, On the performance of a mixed-layer model based on the ??-?? turbulence closure, Journal of Geophysical Research, vol.37, issue.489, pp.8523-8540, 1995.
DOI : 10.1007/BF02226437

H. Burchard and H. Baumert, The Formation of Estuarine Turbidity Maxima Due to Density Effects in the Salt Wedge. A Hydrodynamic Process Study, Journal of Physical Oceanography, vol.28, issue.2, pp.309-321, 1998.
DOI : 10.1175/1520-0485(1998)028<0309:TFOETM>2.0.CO;2

H. Burchard and J. M. Beckers, Non-uniform adaptive vertical grids in one-dimensional numerical ocean models, Ocean Modelling, vol.6, issue.1, pp.51-81, 2004.
DOI : 10.1016/S1463-5003(02)00060-4

H. Burchard and K. Bolding, GETM ? a general estuarine transport model. Scientific Documentation, 2002.

H. Burchard, K. Bolding, and M. R. Villarreal, Three-dimensional modelling of estuarine turbidity maxima in a tidal estuary. Ocean Dyn, pp.250-265, 2004.

H. Burchard, P. D. Craig, J. R. Gemmrich, H. Van-haren, P. P. Mathieu et al., Observational and numerical modeling methods for quantifying coastal ocean turbulence and mixing, Progress in Oceanography, vol.76, issue.4, pp.399-442, 2008.
DOI : 10.1016/j.pocean.2007.09.005

H. Burchard, E. Deleersnijder, and G. Stoyan, Some numerical aspects of turbulence-closure models, Marine Turbulence: Theories, Observations and Models, pp.197-206, 2005.

H. Burchard and O. Petersen, Hybridization between ??- andz-co-ordinates for improving the internal pressure gradient calculation in marine models with steep bottom slopes, International Journal for Numerical Methods in Fluids, vol.31, issue.9, pp.1003-1023, 1997.
DOI : 10.1175/1520-0469(1957)014<0184:ACSHSS>2.0.CO;2

H. Burchard and O. Petersen, Models of turbulence in the marine environment ???a comparative study of two-equation turbulence models, Journal of Marine Systems, vol.21, issue.1-4, pp.29-53, 1999.
DOI : 10.1016/S0924-7963(99)00004-4

H. Burchard, O. Petersen, and T. P. Rippeth, Comparing the performance of the Mellor-Yamada and the ??-?? two-equation turbulence models, Journal of Geophysical Research: Oceans, vol.20, issue.HY3, pp.10543-10554, 1998.
DOI : 10.1016/0017-9310(77)90121-1

H. Burchard and H. Rennau, Comparative quantification of physically and numerically induced mixing in ocean models. Ocean Modell, pp.293-311, 2008.

H. Burchard and T. P. Rippeth, Generation of Bulk Shear Spikes in Shallow Stratified Tidal Seas, Journal of Physical Oceanography, vol.39, issue.4, pp.969-985, 2009.
DOI : 10.1175/2008JPO4074.1

X. Capet, E. J. Campos, and A. M. Paiva, Submesoscale activity over the Argentinian shelf, Geophysical Research Letters, vol.104, issue.15, p.10, 1029.
DOI : 10.1029/2008GL034736

URL : https://hal.archives-ouvertes.fr/hal-00495964

J. R. Carpenter, L. Merckelbach, U. Callies, S. Clark, L. Gaslikova et al., Potential Impacts of Offshore Wind Farms on North Sea Stratification, PLOS ONE, vol.56, issue.6, pp.11-0160830, 2016.
DOI : 10.1371/journal.pone.0160830.s001

V. Casulli and E. Cattani, Stability, accuracy and efficiency of a semi-implicit method for three-dimensional shallow water flow, Computers & Mathematics with Applications, vol.27, issue.4, pp.99-112, 1994.
DOI : 10.1016/0898-1221(94)90059-0

V. Casulli and R. T. Cheng, Semi-implicit finite difference methods for three-dimensional shallow water flow, International Journal for Numerical Methods in Fluids, vol.IV, issue.6, pp.629-648, 1992.
DOI : 10.1029/CO004p0001

R. T. Cheng, V. Casulli, and J. W. Gartner, Tidal, Residual, Intertidal Mudflat (TRIM) Model and its Applications to San Francisco Bay, California, TRIM) model and its applications to, pp.235-280, 1993.
DOI : 10.1006/ecss.1993.1016

A. J. Chorin, Numerical solution of the Navier-Stokes equations, Mathematics of Computation, vol.22, issue.104, pp.745-762, 1968.
DOI : 10.1090/S0025-5718-1968-0242392-2

D. J. Conley, H. W. Paerl, R. W. Howarth, D. F. Boesch, S. P. Seitzinger et al., ECOLOGY: Controlling Eutrophication: Nitrogen and Phosphorus, Science, vol.323, issue.5917, pp.1014-1015, 2009.
DOI : 10.1126/science.1167755

P. D. Craig, A model of diurnally forced vertical current structure near 30?? latitude, Continental Shelf Research, vol.9, issue.11, pp.965-980, 1989.
DOI : 10.1016/0278-4343(89)90002-2

B. Cushman-roisin and J. M. Beckers, Introduction to geophysical fluid dynamics: physical and numerical aspects, 2011.

G. Danabasoglu, S. G. Yeager, D. Bailey, E. Behrens, M. Bentsen et al., North Atlantic simulations in Coordinated Ocean-ice Reference Experiments phase II (CORE-II). Part I: Mean states, Ocean Modelling, vol.73, pp.76-107, 2014.
DOI : 10.1016/j.ocemod.2013.10.005

URL : https://hal.archives-ouvertes.fr/hal-01491382

S. Danilov, Ocean modeling on unstructured meshes. Ocean Modell, pp.195-210, 2013.
DOI : 10.1016/j.ocemod.2013.05.005

URL : http://epic.awi.de/33287/1/omod_unst.pdf

V. Daru and C. Tenaud, High order one-step monotonicity-preserving schemes for unsteady compressible flow calculations, Journal of Computational Physics, vol.193, issue.2, pp.563-594, 2004.
DOI : 10.1016/j.jcp.2003.08.023

H. C. Davies, A lateral boundary formulation for multi-level prediction models, Quarterly Journal of the Royal Meteorological Society, vol.102, issue.432, pp.405-418, 1976.
DOI : 10.1256/smsqj.43209

L. Debreu and E. Blayo, Two-way embedding algorithms: a review. Ocean Dyn, pp.415-428, 2008.
DOI : 10.1007/s10236-008-0150-9

URL : https://hal.archives-ouvertes.fr/hal-00387449

Z. Defne and N. K. Ganju, Quantifying the Residence Time and Flushing Characteristics of a Shallow, Back-Barrier Estuary: Application of Hydrodynamic and Particle Tracking Models, Estuaries and Coasts, vol.10, issue.2, pp.1719-1734, 2015.
DOI : 10.1016/0077-7579(76)90013-2

E. Deleersnijder, Numerical mass conservation in a free-surface sigma coordinate marine model with mode splitting, Journal of Marine Systems, vol.4, issue.5, pp.365-370, 1993.
DOI : 10.1016/0924-7963(93)90021-D

E. Deleersnijder and J. M. Beckers, On the use of the ??-coordinate system in regions of large bathymetric variations, Journal of Marine Systems, vol.3, issue.4-5, pp.381-390, 1992.
DOI : 10.1016/0924-7963(92)90011-V

E. Deleersnijder, J. M. Beckers, J. M. Campin, M. Mohajir, T. Fichefet et al., Some mathematical problems associated with the development and use of marine models The mathematics of models for climatology and environment, pp.41-86, 1997.

E. J. Delhez, M. Grégoire, J. C. Nihoul, and J. M. Beckers, Dissection of the GHER turbulence closure scheme, Journal of Marine Systems, vol.21, issue.1-4, pp.379-397, 1999.
DOI : 10.1016/S0924-7963(99)00023-8

J. Demange, L. Debreu, P. Marchesiello, F. Lemarié, and E. Blayo, Numerical representation of internal waves propagation, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01063417

R. J. Diaz and R. Rosenberg, Spreading Dead Zones and Consequences for Marine Ecosystems, Science, vol.52, issue.5865, pp.926-929, 2008.
DOI : 10.1126/science.1149016

D. S. Dukhovskoy, S. L. Moreay, P. J. Martin, J. J. O-'brien, and C. Cooper, Application of a vanishing, quasi-sigma, vertical coordinate for simulation of high-speed, deep currents over the Sigsbee Escarpment in the Gulf of Mexico, Ocean Modelling, vol.28, issue.4, pp.250-265, 2009.
DOI : 10.1016/j.ocemod.2009.02.009

J. K. Dukowicz, Reduction of Density and Pressure Gradient Errors in Ocean Simulations, Journal of Physical Oceanography, vol.31, issue.7, pp.1915-1921, 2001.
DOI : 10.1175/1520-0485(2001)031<1915:RODAPG>2.0.CO;2

D. R. Durran, Numerical Methods for Fluid Dynamics With Applications to Geophysics, 2010.

S. M. Durski, S. M. Glenn, and D. B. Haidvogel, Vertical mixing schemes in the coastal ocean: Comparison of the level 2.5 Mellor-Yamada scheme with an enhanced version of the K profile parameterization, Journal of Geophysical Research, vol.108, issue.C3, pp.101510-1029, 2004.
DOI : 10.1029/CO004p0001

C. Eden, L. Czeschel, and D. Olbers, Toward Energetically Consistent Ocean Models, Journal of Physical Oceanography, vol.44, issue.12, pp.3160-3184, 2014.
DOI : 10.1175/JPO-D-13-0260.1

URL : http://epic.awi.de/36666/1/jpo-d-13-0260.pdf

C. Eden and R. J. Greatbatch, Towards a mesoscale eddy closure. Ocean Modell, pp.223-239, 2008.
DOI : 10.1016/j.ocemod.2007.09.002

T. O. Espelid, J. Berntsen, and K. Barthel, Conservation of energy for schemes applied to the propagation of shallow-water inertia-gravity waves in regions with varying depth, International Journal for Numerical Methods in Engineering, vol.14, issue.12, pp.1521-1545, 2000.
DOI : 10.1142/1970

T. Ezer and G. L. Mellor, A generalised coordinate ocean model and a comparison of the bottom boundary layer dynamics in terrain-following and in z-level grids. Øcean Modell, pp.379-403, 2004.

C. W. Fairall, E. F. Bradley, D. P. Rogers, J. B. Edson, and G. S. Young, Bulk parameterization of air-sea fluxes for Tropical Ocean-Global Atmosphere Coupled-Ocean Atmosphere Response Experiment, Journal of Geophysical Research: Oceans, vol.123, issue.C2, pp.3747-3764, 1996.
DOI : 10.1175/1520-0493(1995)123<0110:CWITEW>2.0.CO;2

R. A. Feagin, D. J. Sherman, and W. E. Grant, Coastal erosion, global sea-level rise, and the loss of sand dune plant habitats, Frontiers in Ecology and the Environment, vol.3, issue.7, pp.359-364, 2005.
DOI : 10.1890/1540-9295(2005)003[0359:CEGSRA]2.0.CO;2

W. Fennel, T. Seifert, and B. Kayser, Rossby radii and phase speeds in the Baltic Sea, Continental Shelf Research, vol.11, issue.1, pp.23-36, 1991.
DOI : 10.1016/0278-4343(91)90032-2

R. Flather, A tidal model of the north-west european continental shelf, Memoires de la Societe Royale des Sciences de Liege 6, pp.141-164, 1976.

R. A. Flather and N. S. Heaps, Tidal Computations for Morecambe Bay, Geophysical Journal of the Royal Astronomical Society, vol.6, issue.580, pp.489-517, 1975.
DOI : 10.1090/S0025-5718-1966-0198702-6

URL : https://academic.oup.com/gji/article-pdf/42/2/489/1832979/42-2-489.pdf

N. P. Fofonoff, M. Jr, and R. C. , Algorithms for computation of fundamental properties of seawater, Unesco technical papers in marine science 44, 1983.

B. Fox-kemper, G. Danabasoglu, R. Ferrari, S. Griffies, R. Hallberg et al., Parameterization of mixed layer eddies. III: Implementation and impact in global ocean climate simulations, Ocean Modelling, vol.39, issue.1-2, pp.61-78, 2011.
DOI : 10.1016/j.ocemod.2010.09.002

B. Fox-kemper and D. Menemenlis, Can large eddy simulation techniques improve mesoscale rich ocean models?, AGU. number 177 in Geophysical Monograph Series, pp.319-337, 2008.
DOI : 10.1007/978-1-4612-4636-7_4

B. Galperin, L. H. Kantha, S. Hassid, and A. Rosati, A Quasi-equilibrium Turbulent Energy Model for Geophysical Flows, Journal of the Atmospheric Sciences, vol.45, issue.1, pp.55-62, 1988.
DOI : 10.1175/1520-0469(1988)045<0055:AQETEM>2.0.CO;2

URL : http://journals.ametsoc.org/doi/pdf/10.1175/1520-0469%281988%29045%3C0055%3AAQETEM%3E2.0.CO%3B2

X. Gao and C. T. Chen, Heavy metal pollution status in surface sediments of the coastal Bohai Bay, Water Research, vol.46, issue.6, 1901.
DOI : 10.1016/j.watres.2012.01.007

P. Gaspar, Y. Gregoris, and J. Lefevre, A simple eddy kinetic energy model for simulations of the oceanic vertical mixing: Tests at station Papa and long-term upper ocean study site, Journal of Geophysical Research, vol.105, issue.C9, pp.16179-16193, 1990.
DOI : 10.1002/qj.49710544403

P. R. Gent and J. C. Mcwilliams, Isopycnal Mixing in Ocean Circulation Models, Journal of Physical Oceanography, vol.20, issue.1, pp.150-155, 1990.
DOI : 10.1175/1520-0485(1990)020<0150:IMIOCM>2.0.CO;2

URL : http://journals.ametsoc.org/doi/pdf/10.1175/1520-0485%281990%29020%3C0150%3AIMIOCM%3E2.0.CO%3B2

R. Gerdes, A primitive equation ocean circulation model using a general vertical coordinate transformation: 1. Description and testing of the model, Journal of Geophysical Research, vol.31, issue.C8, pp.14683-14701, 1993.
DOI : 10.1016/0021-9991(79)90051-2

H. Gerritsen, E. De-goede, M. Genseberger, and R. Uittenbogaard, Validation Document Delft3D- FLOW, 2004.

S. Gottlieb and C. W. Shu, Total variation diminishing Runge-Kutta schemes, Mathematics of Computation of the American Mathematical Society, vol.67, issue.221, pp.73-85, 1998.
DOI : 10.1090/S0025-5718-98-00913-2

URL : http://www.ams.org/mcom/1998-67-221/S0025-5718-98-00913-2/S0025-5718-98-00913-2.pdf

U. Gräwe, G. Flöser, T. Gerkema, M. Duran-matute, T. Badewien et al., A numerical model for the entire Wadden Sea: Skill assessment and analysis of hydrodynamics, Journal of Geophysical Research: Oceans, vol.10, issue.7, pp.5231-5251, 2016.
DOI : 10.1016/0077-7579(76)90013-2

U. Gräwe, P. Holtermann, K. Klingbeil, and H. Burchard, Advantages of vertically adaptive coordinates in numerical models of stratified shelf seas. Ocean Modell, pp.56-68, 2015.

S. Griffies, A. Adcroft, and D. C. , Formulating the equations of ocean models Ocean Modeling in an Eddying Regime, pp.281-317, 2008.

S. M. Griffies, Fundamentals of ocean climate models, 2004.

S. M. Griffies, Elements of mom4p1, 2007.

S. M. Griffies, A. Gnanadesikan, R. C. Pacanowski, V. D. Larichev, J. K. Dukowicz et al., -Coordinate Ocean Model, Journal of Physical Oceanography, vol.28, issue.5, pp.805-830, 1998.
DOI : 10.1175/1520-0485(1998)028<0805:IDIAZC>2.0.CO;2

S. M. Griffies and R. W. Hallberg, Biharmonic Friction with a Smagorinsky-Like Viscosity for Use in Large-Scale Eddy-Permitting Ocean Models, Monthly Weather Review, vol.128, issue.8, pp.2935-2946, 2000.
DOI : 10.1175/1520-0493(2000)128<2935:BFWASL>2.0.CO;2

M. Gröger, C. Dieterich, M. H. Meier, and S. Schimanke, Thermal air-sea coupling in hindcast simulations for the North Sea, 2015.

D. B. Haidvogel, H. G. Arango, K. Hedstrom, A. Beckmann, P. Malanotte-rizzoli et al., Model evaluation experiments in the North Atlantic Basin: simulations in nonlinear terrain-following coordinates, Dynamics of Atmospheres and Oceans, vol.32, issue.3-4, pp.239-281, 2000.
DOI : 10.1016/S0377-0265(00)00049-X

B. S. Halpern, S. Walbridge, K. A. Selkoe, C. V. Kappel, F. Micheli et al., A Global Map of Human Impact on Marine Ecosystems, Science, vol.241, issue.5865, pp.948-952, 2008.
DOI : 10.1126/science.1067728

R. L. Haney, On the Pressure Gradient Force over Steep Topography in Sigma Coordinate Ocean Models, Journal of Physical Oceanography, vol.21, issue.4, pp.610-619, 1991.
DOI : 10.1175/1520-0485(1991)021<0610:OTPGFO>2.0.CO;2

R. R. Harcourt, A Second-Moment Closure Model of Langmuir Turbulence, Journal of Physical Oceanography, vol.43, issue.4, pp.673-697, 2014.
DOI : 10.1175/JPO-D-12-0105.1

H. Van-haren, L. Maas, J. T. Zimmerman, and H. R. Malschaert, Strong inertial currents and marginal internal wave stability in the central North Sea, Geophysical Research Letters, vol.323, issue.19, pp.2993-2996, 1999.
DOI : 10.1098/rsta.1987.0100

A. Harten, High resolution schemes for hyperbolic conservation laws, Journal of Computational Physics, vol.49, issue.3, pp.357-393, 1983.
DOI : 10.1016/0021-9991(83)90136-5

Y. Heggelund, F. Vikebø, J. Berntsen, and G. Furnes, Hydrostatic and non-hydrostatic studies of gravitational adjustment over a slope, Continental Shelf Research, vol.24, issue.18, pp.2133-2148, 2004.
DOI : 10.1016/j.csr.2004.07.005

C. W. Hirt, A. A. Amsden, and J. L. Cook, An arbitrary Lagrangian-Eulerian computing method for all flow speeds, Journal of Computational Physics, vol.14, issue.3, pp.227-253, 1974.
DOI : 10.1016/0021-9991(74)90051-5

R. Hofmeister, K. Bolding, R. D. Hetland, G. Schernewski, H. Siegel et al., The dynamics of cooling water discharge in a shallow, non-tidal embayment, Continental Shelf Research, vol.71, pp.68-77, 2013.
DOI : 10.1016/j.csr.2013.10.006

R. Hofmeister, H. Burchard, and J. M. Beckers, Non-uniform adaptive vertical grids for 3d numerical ocean models. Ocean Modell, pp.70-86, 2010.
DOI : 10.1016/j.ocemod.2009.12.003

J. Holt, J. Harle, R. Proctor, S. Michel, M. Ashworth et al., Modelling the global coastal ocean, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.414, issue.6863, pp.939-951, 2009.
DOI : 10.1038/35107050

URL : http://rsta.royalsocietypublishing.org/content/roypta/367/1890/939.full.pdf

J. T. Holt and I. D. James, coordinate density evolving model of the northwest European continental shelf: 1. Model description and density structure, Journal of Geophysical Research: Oceans, vol.42, issue.1, pp.14015-14034, 2001.
DOI : 10.1006/ecss.1996.0028

J. T. Holt and I. D. James, An assessment of the fine-scale eddies in a high-resolution model of the shelf seas west of Great Britain, Ocean Modelling, vol.13, issue.3-4, pp.271-291, 2006.
DOI : 10.1016/j.ocemod.2006.02.005

R. Hordoir, L. Axell, U. Löptien, H. Dietze, and I. Kuznetsov, Influence of sea level rise on the dynamics of salt inflows in the Baltic Sea, Journal of Geophysical Research: Oceans, vol.27, issue.1-2, pp.6653-6668, 2015.
DOI : 10.1016/j.ocemod.2008.10.005

A. R. Horner-devine, R. D. Hetland, and D. G. Macdonald, Mixing and Transport in Coastal River Plumes, Annual Review of Fluid Mechanics, vol.47, issue.1, pp.569-594, 2015.
DOI : 10.1146/annurev-fluid-010313-141408

W. Hundsdorfer and R. A. Trompert, Method of lines and direct discretization: a comparison for linear advection, Applied Numerical Mathematics, vol.13, issue.6, pp.469-490, 1994.
DOI : 10.1016/0168-9274(94)90009-4

J. M. Huthnance, Circulation, exchange and water masses at the ocean margin: the role of physical processes at the shelf edge, Progress in Oceanography, vol.35, issue.4, pp.353-431, 1995.
DOI : 10.1016/0079-6611(95)80003-C

M. Ilicak, A. J. Adcroft, S. M. Griffies, and R. W. Hallberg, Spurious dianeutral mixing and the role of momentum closure. Ocean Modell, pp.45-46, 2012.

J. B. Jackson, M. X. Kirby, W. H. Berger, K. A. Bjorndal, L. W. Botsford et al., Historical Overfishing and the Recent Collapse of Coastal Ecosystems, Science, vol.293, issue.5530, pp.629-637, 2001.
DOI : 10.1126/science.1059199

L. Jackson, R. Hallberg, and S. Legg, A Parameterization of Shear-Driven Turbulence for Ocean Climate Models, Journal of Physical Oceanography, vol.38, issue.5, pp.1033-1053, 2008.
DOI : 10.1175/2007JPO3779.1

I. James, A high-performance explicit vertical advection scheme for ocean models: how PPM can beat the CFL condition, Applied Mathematical Modelling, vol.24, issue.1, pp.1-9, 2000.
DOI : 10.1016/S0307-904X(99)00022-0

D. A. Jay and J. D. Musiak, Particle trapping in estuarine tidal flows, Journal of Geophysical Research, vol.38, issue.C10, pp.20445-20461, 1994.
DOI : 10.1016/0272-7714(83)90075-6

T. G. Jensen, Open boundary conditions in stratified ocean models, Journal of Marine Systems, vol.16, issue.3-4, pp.297-322, 1998.
DOI : 10.1016/S0924-7963(97)00023-7

B. Johns, P. Marsaleix, C. Estournel, and R. Vhil, On the wind-driven coastal upwelling in the Gulf of Lions, Journal of Marine Systems, vol.3, issue.4-5, pp.309-320, 1992.
DOI : 10.1016/0924-7963(92)90008-V

J. H. Jungclaus and J. O. Backhaus, Application of a transient reduced gravity plume model to the Denmark Strait Overflow, Journal of Geophysical Research, vol.16, issue.C6, pp.12375-12396, 1994.
DOI : 10.1029/JC095iC06p09585

P. Kållberg, Test of a lateral boundary relaxation scheme in a barotropic model, 1977.

J. Van-kan, A Second-Order Accurate Pressure-Correction Scheme for Viscous Incompressible Flow, SIAM Journal on Scientific and Statistical Computing, vol.7, issue.3, pp.870-891, 1986.
DOI : 10.1137/0907059

Y. Kanarska and V. Maderich, A non-hydrostatic numerical model for calculating free-surface stratified flows, Ocean Dynamics, vol.53, issue.3, pp.176-185, 2003.
DOI : 10.1007/s10236-003-0039-6

Y. Kanarska, A. Shchepetkin, and J. Mcwilliams, Algorithm for non-hydrostatic dynamics in the Regional Oceanic Modeling System. Ocean Modell, pp.143-174, 2007.

L. H. Kantha and C. A. Clayson, Numerical models of oceans and oceanic processes, International Geophysics Series, vol.66, 2000.

L. H. Kantha and C. A. Clayson, Small-scale processes in geophysical fluid flows, International Geophysics Series, vol.67, 2000.

A. Kasahara, Various Vertical Coordinate Systems Used for Numerical Weather Prediction, Monthly Weather Review, vol.102, issue.7, pp.509-522, 1974.
DOI : 10.1175/1520-0493(1974)102<0509:VVCSUF>2.0.CO;2

URL : http://journals.ametsoc.org/doi/pdf/10.1175/1520-0493%281974%29102%3C0509%3AVVCSUF%3E2.0.CO%3B2

E. Keilegavlen and J. Berntsen, Non-hydrostatic pressure in ??-coordinate ocean models, Ocean Modelling, vol.28, issue.4, pp.240-249, 2009.
DOI : 10.1016/j.ocemod.2009.02.006

URL : http://folk.uib.no/nmajb/KB07.pdf

K. Klingbeil and H. Burchard, Implementation of a direct nonhydrostatic pressure gradient discretisation into a layered ocean model. Ocean Modell, pp.64-77, 2013.

K. Klingbeil, M. Mohammadi-aragh, U. Gräwe, and H. Burchard, Quantification of spurious dissipation and mixing -discrete variance decay in a finite-volume framework. Ocean Modell, pp.49-64, 2014.

P. J. Knight, M. J. Howarth, and T. P. Rippeth, Inertial currents in the northern North sea, Journal of Sea Research, vol.47, issue.3-4, pp.269-284, 2002.
DOI : 10.1016/S1385-1101(02)00122-3

J. Kondo, Air-sea bulk transfer coefficients in diabatic conditions. Bound. Layer Meteor, pp.91-112, 1975.
DOI : 10.1007/bf00232256

S. Lahaye, F. Gouillon, R. Baraille, A. Pichon, L. Pineau-guillou et al., A numerical scheme for modeling tidal wetting and drying, Journal of Geophysical Research, vol.3, issue.6, p.3028, 2011.
DOI : 10.1016/0021-9991(79)90051-2

URL : http://onlinelibrary.wiley.com/doi/10.1029/2010JC006666/pdf

W. G. Large, J. C. Mcwilliams, and S. C. Doney, Oceanic vertical mixing: A review and a model with a nonlocal boundary layer parameterization, Reviews of Geophysics, vol.33, issue.11, pp.363-403, 1994.
DOI : 10.1017/CBO9780511608827

P. Lazure and J. C. Salomon, Coupled 2-d and 3-d modeling of coastal hydrodynamics, Oceanol. Acta, vol.14, pp.173-180, 1991.

M. Leclair and G. Madec, ? z-coordinate, an arbitrary lagrangian-eulerian coordinate separating high and low frequency motions. Ocean Modell, pp.139-152, 2011.

F. Lemarié, L. Debreu, G. Madec, J. Demange, J. Molines et al., Stability constraints for oceanic numerical models: implications for the formulation of time and space discretizations, Ocean Modelling, vol.92, pp.124-148, 2015.
DOI : 10.1016/j.ocemod.2015.06.006

F. Lemarié, L. Debreu, A. Shchepetkin, and J. Mcwilliams, On the stability and accuracy of the harmonic and biharmonic isoneutral mixing operators in ocean models. Ocean Modell, pp.52-53, 2012.

F. Lemarié, J. Kurian, A. F. Shchepetkin, M. J. Molemaker, F. Colas et al., Are There Inescapable Issues Prohibiting the use of Terrain-Following Coordinates in Climate Models ? Ocean Modell, pp.57-79, 2012.

H. J. Lenhart, D. K. Mills, H. Baretta-bekker, S. M. Van-leeuwen, J. Van-der-molen et al., Predicting the consequences of nutrient reduction on the eutrophication status of the North Sea, Journal of Marine Systems, vol.81, issue.1-2, pp.148-170, 2010.
DOI : 10.1016/j.jmarsys.2009.12.014

DOI : 10.1175/1520-0493(1965)093<0011:OTCSON>2.3.CO;2

S. J. Lin, A finite-volume integration method for computing pressure gradient force in general vertical coordinates, Quarterly Journal of the Royal Meteorological Society, vol.18, issue.542, pp.1749-1762, 1997.
DOI : 10.1175/1520-0469(1957)014<0184:ACSHSS>2.0.CO;2

E. N. Lorenz, Energy and Numerical Weather Prediction, Tellus, vol.12, pp.364-373, 1960.
DOI : 10.1111/j.2153-3490.1960.tb01323.x

H. K. Lotze, H. S. Lenihan, B. J. Bourque, R. H. Bradbury, R. G. Cooke et al., Depletion, Degradation, and Recovery Potential of Estuaries and Coastal Seas, Science, vol.312, issue.5781, pp.1806-1809, 2006.
DOI : 10.1126/science.1128035

K. A. Lundquist, F. K. Chow, and J. K. Lundquist, An Immersed Boundary Method for the Weather Research and Forecasting Model, Monthly Weather Review, vol.138, issue.3, pp.796-817, 2010.
DOI : 10.1175/2009MWR2990.1

P. Luyten, J. Jones, R. Proctor, A. Tabor, P. Tett et al., COHERENS -A coupled hydrodynamical-ecological model for regional and shelf seas: User Documentation, 1999.

P. Maccready and W. R. Geyer, Advances in Estuarine Physics, Annual Review of Marine Science, vol.2, issue.1, pp.35-58, 2010.
DOI : 10.1146/annurev-marine-120308-081015

R. V. Madala and S. A. Piacsek, A semi-implicit numerical model for baroclinic oceans, Journal of Computational Physics, vol.23, issue.2, pp.167-178, 1977.
DOI : 10.1016/0021-9991(77)90119-X

G. Madec, P. Delecluse, M. Crepon, and M. Chartier, A Three-Dimensional Numerical Study of Deep-Water Formation in the Northwestern Mediterranean Sea, Journal of Physical Oceanography, vol.21, issue.9, pp.1349-1371, 1991.
DOI : 10.1175/1520-0485(1991)021<1349:ATDNSO>2.0.CO;2

URL : https://hal.archives-ouvertes.fr/hal-00153956

P. Marchesiello, L. Debreu, and X. Couvelard, Spurious diapycnal mixing in terrain-following coordinate models: The problem and a solution, Ocean Modelling, vol.26, issue.3-4, pp.159-169, 2009.
DOI : 10.1016/j.ocemod.2008.09.004

URL : https://hal.archives-ouvertes.fr/hal-00409317

P. Marchesiello, J. C. Mcwilliams, and A. Shchepetkin, Open boundary conditions for long-term integration of regional oceanic models. Ocean Modell, pp.1-20, 2001.

P. Marsaleix, F. Auclair, C. Estournel, C. Nguyen, and C. Ulses, An accurate implementation of the compressibility terms in the equation of state in a low order pressure gradient scheme for sigma coordinate ocean models, Ocean Modelling, vol.40, issue.1, pp.1-13, 2011.
DOI : 10.1016/j.ocemod.2011.07.004

P. Marsaleix, F. Auclair, J. W. Floor, M. J. Herrmann, C. Estournel et al., Energy conservation issues in sigma-coordinate free-surface ocean models. Ocean Modell, pp.61-89, 2008.
DOI : 10.1016/j.ocemod.2007.07.005

URL : https://hal.archives-ouvertes.fr/hal-00518955

P. Marsaleix, C. Estournel, V. Kondrachoff, and R. Vehil, A numerical study of the formation of the Rh??ne River plume, Journal of Marine Systems, vol.14, issue.1-2, pp.99-115, 1998.
DOI : 10.1016/S0924-7963(97)00011-0

J. Marshall, C. Hill, L. Perelman, and A. J. Adcroft, Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling, Journal of Geophysical Research: Oceans, vol.37, issue.C11, pp.5733-5752, 1997.
DOI : 10.1017/S002211206900084X

URL : http://onlinelibrary.wiley.com/doi/10.1029/96JC02776/pdf

P. J. Martin, Simulation of the mixed layer at OWS November and Papa with several models, Journal of Geophysical Research, vol.33, issue.C1, pp.903-916, 1985.
DOI : 10.1175/1520-0469(1976)033<1974:MBDML>2.0.CO;2

P. J. Martin, Description of the Navy Coastal Ocean Model Version 1.0, 2000.
DOI : 10.21236/ADA389503

A. S. Martinho and M. L. Batteen, On reducing the slope parameter in terrain-following numerical ocean models. Ocean Modell, pp.166-175, 2006.

F. Martins, P. Leitão, A. Silva, and R. Neves, 3D modelling in the Sado estuary using a new generic vertical discretization approach, Oceanologica Acta, vol.24, pp.51-62, 2001.
DOI : 10.1016/S0399-1784(01)00092-5

E. A. Martinsen and H. Engedahl, Implementation and testing of a lateral boundary scheme as an open boundary condition in a barotropic ocean model, Coastal Engineering, vol.11, issue.5-6, pp.603-627, 1987.
DOI : 10.1016/0378-3839(87)90028-7

E. Mason, J. Molemaker, A. F. Shchepetkin, F. Colas, J. C. Mcwilliams et al., Procedures for offline grid nesting in regional ocean models. Ocean Modell, pp.1-15, 2010.

M. Mathis, A. Elizalde, U. Mikolajewicz, and T. Pohlmann, Variability patterns of the general circulation and sea water temperature in the North Sea, Progress in Oceanography, vol.135, pp.91-112, 2015.
DOI : 10.1016/j.pocean.2015.04.009

J. D. Mccalpin, A comparison of second-order and fourth-order pressure gradient algorithms in a ??-co-ordinate ocean model, International Journal for Numerical Methods in Fluids, vol.113, issue.4, pp.361-383, 1994.
DOI : 10.1002/fld.1650180404

H. E. Meier, E. Kjellström, and L. P. Graham, Estimating uncertainties of projected Baltic Sea salinity in the late 21st century, Geophysical Research Letters, vol.9, issue.D14, p.10, 1029.
DOI : 10.1029/2006GL026488

G. L. Mellor, Oscillatory Bottom Boundary Layers, Journal of Physical Oceanography, vol.32, issue.11, pp.3075-3088, 2002.
DOI : 10.1175/1520-0485(2002)032<3075:OBBL>2.0.CO;2

G. L. Mellor and A. F. Blumberg, Modeling Vertical and Horizontal Diffusivities with the Sigma Coordinate System, Monthly Weather Review, vol.113, issue.8, pp.1379-1383, 1985.
DOI : 10.1175/1520-0493(1985)113<1379:MVAHDW>2.0.CO;2

G. L. Mellor, T. Ezer, and L. Y. Oey, The Pressure Gradient Conundrum of Sigma Coordinate Ocean Models, Journal of Atmospheric and Oceanic Technology, vol.11, issue.4, pp.1126-1134, 1994.
DOI : 10.1175/1520-0426(1994)011<1126:TPGCOS>2.0.CO;2

G. L. Mellor and T. Yamada, Development of a turbulence closure model for geophysical fluid problems, Reviews of Geophysics, vol.33, issue.4, pp.851-875, 1982.
DOI : 10.2514/8.3651

F. Mesinger and A. Arakawa, Numerical Methods used in atmospheric models, 1976.

M. Mohammadi-aragh, K. Klingbeil, N. Brüggemann, C. Eden, and H. Burchard, The impact of advection schemes on restratifiction due to lateral shear and baroclinic instabilities. Ocean Modell, pp.112-127, 2015.

F. Nataf, Absorbing boundary conditions and perfectly matched layers in wave propagation problems, Direct and Inverse problems in Wave Propagation and Applications, pp.219-231, 2013.
DOI : 10.1515/9783110282283.219

URL : https://hal.archives-ouvertes.fr/hal-00799759

T. Neumann, W. Fennel, and C. Kremp, Experimental simulations with an ecosystem model of the Baltic Sea: A nutrient load reduction experiment, Global Biogeochemical Cycles, vol.4, issue.3, 1029.
DOI : 10.1002/iroh.19970820205

R. J. Nicholls, F. M. Hoozemans, and M. Marchand, Increasing flood risk and wetland losses due to global sea-level rise: regional and global analyses, Global Environmental Change, vol.9, pp.69-87, 1999.
DOI : 10.1016/S0959-3780(99)00019-9

J. C. Nihoul, F. Waleffe, and S. Djenidi, A 3D-numerical model of the Northern Bering Sea, Environmental Software, vol.1, issue.2, pp.76-81, 1986.
DOI : 10.1016/0266-9838(86)90002-X

O. Dea, E. J. Arnold, A. K. Edwards, K. P. Furner, R. Hydler et al., An operational ocean forecast system incorporating NEMO and SST data assimilation for the tidally driven European North-West shelf, Journal of Operational Oceanography, vol.5, pp.3-17, 2012.

L. Y. Oey, A wetting and drying scheme for POM. Ocean Modell, pp.133-150, 2005.
DOI : 10.1016/j.ocemod.2004.06.002

D. Olbers, J. Willebrand, and C. Eden, Ocean dynamics, 2012.
DOI : 10.1007/978-3-642-23450-7

J. Oliger and A. Sundström, Theoretical and Practical Aspects of Some Initial Boundary Value Problems in Fluid Dynamics, SIAM Journal on Applied Mathematics, vol.35, issue.3, pp.419-446, 1978.
DOI : 10.1137/0135035

I. Orlanski, A simple boundary condition for unbounded hyperbolic flows, Journal of Computational Physics, vol.21, issue.3, pp.251-269, 1976.
DOI : 10.1016/0021-9991(76)90023-1

A. Oschlies, Improved Representation of Upper-Ocean Dynamics and Mixed Layer Depths in a Model of the North Atlantic on Switching from Eddy-Permitting to Eddy-Resolving Grid Resolution, Journal of Physical Oceanography, vol.32, issue.8, 2002.
DOI : 10.1175/1520-0485(2002)032<2277:IROUOD>2.0.CO;2

E. D. Palma and R. P. Matano, On the implementation of open boundary conditions for a general circulation model: The three-dimensional case, Journal of Geophysical Research: Oceans, vol.15, issue.C4, pp.8605-8627, 2000.
DOI : 10.1007/s00585-997-0113-3

S. V. Patankar, Numerical Heat Transfer and Fluid Flow, 1980.

C. A. Paulson and J. J. Simpson, Irradiance Measurements in the Upper Ocean, Journal of Physical Oceanography, vol.7, issue.6, pp.952-956, 1977.
DOI : 10.1175/1520-0485(1977)007<0952:IMITUO>2.0.CO;2

D. W. Peaceman, J. Rachford, and H. H. , The Numerical Solution of Parabolic and Elliptic Differential Equations, Journal of the Society for Industrial and Applied Mathematics, vol.3, issue.1, pp.28-41, 1955.
DOI : 10.1137/0103003

B. Pearson, B. Fox-kemper, S. Bachman, and F. Bryan, Evaluation of scale-aware subgrid mesoscale eddy models in a global eddy-rich model, Ocean Modelling, vol.115, pp.42-58, 2017.
DOI : 10.1016/j.ocemod.2017.05.007

P. Penven, L. Debreu, P. Marchesiello, and J. C. Mcwilliams, Evaluation and application of the roms 1-way embedding procedure to the central california upwelling system. Ocean Modell, pp.157-187, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00280334

A. L. Perkins, L. F. Smedstad, D. W. Blake, G. W. Heburn, and A. J. Wallcraft, A new nested boundary condition for a primitive equation ocean model, Journal of Geophysical Research: Oceans, vol.114, issue.2, pp.3483-3500, 1997.
DOI : 10.1175/1520-0493(1986)114<1330:ATWINP>2.0.CO;2

J. Pietrzak, J. B. Jakobson, H. Burchard, H. J. Vested, and O. Petersen, A three-dimensional hydrostatic model for coastal and ocean modelling using a generalised topography following co-ordinate system. Ocean Modell, pp.173-205, 2002.

M. Quante and F. Colijn, North Sea Region Climate Change Assessment, 2016.
DOI : 10.1007/978-3-319-39745-0

W. H. Raymond and H. L. Kuo, A radiation boundary condition for multi-dimensional flows, Quarterly Journal of the Royal Meteorological Society, vol.39, issue.464, pp.535-551, 1984.
DOI : 10.1002/qj.49711046414

H. Rennau, S. Schimmels, and H. Burchard, On the effect of structure-induced resistance and mixing on inflows into the Baltic Sea: A numerical model study, Coastal Engineering, vol.60, pp.53-68, 2012.
DOI : 10.1016/j.coastaleng.2011.08.002

T. P. Rippeth, N. Fisher, and J. H. Simpson, The Cycle of Turbulent Dissipation in the Presence of Tidal Straining, Journal of Physical Oceanography, vol.31, issue.8, pp.2458-2471, 2001.
DOI : 10.1175/1520-0485(2001)031<2458:TCOTDI>2.0.CO;2

W. Rodi, Examples of calculation methods for flow and mixing in stratified fluids, Journal of Geophysical Research, vol.33, issue.C5, pp.5305-5328, 1987.
DOI : 10.1175/1520-0469(1976)033<1974:MBDML>2.0.CO;2

F. Roquet, G. Madec, T. J. Mcdougall, and P. M. Barkerd, Accurate polynomial expressions for the density and specific volume of seawater using the TEOS-10 standard. Ocean Modell, pp.29-43, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01234088

M. A. Ross and A. J. Mehta, On the mechanics of lutoclines and fluid mud, J. Coastal Res, pp.51-62, 1989.

F. J. Rueda, E. Sanmiguel-rojas, and B. R. Hodges, Baroclinic stability for a family of two-level, semi-implicit numerical methods for the 3D shallow water equations, International Journal for Numerical Methods in Fluids, vol.60, issue.3, pp.237-268, 2007.
DOI : 10.1142/1970

C. Schär, D. Leuenberger, O. Fuhrer, D. Lüthi, and C. Girard, A New Terrain-Following Vertical Coordinate Formulation for Atmospheric Prediction Models, Monthly Weather Review, vol.130, issue.10, pp.2459-2480, 2002.
DOI : 10.1175/1520-0493(2002)130<2459:ANTFVC>2.0.CO;2

A. Scotti and J. Pineda, Observation of very large and steep internal waves of elevation near the Massachusetts coast, Geophysical Research Letters, vol.289, issue.52, p.10, 1029.
DOI : 10.1142/9789812797568_0001

J. A. Screen and I. Simmonds, The central role of diminishing sea ice in recent Arctic temperature amplification, Nature, vol.464, issue.7293, pp.1334-1337, 2010.
DOI : 10.1038/nature09051

G. Shapiro, M. Luneva, J. Pickering, and D. Storkey, The effect of various vertical discretization schemes and horizontal diffusion parameterization on the performance of a 3-D ocean model: the Black Sea case study, Ocean Science, vol.9, issue.2, pp.377-390, 2013.
DOI : 10.5194/os-9-377-2013

A. F. Shchepetkin, An adaptive, courant-number-dependent implicit scheme for vertical advection in oceanic modeling. Ocean Modell, pp.38-69, 2015.

A. F. Shchepetkin and J. C. Mcwilliams, A method for computing horizontal pressure-gradient force in an oceanic model with a nonaligned vertical coordinate, Journal of Geophysical Research, vol.48, issue.4, pp.3090-3124, 2003.
DOI : 10.1142/p097

A. F. Shchepetkin and J. C. Mcwilliams, The Regional Oceanic Modeling System: A split-explicit, free-surface, topography-following-coordinate ocean model. Ocean Modell, pp.347-404, 2005.

A. F. Shchepetkin and J. C. Mcwilliams, Computational kernel algorithms for fine-scale, multiprocess, longtime oceanic simulations Computational methods for the atmosphere and the oceans Special Volume, pp.121-183, 2009.

A. F. Shchepetkin, J. C. Mcwilliams, and . Haidvogel, Correction and commentary for " ocean forecasting in terrainfollowing coordinates: Formulation and skill assessment of the regional ocean modeling system, J. Comp. Phys. J. Comput. Phys, vol.227, issue.228, pp.3595-3624, 2009.

J. Sheng, R. J. Greatbatch, X. Zhai, and L. Tang, A new two-way nesting technique for ocean modeling based on the smoothed semi-prognostic method. Ocean Dyn, pp.162-177, 2005.

C. W. Shu, TVB uniformly high-order schemes for conservation laws, Mathematics of Computation, vol.49, issue.179, pp.105-121, 1987.
DOI : 10.1090/S0025-5718-1987-0890256-5

URL : http://www.ams.org/mcom/1987-49-179/S0025-5718-1987-0890256-5/S0025-5718-1987-0890256-5.pdf

C. W. Shu, Total-Variation-Diminishing Time Discretizations, SIAM Journal on Scientific and Statistical Computing, vol.9, issue.6, pp.1073-1084, 1988.
DOI : 10.1137/0909073

T. J. Simons, Verification of Numerical Models of Lake Ontario: Part I. Circulation in Spring and Early Summer, Journal of Physical Oceanography, vol.4, issue.4, pp.507-523, 1974.
DOI : 10.1175/1520-0485(1974)004<0507:VONMOL>2.0.CO;2

J. H. Simpson, J. Brown, J. Matthews, and G. Allen, Tidal Straining, Density Currents, and Stirring in the Control of Estuarine Stratification, Estuaries, vol.13, issue.2, pp.125-132, 1990.
DOI : 10.2307/1351581

J. Smagorinsky, GENERAL CIRCULATION EXPERIMENTS WITH THE PRIMITIVE EQUATIONS, Monthly Weather Review, vol.91, issue.3, pp.99-164, 1963.
DOI : 10.1175/1520-0493(1963)091<0099:GCEWTP>2.3.CO;2

W. D. Smyth, E. D. Skyllingstad, G. B. Crawford, and H. Wijesekera, Nonlocal fluxes and stokes drift effects in the K-profile parameterization. Ocean Dyn, pp.104-115, 2002.

Y. Song and D. B. Haidvogel, A Semi-implicit Ocean Circulation Model Using a Generalized Topography-Following Coordinate System, Journal of Computational Physics, vol.115, issue.1, pp.228-244, 1994.
DOI : 10.1006/jcph.1994.1189

Y. Soufflet, P. Marchesiello, F. Lemarié, J. Jouanno, X. Capet et al., On effective resolution in ocean models. Ocean Modell, pp.36-50, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01250231

V. P. Starr, A QUASI-LAGRANGIAN SYSTEM OF HYDRODYNAMICAL EQUATIONS, Journal of Meteorology, vol.2, issue.4, pp.227-237, 1945.
DOI : 10.1175/1520-0469(1945)002<0227:AQLSOH>2.0.CO;2

G. S. Stelling and S. P. Duinmeijer, A staggered conservative scheme for every Froude number in rapidly varied shallow water flows, International Journal for Numerical Methods in Fluids, vol.360, issue.12, pp.1329-1354, 2003.
DOI : 10.1007/978-3-662-03915-1

G. S. Stelling and J. A. Van-kester, On the approximation of horizontal gradients in sigma co-ordinates for bathymetry with steep bottom slopes, International Journal for Numerical Methods in Fluids, vol.88, issue.10, pp.915-935, 1994.
DOI : 10.1007/978-3-642-85952-6

H. F. Stockdon, R. A. Holman, P. A. Howd, and A. H. Sallenger, Empirical parameterization of setup, swash, and runup, Coastal Engineering, vol.53, issue.7, pp.573-588, 2006.
DOI : 10.1016/j.coastaleng.2005.12.005

A. Suresh and H. Huynh, Accurate Monotonicity-Preserving Schemes with Runge???Kutta Time Stepping, Journal of Computational Physics, vol.136, issue.1, pp.83-99, 1997.
DOI : 10.1006/jcph.1997.5745

E. Svendsen, J. Berntsen, M. Skogen, B. Dlandsvik, and E. Martinsen, Model simulation of the Skagerrak circulation and hydrography during Skagex, Journal of Marine Systems, vol.8, issue.3-4, pp.219-236, 1996.
DOI : 10.1016/0924-7963(96)00007-3

W. J. Sydeman, M. García-reyes, D. S. Schoeman, R. R. Rykaczewski, S. A. Thompson et al., Climate change and wind intensification in coastal upwelling ecosystems, Science, vol.17, issue.6050, pp.77-80, 2014.
DOI : 10.1111/j.1365-2486.2011.02531.x

R. Témam, Sur l'Approximation de la Solution dé Equations de Navier-Stokes par la Méthode de Pas Fractionnaires (II), Arch. Rational Mech. Anal, vol.32, pp.377-385, 1969.

R. Témam and J. Tribbia, Open Boundary Conditions for the Primitive and Boussinesq Equations, Journal of the Atmospheric Sciences, vol.60, issue.21, pp.2647-2660, 2003.
DOI : 10.1175/1520-0469(2003)060<2647:OBCFTP>2.0.CO;2

Y. Uchiyama, J. C. Mcwilliams, and A. F. Shchepetkin, Wave???current interaction in an oceanic circulation model with a vortex-force formalism: Application to the surf zone, Ocean Modelling, vol.34, issue.1-2, pp.16-35, 2010.
DOI : 10.1016/j.ocemod.2010.04.002

L. Umlauf and H. Burchard, A generic length-scale equation for geophysical turbulence models, Journal of Marine Research, vol.61, issue.2, pp.235-265, 2003.
DOI : 10.1357/002224003322005087

L. Umlauf and H. Burchard, Second-order turbulence closure models for geophysical boundary layers. A review of recent work, Continental Shelf Research, vol.25, issue.7-8, pp.795-827, 2005.
DOI : 10.1016/j.csr.2004.08.004

D. S. Van-maren, A. P. Oost, Z. B. Wang, and P. C. Vos, The effect of land reclamations and sediment extraction on the suspended sediment concentration in the Ems Estuary, Marine Geology, vol.376, pp.147-157, 2016.
DOI : 10.1016/j.margeo.2016.03.007

S. Vitousek and O. Fringer, Physical vs numerical dispersion in nonhydrostatic ocean modeling. Ocean Modell, pp.72-86, 2011.

T. Wahl, I. D. Haigh, P. L. Woodworth, F. Albrecht, D. Dillingh et al., Observed mean sea level changes around the North Sea coastline from 1800 to present, Earth-Science Reviews, vol.124, pp.51-67, 2013.
DOI : 10.1016/j.earscirev.2013.05.003

URL : https://hal.archives-ouvertes.fr/hal-01247763

K. M. Waldron, J. Paegle, and J. D. Horel, Sensitivity of a Spectrally Filtered and Nudged Limited-Area Model to Outer Model Options, Monthly Weather Review, vol.124, issue.3, pp.529-547, 1996.
DOI : 10.1175/1520-0493(1996)124<0529:SOASFA>2.0.CO;2

R. A. Walters, E. M. Lane, and E. Hanert, Useful time-stepping methods for the Coriolis term in a shallow water model. Ocean Modell, pp.66-74, 2009.

J. C. Warner, Z. Defne, K. Haas, and H. G. Arango, A wetting and drying scheme for ROMS, Computers & Geosciences, vol.58, pp.54-61, 2013.
DOI : 10.1016/j.cageo.2013.05.004

URL : http://darchive.mblwhoilibrary.org/bitstream/1912/6207/1/1-s2.0-S0098300413001362-main.pdf

J. C. Warner, C. R. Sherwood, H. G. Arango, and R. P. Signell, Performance of four turbulence closure models implemented using a generic length scale method. Ocean Modell, pp.81-113, 2005.

J. C. Warner, C. R. Sherwood, R. P. Signell, C. K. Harris, and H. G. Arango, Development of a threedimensional , regional, coupled wave, current, and sediment-transport model. Computers & Geosci, pp.1284-1306, 2008.

H. Weller and A. Shahrokhi, Curl-Free Pressure Gradients over Orography in a Solution of the Fully Compressible Euler Equations with Implicit Treatment of Acoustic and Gravity Waves, Monthly Weather Review, vol.142, issue.12, pp.4439-4457, 2014.
DOI : 10.1175/MWR-D-14-00054.1

G. H. Wheless and J. M. Klinck, The Evolution of Density-Driven Circulation over Sloping Bottom Topography, Journal of Physical Oceanography, vol.25, issue.5, pp.888-901, 1995.
DOI : 10.1175/1520-0485(1995)025<0888:TEODDC>2.0.CO;2

L. White, A. Adcroft, and R. Hallberg, High-order regridding???remapping schemes for continuous isopycnal and generalized coordinates in ocean models, Journal of Computational Physics, vol.228, issue.23, pp.8665-8692, 2009.
DOI : 10.1016/j.jcp.2009.08.016

L. White and A. J. Adcroft, A high-order finite volume remapping scheme for nonuniform grids: The piecewise quartic method (PQM), Journal of Computational Physics, vol.227, issue.15, pp.7394-7422, 2008.
DOI : 10.1016/j.jcp.2008.04.026

D. C. Wilcox, Turbulence Modeling for CFD. DCW Industries, 1998.

J. L. Wilkin, H. G. Arango, D. B. Haidvogel, C. Lichtenwalner, S. M. Glenn et al., A regional ocean modeling system for the Long-term Ecosystem Observatory, Journal of Geophysical Research, vol.8, issue.C3, 2005.
DOI : 10.5670/oceanog.2002.39

K. H. Wiltshire and B. F. Manly, The warming trend at Helgoland Roads, North Sea: phytoplankton response, Helgoland Marine Research, vol.44, issue.4, pp.269-273, 2004.
DOI : 10.1007/s10152-004-0196-0

J. C. Winterwerp, Z. B. Wang, A. Van-braeckel, G. Van-holland, and F. Kösters, Man-induced regime shifts in small estuariesII: a comparison of rivers. Ocean Dyn, pp.1293-1306, 2013.