Adcroft, A., and J.-M. Campin, 2004: Re-scaled height coordinates for accurate representation of free-surface flows in ocean circulation models. Ocean Modelling, 7, 269-284, full-text.

Arakawa, A., and Y.-J. G. Hsu, 1990: Energy conserving and potential-enstrophy dissipating schemes for the shallow water equations. Mon. Wea. Rev., 118 (10), 1960-1969.

Arakawa, A., and V. R. Lamb, 1981: A potential enstrophy and energy conserving scheme for the shallow water equations. Mon. Wea. Rev., 109 (1), 18-36.

Asselin, R., 1972: Frequency filter for time integrations. Mon. Wea. Rev., 100 (6), 487-490.

Axell, L. B., 2002: Wind-driven internal waves and langmuir circulations in a numerical ocean model of the southern baltic sea. J. Geophys. Res, 107, full-text.

Barnier, B., and Coauthors, 2006: Impact of partial steps and momentum advection schemes in a global ocean circulation model at eddy-permitting resolution. Ocean Dyn., 56, 543-567, full-text.

Beckmann, A., and R. D"oscher, 1997: A method for improved representation of dense water spreading over topography in geopotential-coordinate models. J. Phys. Oceanogr., 27, 581-591.

Beckmann, A., and H. Goosse, 2003: A parameterization of ice shelf-ocean interaction for climate models. Ocean Modelling, 5, 157-170.

Beckmann, A., and D. B. Haidvogel, 1993: Numerical simulation of flow around a tall isolated seamount. part i - problem formulation and model accuracy. J. Phys. Oceanogr., 23 (8), 1736-1753.

Bernie, D., E. Guilyardi, G. Madec, J. M. Slingo, and S. J. Woolnough, 2007: Impact of resolving the diurnal cycle in an ocean-atmosphere gcm. part 1: a diurnally forced ogcm. Clim. Dyn., 29 (6), 575-590.

Bernie, D. J., S. J. Woolnough, J. M. Slingo, and E. Guilyardi, 2005: Modelling diurnal and intraseasonal variability of the ocean mixed layer. J. Climate, 18 (8), 1190-1200.

Bignami, F., S. Marullo, R. Santoleri, and M. E. Schiano, 1995: Longwave radiation budget in the mediterranean sea. J. Geophys. Res, 100 (C2), 2501-2514, full-text.

Blanke, B., and P. Delecluse, 1993: Low frequency variability of the tropical atlantic ocean simulated by a general circulation model with mixed layer physics. J. Phys. Oceanogr., 23, 1363-1388.

Blanke, B., and S. Raynaud, 1997: Kinematics of the pacific equatorial undercurrent: An eulerian and lagrangian approach from gcm results. J. Phys. Oceanogr., 27 (6), 1038-1053.

Bloom, S. C., L. L. Takacs, A. M. D. Silva, and D. Ledvina, 1996: Data assimilation using incremental analysis updates. Mon. Wea. Rev., 124, 1256-1271.

Bouffard, D., and L. Boegman, 2013: A diapycnal diffusivity model for stratified environmental flows. Dyn. Atmos. Ocean, 61-62, 14-34, full-text.

Bougeault, P., and P. Lacarrere, 1989: Parameterization of orography-induced turbulence in a mesobeta-scale model. Mon. Wea. Rev., 117 (8), 1872-1890.

Bouillon, S., M. M. Maqueda, V. Legat, and T. Fichefet, 2009: An elastic-viscous-plastic sea ice model formulated on arakawa b and c grids. Ocean Modelling, 27, 174-184, full-text.

Brankart, J.-M., 2013: Impact of uncertainties in the horizontal density gradient upon low resolution global ocean modelling. Ocean Modelling, 66, 64-76, full-text.

Brankart, J.-M., G. Candille, F. Garnier, C. Calone, A. Melet, P.-A. Bouttier, P. Brasseur, and J. Verron, 2015: A generic approach to explicit simulation of uncertainty in the nemo ocean model. Geoscientific Model Development, 8 (5), 1285-1297, full-text.

Brodeau, L., B. Barnier, A.-M. Tréguier, T. Penduff, and S. Gulev, 2009: An era40-based atmospheric forcing for global ocean circulation models. Ocean Modelling, 31 (3-4), 88-104.

Brown, J. A., and K. A. Campana, 1978: An economical time-differencing system for numerical weather prediction. Mon. Wea. Rev., 106 (8), 1125-1136.

Bryan, K., 1984: Accelerating the convergence to equilibrium of ocean-climate models. J. Phys. Oceanogr., 14, 666-673.

Burchard, H., 2002: Energy-conserving discretisation of turbulent shear and buoyancy production. Ocean Modelling, 4 (3-4), 347-361, full-text.

Campin, J.-M., A. Adcroft, C. Hill, and J. Marshall, 2004: Conservation of properties in a free-surface model. Ocean Modelling, 6 (3-4), 221-244.

Campin, J.-M., and H. Goosse, 1999: Parameterization of density-driven downsloping flow for a coarse-resolution ocean model in z-coordinate. Tellus, 51, 412-430.

Campin, J.-M., J. Marshall, and D. Ferreira, 2008: Sea ice-ocean coupling using a rescaled vertical coordinate z*. Ocean Modelling, 24 (1-2), 1-14, full-text.

Canuto, V. M., A. Howard, Y. Cheng, and M. S. Dubovikov, 2001: Ocean turbulence. parti: One-point closure model-momentum and heat vertical diffusivities. J. Phys. Oceanogr., 24 (12), 2546-2559.

Carrère, L., and F. Lyard, 2003: Modelling the barotropic response of the global ocean to atmospheric wind and pressure forcing - comparisons with observations. Geophys. Res. Let., 30 (6), full-text.

Castellari, S., N. Pinardi, and K. Leaman, 1998: A model study of air-sea interactions in the mediterranean sea. J. Mar. Sys., 18, 89-114.

Chanut, J., 2005: Nesting code for nemo. Tech. rep., European Union: Marine Environment and Security for the European Area (MERSEA) Integrated Project. MERSEA-WP09-MERCA-TASK-9.1.1.

Chassignet, E. P., L. T. Smith, and G. R. Halliwell, 2003: North atlantic simulations with the hybrid coordinate ocean model (hycom): Impact of the vertical coordinate choice, reference pressure, and thermobaricity. J. Phys. Oceanogr., 33, 2504-2526.

Cox, M., 1987: Isopycnal diffusion in a z-coordinate ocean model. Ocean Modelling, 74, 1-9.

Craig, P. D., and M. L. Banner, 1994: Modeling wave-enhanced turbulence in the ocean surface layer. J. Phys. Oceanogr., 24 (12), 2546-2559.

Craik, A. D. D., and S. Leibovich, 1976: A rational model for langmuir circulations. J. Fluid Mech., 73, 401-426.

D'Alessio, S. J. D., K. Abdella, and N. A. McFarlane, 1998: A new second-order turbulence closure scheme for modeling the oceanic mixed layer. J. Phys. Oceanogr., 28, 1624-1641.

Daley, R., and E. Barker, 2001: NAVDAS Source Book 2001. NRL/PU/7530-01-441, Available from the Naval Research Laboratory, Monterey, CA., 93943-5502, 163pp pp.

Danabasoglu, G., R. Ferrari, and J. C. McWilliams, 2008: Sensitivity of an ocean general circulation model to a parameterization of near-surface eddy fluxes. J. Climate, 21, 1192-1208, full-text.

Davies, H., 1976: A lateral boundary formulation for multi-level prediction models. Quart. J. Roy. Meteor. Soc., 102, 405-418.

de Boyer Montégut, C., G. Madec, A. Fischer, A. Lazar, and D. Iudicone, 2004: Mixed layer depth over the global ocean: An examination of profile data and a profile-based climatology. J. Geophys. Res, 109, C12003, full-text.

de Lavergne, C., G. Madec, J. L. Sommer, A. J. G. Nurser, and A. C. N. Garabato, 2016: The impact of a variable mixing efficiency on the abyssal overturning. Journal of Physical Oceanography, 46, 663-–681, full-text.

Debreu, L., C. Vouland, and E. Blayo, 2008: Agrif: Adaptive grid refinement in fortran. Computers and Geosciences, 34, 8-13.

Delecluse, P., and G. Madec, 2000: Ocean modelling and the role of the ocean in the climate system. In Modeling the Earth's Climate and its Variability, Les Houches, Session, LXVII 1997, Eds. W. R. Holland, S. Joussaume and F. David, Elsevier Science, 237-313.

Dobricic, S., N. Pinardi, M. Adani, M. Tonani, C. Fratianni, A. Bonazzi, and V. Fernandez, 2007: Daily oceanographic analysis by the mediterranean basin scale assimilation system. Ocean Sc., 3, 149-157.

Drijfhout, S. S., 1994: Heat transport by mesoscale eddies in an ocean circulation model. J. Phys. Oceanogr., 24, 353-369.

Dukowicz, J. K., and R. D. Smith, 1994: Implicit free-surface method for the bryan-cox-semtner ocean model. J. Geophys. Res, 99, 7991-8014.

Eby, M., and G. Holloway, 1994: Sensitivity of a large-scale ocean model to a parameterization of topographic stress. J. Phys. Oceanogr., 24, 2577-2587.

Egbert, G., and R. Ray, 2000: Significant dissipation of tidal energy in the deep ocean inferred from satellite altimeter data. Nature, 405, 775-778.

Egbert, G., and R. Ray, 2001: Estimates of m2 tidal energy dissipation from topex/poseidon altimeter data. J. Geophys. Res, 106, 22475-22502.

Eiseman, P. R., and A. P. Stone, 1980: Conservation lows of fluid dynamics - a survey. SIAM Review, 22, 12-27.

Emile-Geay, J., and G. Madec, 2009: Geothermal heating, diapycnal mixing and the abyssal circulation. Ocean Sc., 5, 281-325.

Engerdahl, H., 1995: Use of the flow relaxation scheme in a three-dimensional baroclinic ocean model with realistic topography. Tellus, 47A, 365-382.

Farge, M., 1987: Dynamique non lineaire des ondes et des tourbillons dans les equations de saint venant. Ph.D. thesis, Doctorat es Mathematiques, Paris VI University, France, 401pp pp.

Farrow, D. E., and D. P. Stevens, 1995: A new tracer advection scheme for bryan-cox type ocean general circulation models. J. Phys. Oceanogr., 25, 1731-1741.

Flather, R., 1994: A storm surge prediction model for the northern bay of bengal with application to the cyclone disaster in april 1991. J. Phys. Oceanogr., 24, 172-190.

Fujio, S., and N. Imasato, 1991: Diagnostic calculation for circulation and water mass movement in the deep pacific. J. Geophys. Res, 96, 759-774.

Galperin, B., L. H. Kantha, S. Hassid, and A. Rosati, 1988: A quasi-equilibrium turbulent energy model for geophysical flows. J. Atmos. Sc., 45, 55-62.

Gargett, A. E., 1984: Vertical eddy diffusivity in the ocean interior. J. Mar. Res., 42.

Gaspar, P., Y. Grégoris, and J.-M. Lefevre, 1990: A simple eddy kinetic energy model for simulations of the oceanic vertical mixing Tests at station papa and long-term upper ocean study site. J. Geophys. Res, 95 (C9).

Gent, P. R., and J. C. Mcwilliams, 1990: Isopycnal mixing in ocean circulation models. J. Phys. Oceanogr., 20 (1), 150-155.

Gerdes, R., 1993a: A primitive equation ocean circulation model using a general vertical coordinate transformation 1. description and testing of the model. J. Geophys. Res, 98.

Gerdes, R., 1993b: A primitive equation ocean circulation model using a general vertical coordinate transformation 2. application to an overflow problem. J. Geophys. Res, 98, 14703-14726.

Gerdes, R., C. Köberle, and J. Willebrand, 1991: The influence of numerical advection schemes on the results of ocean general circulation models. Clim. Dynamics, 5 (4), 211-226, full-text.

Gibson, J. K., 1986: Standard software development and maintenance. Tech. rep., Operational Dep., ECMWF, Reading, UK.

Gill, A. E., 1982: Atmosphere-Ocean Dynamics. International Geophysics Series, Academic Press, New-York.

Goff, J. A., 2010: Global prediction of abyssal hill root-mean-square heights from small-scale altimetric gravity variability. Journal of Geophysical Research: Solid Earth, 115 (B12), B12104, full-text.

Goosse, H., E. Deleersnijder, T. Fichefet, and M. England, 1999: Sensitivity of a global coupled ocean-sea ice model to the parameterization of vertical mixing. J. Geophys. Res, 104, 13,681-13,695.

Graham, F., and T. McDougall, 2013: Quantifying the nonconservative production of conservative temperature, potential temperature, and entropy. J. Phys. Oceanogr., 43, 838-862, full-text.

Greatbatch, R. J., 1994: A note on the representation of steric sea level in models that conserve volume rather than mass. J. Geophys. Res, 99 (C6), 12,767-12,771.

Griffies, S., 1998: The gent-mcwilliams skew-flux. J. Phys. Oceanogr., 28, 831-841.

Griffies, S., 2004: Fundamentals of ocean climate models. Princeton University Press, 434pp.

Griffies, S., A. Gnanadesikan, R. Pacanowski, V. Larichev, J. Dukowicz, and R. Smith, 1998: Isoneutral diffusion in a z-coordinate ocean model. J. Phys. Oceanogr., 28 (5), 805-830.

Griffies, S., and R. Hallberg, 2000: Biharmonic friction with a smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models. Mon. Wea. Rev., 128, 2935–-2946, full-text.

Griffies, S., R. Pacanowski, M. Schmidt, and V. Balaji, 2001: Tracer conservation with an explicit free surface method for z-coordinate ocean models. Mon. Wea. Rev., 129 (5), 1081-1098.

Griffies, S., and Coauthors, 2005: Formulation of an ocean model for global climate simulations. Ocean Sc., 1, 45-79.

Griffies, S., and Coauthors, 2009: Coordinated ocean-ice reference experiments (cores). Ocean Modelling, 26 (1-2), 1-46, full-text.

Guilyardi, E., G. Madec, and L. Terray, 2001: The role of lateral ocean physics in the upper ocean thermal balance of a coupled ocean-atmosphere gcm. Clim. Dyn., 17 (8), 589-599.

Haltiner, G. J., and R. T. Williams, 1980: Numerical prediction and dynamic meteorology. John Wiley & Sons Eds., second edition, 477pp pp.

Haney, R. L., 1991: On the pressure gradient force over steep topography in sigma coordinate ocean models. J. Phys. Oceanogr., 21 (4), 610-619.

Hazeleger, W., and S. S. Drijfhout, 1998: Mode water variability in a model of the subtropical gyre: response to anomalous forcing. J. Phys. Oceanogr., 28, 266-288.

Hazeleger, W., and S. S. Drijfhout, 1999: Stochastically forced mode water variability. J. Phys. Oceanogr., 29, 1772-1786.

Hazeleger, W., and S. S. Drijfhout, 2000a: Eddy subduction in a model of the subtropical gyre. J. Phys. Oceanogr., 30, 677-695.

Hazeleger, W., and S. S. Drijfhout, 2000b: A model study on internally generated variability in subtropical mode water formation. J. Geophys. Res, 105, 13,965-13,979.

He, Y., and C. H. Q. Ding, 2001: Using accurate arithmetics to improve numerical reproducibility and stability in parallel applications. J. Supercomputing., 18, 259-277.

Hellerman, S., and M. Rosenstein, 1983: Normal monthly wind stress over the world ocean with error estimates. J. Phys. Oceanogr., 13, 1093-1104.

Hirt, C. W., A. A. Amsden, and J. L. Cook, 1974: An arbitrary lagrangian-eulerian computing method for all flow speeds. J. Comput. Phys., 14, 227-253.

Hofmeister, R., H. Burchard, and J.-M. Beckers, 2009: Non-uniform adaptive vertical grids for 3d numerical ocean models. Ocean Modelling, 33, 70-86, full-text.

Holland, D., and A. Jenkins, 1999: Modeling thermodynamic ice-ocean interactions at the base of an ice shelf. J. Phys. Oceanogr., 29, 1787-1800.

Holloway, G., 1986: A shelf wave/topographic pump drives mean coastal circulation (part i). Ocean Modelling, 68.

Holloway, G., 1992: Representing topographic stress for large-scale ocean models. J. Phys. Oceanogr., 22, 1033-1046.

Holloway, G., and Z. Wang, 2009: Representing eddy stress in an arctic ocean model. J. Geophys. Res, full-text.

Hunke, E., and W. Lipscomb, 2008: Cice: the los alamos sea ice model documentation and software user's manual, version 4.0. Tech. rep., Los Alamos National Laboratory, N.M.

Hunter, J. R., 2006: Specification for test models of ice shelf cavities. Tech. rep., Antarctic Climate & Ecosystems Cooperative Research Centre Private Bag 80, Hobart, Tasmania 7001.

IOC, SCOR, and IAPSO, 2010: The international thermodynamic equation of seawater - 2010: Calculation and use of thermodynamic properties. Tech. rep., Intergovernmental Oceanographic Commission, 196pp pp. URL

Jackson, P. R., and C. R. Rehmann, 2014: Experiments on differential scalar mixing in turbulence in a sheared, stratified flow. J. Phys. Oceanogr., 44 (10), 2661-2680, full-text.

Jenkins, A., 1991: A one-dimensional model of ice shelf-ocean interaction. J. Geophys. Res, 96 (C11), 2298-2312.

Jenkins, A., 2001: The role of meltwater advection in the formulation of conservative boundary conditions at an ice-ocean interface. J. Phys. Oceanogr., 31, 285-296.

Jenkins, A., 2010: observation and parameterization of ablation at the base of ronne ice shelf, antarctica. J. Phys. Oceanogr., 40 (10), 2298-2312.

Jones, P. W., 1998: A user's guide for scrip: A spherical coordinate remapping and interpolation package. version 1.4. Tech. rep., Los Alamos National Laboratory. URL

Kantha, L., and S. Carniel, 2005: Comment on ”generic length-scale equation for geophysical turbulence models” by l. umlauf and h. burchard. J. Mar. Sys., 61, 693-702.

Kantha, L. H., and C. A. Clayson, 1994: An improved mixed layer model for geophysical applications. J. Geophys. Res, 99, 25,235-25,266.

Kasahara, A., 1974: Various vertical coordinate systems used for numerical weather prediction. Mon. Wea. Rev., 102, 509-522.

Killworth, P., D. Stainforth, D. Webb, and S. Paterson, 1991: The development of a free-surface bryan-cox-semtner ocean model. J. Phys. Oceanogr., 21 (9), 1333-1348.

Killworth, P. D., 1989: On the parameterization of deep convection in ocean models. Parameterization of small-scale processes, H. winter workshop, Ed., University of Hawaii at Manoa.

Killworth, P. D., 1992: An equivalent-barotropic mode in the fine resolution antarctic model. J. Phys. Oceanogr., 22, 1379-1387.

Koch-Larrouy, A., M. Lengaigne, P. Terray, G. Madec, and S. Masson, 2010: Tidal mixing in the indonesian seas and its effect on the tropical climate system. Clim. Dyn., 34 (6), 891-904, full-text.

Koch-Larrouy, A., G. Madec, B. Blanke, and R. Molcard, 2008a: Water mass transformation along the indonesian throughflow in an ogcm. Ocean Dyn., 58 (3-4), 289-309, full-text.

Koch-Larrouy, A., G. Madec, P. Bouruet-Aubertot, T. Gerkema, L. Bessieres, and R. Molcard, 2007: Tidal mixing in the indonesian seas and its effect on the tropical climate system. Geophys. Res. Let., 34, L04604, full-text.

Koch-Larrouy, A., G. Madec, D. Iudicone, A. Atmadipoera, and R. Molcard, 2008b: Physical processes contributing to the water mass transformation of the indonesian throughflow. Ocean Dyn., 58 (3-4), 275-288, full-text.

Kolmogorov, A. N., 1942: The equation of turbulent motion in an incompressible fluid. Izv. Akad. Nauk SSSR, Ser. Fiz., 6, 56-58.

Kondo, J., 1975: Air-sea bulk transfer coefficients in diabatic conditions. Boundary-Layer Meteorol, 9, 91-112.

Large, W. G., and S. Yeager, 2004: Diurnal to decadal global forcing for ocean and sea-ice models: the data sets and flux climatologies. NCAR Technical Note, NCAR/TN-460+STR, CGD Division of the National Center for Atmospheric Research.

Lazar, A., 1997: La branche froide de la circulation thermohaline - sensibilité à la diffusion turbulente dans un modèle de circulation générale idéalisée. Ph.D. thesis, Université Pierre et Marie Curie, Paris, France, 200pp.

Lazar, A., G. Madec, and P. Delecluse, 1999: The deep interior downwelling, the veronis effect, and mesoscale tracer transport parameterizations in an ogcm. J. Phys. Oceanogr., 29 (11), 2945-2961.

Le Sommer, J., T. Penduff, S. Theetten, G. Madec, and B. Barnier, 2009: How momentum advection schemes influence current-topography interactions at eddy permitting resolution. Ocean Modelling, 29 (1), 1-14, full-text.

Leclair, M., 2010: introduction d'une coordonnée verticale arbitrairement lagrangienne eulérienne dans le code nemo, 180pp. Ph.D. thesis, Université Pierre and Marie Curie.

Leclair, M., and G. Madec, 2009: A conservative leap-frog time stepping method. Ocean Modelling, 30 (2-3), 88-94, full-text.

Leclair, M., and G. Madec, 2011: $ \tilde{z}$-coordinate, an arbitrary lagrangian-eulerian coordinate separating high and low frequency. Ocean Modelling, 37, 139-152, full-text.

Lemarié, F., L. Debreu, J. Demange, G. Madec, J. Molines, and M. Honnorat, 2015: Stability constraints for oceanic numerical models: Implications for the formulation of time and space discretizations. Ocean Modelling, 92, 124-148, full-text.

Lengaigne, M., G. Madec, G. Alory, and C. Menkes, 2003: Sensitivity of the tropical pacific ocean to isopycnal diffusion on tracer and dynamics. J. Geophys. Res, 108 (C11), 3345, full-text.

Lengaigne, M., C. Menkes, O. Aumont, T. Gorgues, L. Bopp, and J.-M. A. G. Madec, 2007: Bio-physical feedbacks on the tropical pacific climate in a coupled general circulation model. Clim. Dyn., 28, 503-516.

Leonard, B. P., 1979: A stable and accurate convective modelling procedure based on quadratic upstream interpolation. Computer Methods in Applied Mechanics and Engineering, 19, 59-98.

Leonard, B. P., 1991: The ultimate conservative difference scheme applied to unsteady one-dimensional advection. Computer Methods in Applied Mechanics and Engineering, 17-74.

Lermusiaux, P. F. J., 2001: Evolving the subspace of three-dimensional miltiscale ocean variability: Massachusetts bay. J. Mar. Sys., 29, 385-422.

Levier, B., A.-M. Tréguier, G. Madec, and V. Garnier, 2007: Free surface and variable volume in the nemo code. Tech. rep., MERSEA MERSEA IP report WP09-CNRS-STR-03-1A, 47pp, available on the NEMO web site.

Lévy, M., A. Estubier, and G. Madec, 2001: Choice of an advection scheme for biogeochemical models. Geophys. Res. Let., 28.

Lévy, M., P. Klein, A.-M. Tréguier, D. Iovino, G. Madec, S. Masson, and T. Takahashi, 2010: Impacts of sub-mesoscale physics on idealized gyres. Ocean Modelling, 34 (1-2), full-text.

Li, M., and C. Garrett, 1993: Cell merging and the jet/downwelling ratio in langmuir circulation. J. Mar. Res., 51, 737-769.

Losch, M., 2008: Modeling ice shelf cavities in a z coordinate ocean general circulation model. J. Geophys. Res, 113 (C13).

Lott, F., G. Madec, and J. Verron, 1990: Topographic experiments in an ocean general circulation model. Ocean Modelling, 88, 1-4.

Madec, G., 1990: La formation d'eau profonde et son impact sur la circulation régionale en méditerranée occidentale - une approche numérique. Ph.D. thesis, Université Pierre et Marie Curie, Paris, France, 194pp.

Madec, G., M. Chartier, and M. Crépon, 1991a: Effect of thermohaline forcing variability on deep water formation in the northwestern mediterranean sea - a high resulution three-dimensional study. Dyn. Atmos. Ocean, 15, 301-332.

Madec, G., M. Chartier, P. Delecluse, and M. Crépon, 1991b: A three-dimensional numerical study of deep water formation in the northwestern mediterranean sea . J. Phys. Oceanogr., 21, 1349-1371.

Madec, G., and M. Crépon, 1991: Deep convection and deep water formation in the oceans, chap. Thermohaline-driven deep water formation in the Northwestern Mediterranean Sea, 241-265. Elsevier Oceanographic Series, P.C. Chu and J.C. Gascard (Eds.).

Madec, G., and P. Delecluse, 1997: The opa/arpege and opa/lmd global ocean-atmosphere coupled model. Int. WOCE Newsletter, 26, 12-15.

Madec, G., P. Delecluse, M. Imbard, and C. Levy, 1998: Opa 8 ocean general circulation model - reference manual. Tech. rep., LODYC/IPSL Note 11.

Madec, G., and M. Imbard, 1996: A global ocean mesh to overcome the north pole singularity. Clim. Dyn., 12, 381-388.

Madec, G., F. Lott, P. Delecluse, and M. Crépon, 1996: Large-scale preconditioning of deep-water formation in the northwestern mediterranean sea. J. Phys. Oceanogr., 26 (8), 1393-1408.

Madec, G., C. Rahier, and M. Chartier, 1988: A comparison of two-dimensional elliptic solvers for the streamfunction in a multilevel ogcm. Ocean Modelling, 78, 1-6.

Maggiore, A., M. Zavatarelli, M. G. Angelucci, and N. Pinardi, 1998: Surface heat and water fluxes in the adriatic sea: seasonal and interannual variability. Phys Chem Earth, 23, 561-567.

Maltrud, M., and G. Holloway, 2008: Implementing biharmonic neptune in a global eddying ocean model. Ocean Modelling, 21, 22-34.

Maltrud, M. E., R. D. Smith, A. J. Semtner, and R. C. Malone, 1998: Global eddy-resolving ocean simulations driven by 1985-1995 atmospheric winds. J. Geophys. Res, 103 (C13), 30,825-30,854.

Marsaleix, P., F. Auclair, J. W. Floor, M. J. Herrmann, C. Estournel, I. Pairaud, and C. Ulses, 2008: Energy conservation issues in sigma-coordinate free-surface ocean models. Ocean Modelling, 20 (1), 61-89, full-text.

Marsh, R., and Coauthors, 2015: Nemo-icb (v1.0): interactive icebergs in the nemo ocean model globally configured at eddy-permitting resolution. Geoscientific Model Development, 8 (5), 1547-1562, full-text.

Marti, O., 1992: Etude de l'océan mondial : modélisation de la circulation et du transport de traceurs anthropogéniques. Ph.D. thesis, Université Pierre et Marie Curie, Paris, France, 201pp.

Marti, O., G. Madec, and P. Delecluse, 1992: Comment on "net diffusivity in ocean general circulation models with nonuniform grids" by f. l. yin and i. y. fung. J. Geophys. Res, 97, 12,763-12,766.

Martin, T., and A. Adcroft, 2010: Parameterizing the fresh-water flux from land ice to ocean with interactive icebergs in a coupled climate model. Ocean Modelling, 34 (3-4), 111-124, full-text.

McDougall, T. J., 1987: Neutral surfaces. J. Phys. Oceanogr., 17 (11), 1950-1964.

McDougall, T. J., and J. R. Taylor, 1984: Flux measurements across a finger interface at low values of the stability ratio. J. Mar. Res., 42, 1-14.

Mellor, G., and A. Blumberg, 2004: Wave breaking and ocean surface layer thermal response. J. Phys. Oceanogr., 34 (3), 693-698, full-text.

Mellor, G. L., and T. Yamada, 1982: Development of a turbulence closure model for geophysical fluid problems. Rev. Geophys. Space Phys., 20, 851-875.

Merryfield, W. J., G. Holloway, and A. E. Gargett, 1999: A global ocean model with double-diffusive mixing. J. Phys. Oceanogr., 29 (6), 1124-1142.

Mesinger, F., and A. Arakawa, 1976: Numerical methods used in Atmospheric models. GARP Publication Series No 17.

Morel, A., 1988: Optical modeling of the upper ocean in relation to its biogenous matter content (case i waters). J. Geophys. Res, 93, 10,749-10,768.

Morel, A., and J.-F. Berthon, 1989: Surface pigments, algal biomass profiles, and potential production of the euphotic layer: Relationships reinvestigated in view of remote-sensing applications. Limnol. Oceanogr., 34(8), 1545-1562.

Morel, A., and S. Maritorena, 2001: Bio-optical properties of oceanic waters: a reappraisal. J. Geophys. Res, 106 (C4), 7163-7180.

Murray, R. J., 1996: Explicit generation of orthogonal grids for ocean models. J. Comput. Phys., 126 (2), 251-273.

Oddo, P., M. Adani, N. Pinardi, C. Fratianni, M. Tonani, and D. Pettenuzzo, 2009: A nested atlantic-mediterranean sea general circulation model for operational forecasting. Ocean Sc., 5, 1-13.

Olivier, F., 2001: Etude de l'activité biologique et de la circulation océanique dans un jet géostrophique: le front alméria-oran. Ph.D. thesis, Université Pierre et Marie Curie, Paris, France.

Osborn, T., 1980: Estimates of the local rate of vertical diffusion from dissipation measurements. J. Phys. Oceanogr., 10, 83-89.

Pacanowski, R., and S. Philander, 1981: Parameterization of vertical mixing in numerical models of tropical oceans. J. Phys. Oceanogr., 11 (11), 1443-1451.

Pacanowski, R. C., and A. Gnanadesikan, 1998: Transient response in a z-level ocean model that resolves topography with partial-cells. Mon. Wea. Rev., 126, 3248-3270.

Paulson, C. A., and J. J. Simpson, 1977: Irradiance measurements in the upper ocean. J. Phys. Oceanogr., 7 (6), 952-956.

Payne, R. E., 1972: Albedo of the sea surface. J. Atmos. Sc., 29, 959-970.

Penduff, T., J. L. Sommer, B. Barnier, A. Treguier, J. Molines, and G. Madec, 2007: Influence of numerical schemes on current-topography interactions in 1/4$ ^{\circ }$ global ocean simulations. Ocean Sc., 3, 509-524.

Redi, M. H., 1982: Oceanic isopycnal mixing by coordinate rotation. J. Phys. Oceanogr., 13, 1154-1158.

Reed, R. K., 1977: On estimating insolation over the ocean. J. Phys. Oceanogr., 1, 874-971.

Reverdin, G., P. Delecluse, C. Lévy, P. Andrich, A. Morlière, and J. M. Verstraete, 1991: The near surface tropical atlantic in 1982-1984 : results from a numerical simulation and a data analysis. Prog. Oceangr., 27, 273-340.

Richtmyer, R. D., and K. W. Morton, 1967: Difference methods for initial-value problems. Interscience Publisher, Second Edition, 405pp pp.

Robert, A. J., 1966: The integration of a low order spectral form of the primitive meteorological equations. J. Met. Soc. Japan, 44 (2).

Rodgers, K. B., and Coauthors, 2014: Strong sensitivity of southern ocean carbon uptake and nutrient cycling to wind stirring. Biogeosciences, 11 (15), 4077-4098, full-text.

Rodi, W., 1987: Examples of calculation methods for flow and mixing in stratified fluids. J. Geophys. Res, 92 (C5), 5305-5328.

Roquet, F., G. Madec, L. Brodeau, and J. Nycander, 2015a: Defining a simplified yet realistic equation of state for seawater. J. Phys. Oceanogr., 45, 2564-2579, full-text.

Roquet, F., G. Madec, T. McDougall, and P. Barker, 2015b: Accurate polynomial expressions for the density and specific volume of seawater using the teos-10 standard. Ocean Modelling, 90, 29-43, full-text.

Roullet, G., and G. Madec, 2000: salt conservation, free surface, and varying levels: a new formulation for ocean general circulation models. J. Geophys. Res, 105, 23,927-23,942.

Rousset, C., and Coauthors, 2015: The louvain-la-neuve sea-ice model lim3.6: Global and regional capabilities. Geoscientific Model Development, 8, 2991-3005, full-text.

Sarmiento, J. L., and K. Bryan, 1982: Ocean transport model for the north atlantic. J. Geophys. Res, 87, 394-409.

Shchepetkin, A. F., and J. C. McWilliams, 2005: The regional oceanic modeling system (roms) - a split-explicit, free-surface, topography-following-coordinate oceanic modelr. Ocean Modelling, 9 (4), 347-404.

Shchepetkin, A. F., and J. C. McWilliams, 2008: Handbook of Numerical Analysis, Vol. XIV: Computational Methods for the Ocean and the Atmosphere, pp 121-183. P. G. Ciarlet, editor, R. Temam and J. Tribbia, guest eds., Elsevier Science, 784 pp.

Shchepetkin, A. F., and J. J. O'Brien, 1996: A physically consistent formulation of lateral friction in shallow-water equation ocean models. Mon. Wea. Rev., 124 (6), 1285-1300.

Siddorn, J., and R. Furner, 2012: An analytical stretching function that combines the best attributes of geopotential and terrain-following vertical coordinates. Ocean Modelling, submitted.

Simmons, H. L., S. R. Jayne, L. C. St. Laurent, and A. J. Weaver, 2004: Tidally driven mixing in a numerical model of the ocean general circulation. Ocean Modelling, 245-263.

Smagorinsky, J., 1993: Large Eddy Simulation of Complex Engineering and Geophysical Flows, chap. Some historical remarks on the use of non-linear viscosities, 3-36. Cambridge University Press, B. Galperin and S. A. Orszag (eds.).

Song, Y., and D. Haidvogel, 1994: A semi-implicit ocean circulation model using a generalized topography-following coordinate system. J. Comput. Phys., 115 (1), 228-244.

Song, Y. T., 1998: A general pressure gradient formulation for ocean models. part i: Scheme design and diagnostic analysis. Mon. Wea. Rev., 126 (12), 3213-3230.

St. Laurent, L., and J. D. Nash, 2004: An examination of the radiative and dissipative properties of deep ocean internal tides. Deep-Sea Res., II (51), 3029-3042, full-text.

St. Laurent, L., H. Simmons, and S. Jayne, 2002: Estimating tidally driven mixing in the deep ocean. Geophys. Res. Let., 29, 2106, full-text.

Stacey, M. W., 1999: Simulations of the wind-forced near-surface circulation in knight inlet: A parameterization of the roughness length. J. Phys. Oceanogr., 29, 1363-1367.

Steele, M., R. Morley, and W. Ermold, 2001: Phc- a global ocean hydrography with a high-quality arctic ocean. J. Climate, 14 (9), 2079-2087.

Stein, C. A., and S. Stein, 1992: A model for the global variation in oceanic depth and heat flow with lithospheric age. Nature, 359, 123-129.

Talagrand, O., 1972: On the damping of high-frequency motions in four-dimensional assimilation of meteorological data. J. Atmos. Sc., 29, 1571-1574.

Tonani, M., N. Pinardi, S. Dobricic, I. Pujol, and C. Fratianni, 2008: A high-resolution free-surface model of the mediterranean sea. Ocean Sc., 4, 1-14.

Tréguier, A., 1992: Kinetic energy analysis of an eddy resolving, primitive equation north atlantic model. J. Geophys. Res, 97, 687-701.

Tréguier, A.-M., J. Dukowicz, and K. Bryan, 1996: Properties of nonuniform grids used in ocean general circulation models. J. Geophys. Res, 101, 20,877-20,881.

Tréguier, A. M., I. M. Held, and V. D. Larichev, 1997: Parameterization of quasigeostrophic eddies in primitive equation ocean models. J. Phys. Oceanogr., 27 (4), 567-580.

Umlauf, L., and H. Burchard, 2003: A generic length-scale equation for geophysical turbulence models. J. Mar. Sys., 61 (2), 235-265.

Umlauf, L., and H. Burchard, 2005: Second-order turbulence closure models for geophysical boundary layers. a review of recent work. J. Mar. Sys., 25, 795-827.

UNESCO, 1983: Algorithms for computation of fundamental property of sea water. Techn. Paper in Mar. Sci, 44, UNESCO.

Valcke, S., 2006: Oasis3 user guide (prism_2-5). Tech. rep., PRISM Support Initiative Report No 3, CERFACS, Toulouse, France, 64pp pp.

Vallis, G. K., 2006: Atmospheric and Oceanic Fluid Dynamics. Cambridge University Press, Cambridge, U.K., 745 pp.

Vancoppenolle, M., T. Fichefet, and H. Goosse, 2009a: Simulating the mass balance and salinity of arctic and antarctic sea ice. 2. importance of sea ice salinity variations. Ocean Modelling, 27, 54-69.

Vancoppenolle, M., T. Fichefet, H. Goosse, S. Bouillon, G. Madec, and M. A. M. Maqueda, 2009b: Simulating the mass balance and salinity of arctic and antarctic sea ice. 1. model description and validation. Ocean Modelling, 27, 33-53, full-text.

Warner, J. C., C. R. Sherwood, H. G. Arango, and R. P. Signell, 2005: Performance of four turbulence closure models implemented using a generic length scale method. Ocean Modelling, 8, 81-113, full-text.

Weatherly, G. L., 1984: An estimate of bottom frictional dissipation by gulf stream fluctuations. J. Mar. Res., 42 (2), 289-301.

Weaver, A. J., and M. Eby, 1997: On the numerical implementation of advection schemes for use in conjuction with various mixing parameterizations in the gfdl ocean model. J. Phys. Oceanogr., 27.

Webb, D. J., B. A. de Cuevas, and C. S. Richmond, 1998: Improved advection schemes for ocean models. J. Atmos. Ocean Tech., 15 (5), 1171-1187.

White, L., A. Adcroft, and R. Hallberg, 2009: High-order regridding-remapping schemes for continuous isopycnal and generalized coordinates in ocean models. J. Climate, 228, 8665-8692.

Wilcox, D. C., 1988: Reassessment of the scale-determining equation for advanced turbulence models. AIAA journal, 26 (11), 1299-1310.

Willebrand, J., and Coauthors, 2001: Circulation characteristics in three eddy-permitting models of the north atlantic. Prog. Oceangr., 48 (2), 123-161.

Zalesak, S. T., 1979: Fully multidimensional flux corrected transport algorithms for fluids. J. Comput. Phys., 31.

Zhang, R.-H., and M. Endoh, 1992: A free surface general circulation model for the tropical pacific ocean. J. Geophys. Res, 97, 11,237-11,255.

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