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@STRING{AP = {Academic Press}}

@STRING{AREPS = {Annual Review of Earth Planetary Science}}

@STRING{ARFM = {Annual Review of Fluid Mechanics}}

@STRING{ASL = {Atmospheric Science Letters}}

@STRING{AW = {Addison-Wesley}}

@STRING{CD = {Clim. Dyn.}}

@STRING{CP = {Clarendon Press}}

@STRING{CUP = {Cambridge University Press}}

@STRING{D = {Dover Publications}}

@STRING{DAO = {Dyn. Atmos. Ocean}}

@STRING{DSR = {Deep-Sea Res.}}

@STRING{E = {Eyrolles}}

@STRING{GRL = {Geophys. Res. Let.}}

@STRING{I = {Interscience}}

@STRING{JAOT = {J. Atmos. Ocean Tech.}}

@STRING{JAS = {J. Atmos. Sc.}}

@STRING{JC = {J. Climate}}

@STRING{JCP = {J. Comput. Phys.}}

@STRING{JGR = {J. Geophys. Res}}

@STRING{JHUP = {The Johns Hopkins University Press}}

@STRING{JMR = {J. Mar. Res.}}

@STRING{JMS = {J. Mar. Sys.}}

@STRING{JMSJ = {J. Met. Soc. Japan}}

@STRING{JPO = {J. Phys. Oceanogr.}}

@STRING{JWS = {John Wiley and Sons}}

@STRING{M = {Macmillan}}

@STRING{MGH = {McGraw-Hill}}

@STRING{MWR = {Mon. Wea. Rev.}}

@STRING{Nature = {Nat.}}

@STRING{NH = {North-Holland}}

@STRING{Ocean = {Oceanology}}

@STRING{OS = {Ocean Science}}

@STRING{OUP = {Oxford University Press}}

@STRING{PH = {Prentice-Hall}}

@STRING{PO = {Prog. Oceangr.}}

@STRING{PP = {Pergamon Press}}

@STRING{PRSL = {Proceedings of the Royal Society of London}}

@STRING{QJRMS = {Quart J Roy Meteor Soc}}

@STRING{Recherche = {La Recherche}}

@STRING{Science = {Science}}

@STRING{SV = {Springer-Verlag}}

@STRING{Tellus = {Tellus}}

@ARTICLE{Arakawa1966,
  author = {A. Arakawa},
  title = {Computational design for long term numerical integration of the equations
   of fluid motion, two-dimensional incompressible flow, Part. I.},
  journal = JCP,
  year = {1966},
  volume = {I},
  pages = {119-149},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Arakawa1990,
  author = {A. Arakawa and Y.-J. G. Hsu},
  title = {Energy Conserving and Potential-Enstrophy Dissipating Schemes for
   the Shallow Water Equations},
  journal = MWR,
  year = {1990},
  volume = {118},
  pages = {1960--1969
   
   },
  number = {10},
  abstract = {To incorporate potential enstrophy dissipation into discrete shallow
   water equations with no or arbitrarily small energy dissipation,
   a family of finite-difference schemes have been derived with which
   potential enstrophy is guaranteed to decrease while energy is conserved
   (when the mass flux is nondivergent and time is continuous). Among
   this family of schemes, there is a member that minimizes the spurious
   impact of infinite potential vorticities associated with infinitesimal
   fluid depth. The scheme is, therefore, useful for problems in which
   the free surface may intersect with the lower boundary.},
  date = {October 01, 1990},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Arakawa1981,
  author = {Arakawa, Akio and Lamb, Vivian R.},
  title = {A Potential Enstrophy and Energy Conserving Scheme for the Shallow
   Water Equations},
  journal = MWR,
  year = {1981},
  volume = {109},
  pages = {18--36
   
   },
  number = {1},
  abstract = {To improve the simulation of nonlinear aspects of the flow over steep
   topography, a potential enstrophy and energy conserving scheme for
   the shallow water equations is derived. It is pointed out that a
   family of schemes can conserve total energy for general flow and
   potential enstrophy for flow with no mass flux divergence. The newly
   derived scheme is a unique member of this family, that conserves
   both potential enstrophy and energy for general flow. Comparison
   by means of numerical experiment with a scheme that conserves (potential)
   enstrophy for purely horizontal nondivergent flow demonstrated the
   considerable superiority of the newly derived potential enstrophy
   and energy conserving scheme, not only in suppressing a spurious
   energy cascade but also in determining the overall flow regime. The
   potential enstrophy and energy conserving scheme for a spherical
   grid is also presented.},
  date = {January 01, 1981},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{ASSELIN1972,
  author = {R. Asselin},
  title = {Frequency Filter for Time Integrations},
  journal = MWR,
  year = {1972},
  volume = {100},
  pages = {487-490},
  number = {6},
  abstract = {A simple filter for controlling high-frequency computational and physical
   modes arising in time integrations is proposed. A linear analysis
   of the filter with leapfrog, implicit, and semi-implicit, differences
   is made. The filter very quickly removes the computational mode and
   is also very useful in damping high-frequency physical waves. The
   stability of the leapfrog scheme is adversely affected when a large
   filter parameter is used, but the analysis shows that the use of
   centered differences with frequency filter is still more advantageous
   than the use of the Euler-backward method. An example of the use
   of the filter in an actual forecast with the meteorological equations
   is shown.},
  date = {June 01, 1972},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Beckmann1998,
  author = {A. Beckmann},
  title = {The representation of bottom boundary layer processes in numerical
   ocean circulation models.},
  journal = {Ocean modelling and parameterization, E. P. Chassignet and J. Verron
   (eds.), NATO Science Series, Kluwer Academic Publishers},
  year = {1998},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{BeckDos1998,
  author = {A. Beckmann and R. D\"{o}scher},
  title = {A method for improved representation of dense water spreading over
   topography in geopotential-coordinate models},
  journal = JPO,
  year = {1998},
  volume = {27},
  pages = {581-591},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Beckmann1993,
  author = {A. Beckmann and D. B. Haidvogel},
  title = {Numerical Simulation of Flow around a Tall Isolated Seamount. Part
   I - Problem Formulation and Model Accuracy},
  journal = {Journal of Physical Oceanography},
  year = {1993},
  volume = {23},
  pages = {1736--1753
   
   },
  number = {8},
  abstract = {A sigma coordinate ocean circulation model is employed to study flow
   trapped to a tall seamount in a periodic f-plane channel. In Part
   I, errors arising from the pressure gradient formulation in the steep
   topography/strong stratification limit are examined. To illustrate
   the error properties, a linearized adiabatic version of the model
   is considered, both with and without forcing, and starting from a
   resting state with level isopycnals. The systematic discretization
   errors from the horizontal pressure gradient terms are shown analytically
   to increase with steeper topography (relative to a fixed horizontal
   grid) and for stronger stratification (as measured by the Burger
   number). For an initially quiescent unforced ocean, the pressure
   gradient errors produce a spurious oscillating current that, at the
   end of 10 days, is approximately 1 cm s−1 in amplitude. The
   period of the spurious oscillation (about 0.5 days) is shown to be
   a consequence of the particular form of the pressure gradient terms
   in the sigma coordinate system. With the addition of an alongchannel
   diurnal forcing, resonantly generated seamount-trapped waves are
   observed to form. Error levels in these solutions are less than those
   in the unforced cases; spurious time-mean currents are several orders
   of magnitude less in amplitude than the resonant propagating waves.
   However, numerical instability is encountered in a wider range of
   parameter space. The properties of these resonantly generated waves
   is explored in detail in Part II of this study. Several new formulations
   of the pressure gradient terms are tested. Two of the formulations—constructed
   to have additional conservation properties relative to the traditional
   form of the pressure gradient terms (conservation of JEBAR and conservation
   of energy)—are found to have error properties generally similar
   to those of the traditional formulation. A corrected gradient algorithm,
   based upon vertical interpolation of the pressure field, has a dramatically
   reduced error level but a much more restrictive range of stable behavior.},
  date = {August 01, 1993},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Blanke1993,
  author = {B. Blanke and P. Delecluse},
  title = {Low frequency variability of the tropical Atlantic ocean simulated
   by a general circulation model with mixed layer physics},
  journal = JPO,
  year = {1993},
  volume = {23},
  pages = {1363-1388}
}

@ARTICLE{blanketal97,
  author = {B. Blanke and J. D. Neelin and D. Gutzler},
  title = {Estimating the effect of stochastic wind forcing on ENSO irregularity},
  journal = JC,
  year = {1997},
  volume = {10},
  pages = {1473-1486},
  abstract = {One open question in El Nin˜o–Southern Oscillation (ENSO) simulation
   and predictability is the role of random
   
   forcing by atmospheric variability with short correlation times, on
   coupled variability with interannual timescales.
   
   The discussion of this question requires a quantitative assessment
   of the stochastic component of the wind stress
   
   forcing. Self-consistent estimates of this noise (the stochastic forcing)
   can be made quite naturally in an empirical
   
   atmospheric model that uses a statistical estimate of the relationship
   between sea surface temperature (SST) and
   
   wind stress anomaly patterns as the deterministic feedback between
   the ocean and the atmosphere. The authors
   
   use such an empirical model as the atmospheric component of a hybrid
   coupled model, coupled to the GFDL
   
   ocean general circulation model. The authors define as residual the
   fraction of the Florida State University wind
   
   stress not explained by the empirical atmosphere run from observed
   SST, and a noise product is constructed by
   
   random picks among monthly maps of this residual.
   
   The impact of included or excluded noise is assessed with several
   ensembles of simulations. The model is
   
   run in coupled regimes where, in the absence of noise, it is perfectly
   periodic: in the presence of prescribed
   
   seasonal variability, the model is strongly frequency locked on a
   2-yr period; in annual average conditions it
   
   has a somewhat longer inherent ENSO period (30 months). Addition of
   noise brings an irregular behavior that
   
   is considerably richer in spatial patterns as well as in temporal
   structures. The broadening of the model ENSO
   
   spectral peak is roughly comparable to observed. The tendency to frequency
   lock to subharmonic resonances
   
   of the seasonal cycle tends to increase the broadening and to emphasize
   lower frequencies. An inclination to
   
   phase lock to preferred seasons persists even in the presence of noise-induced
   irregularity. Natural uncoupled
   
   atmospheric variability is thus a strong candidate for explaining
   the observed aperiodicity in ENSO time series.
   
   Model–model hindcast experiments also suggest the importance of atmospheric
   noise in setting limits to ENSO
   
   predictability.},
  pdf = {Blanke_etal_JC97.pdf}
}

@ARTICLE{Bougeault1989,
  author = {P. Bougeault and P. Lacarrere},
  title = {Parameterization of Orography-Induced Turbulence in a Mesobeta--Scale
   Model},
  journal = MWR,
  year = {1989},
  volume = {117},
  pages = {1872-1890},
  number = {8},
  abstract = {The possibility of extending existing techniques for turbulence parameterization
   in the planetary boundary layer to attitude, orography-induced turbulence
   events is examined. Starting from a well-tested scheme, we show that
   it is possible to generalize the specification method of the length
   scales, with no deterioration of the scheme performance in the boundary
   layer. The new scheme is implemented in a two-dimensional version
   of a limited-area, numerical model used for the simulation of mesobeta-scale
   atmospheric flows. Three well-known cases of orographically induced
   turbulence are studied. The comparison with observations and former
   studies shows a satisfactory behavior of the new scheme.},
  date = {August 01, 1989},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Brown1978,
  author = {J. A. Brown and K. A. Campana},
  title = {An Economical Time-Differencing System for Numerical Weather Prediction},
  journal = MWR,
  year = {1978},
  volume = {106},
  pages = {1125-1136},
  number = {8},
  month = aug,
  abstract = {A simple method for integrating the primitive equations is presented
   which allows for a timestep increment up to twice that of the conventional
   leapfrog scheme. It consists of a time-averaging operator, which
   incorporates three consecutive time levels, on the pressure gradient
   terms in the equations of motion. An attractive feature of the method
   is its case in programming, since the resulting finite-difference
   equations can he solved explicitly.Presented here are linear analyses
   of the method applied to the barotropic and two-layer baroclinic
   gravity waves. Also presented is an analysis of the method with a
   time-damping device incorporated, which is an alternative in controlling
   linearly amplifying computational modes.},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Bryan1997,
  author = {K. Bryan},
  title = {A Numerical Method for the Study of the Circulation of the World
   Ocean},
  journal = JCP,
  year = {1997},
  volume = {135, 2},
  owner = {gm},
  timestamp = {2007.08.10}
}

@ARTICLE{Bryan1984,
  author = {K. Bryan},
  title = {Accelerating the convergence to equilibrium of ocean-climate models},
  journal = JPO,
  year = {1984},
  volume = {14},
  owner = {gm},
  timestamp = {2007.08.10}
}

@ARTICLE{Bryden1973,
  author = {H. L. Bryden},
  title = {New polynomials for thermal expansion, adiabatic temperature gradient
   
   and potential temperature of sea water},
  journal = DSR,
  year = {1973},
  volume = {20},
  pages = {401-408},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Campin2004,
  author = {J.-M. Campin and A. Adcroft and C. Hill and J. Marshall},
  title = {Conservation of properties in a free-surface model},
  journal = {Ocean Modelling},
  year = {2004},
  volume = {6, 3-4},
  pages = {221-244},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Cox1987,
  author = {M. Cox},
  title = {Isopycnal diffusion in a z-coordinate ocean model},
  journal = {Ocean Modelling},
  year = {1987},
  volume = {74},
  pages = {1-5},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Dukowicz1994,
  author = {J. K. Dukowicz and R. D. Smith},
  title = {Implicit free-surface method for the Bryan-Cox-Semtner ocean model},
  journal = JGR,
  year = {1994},
  volume = {99},
  pages = {7991-8014},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Dutay.J.C2004,
  author = {J. -C. Dutay and P. J. -Baptiste and J. -M. Campin and A. Ishida
   and E. M. -Reimer and R. J. Matear and A. Mouchet and I. J. Totterdell
   and Y. Yamanaka and K. Rodgers and G. Madec and J.C. Orr},
  title = {Evaluation of OCMIP-2 ocean models’ deep circulation
   
   with mantle helium-3},
  journal = {Journal of Marine Systems},
  year = {2004},
  pages = {1-22},
  abstract = {We compare simulations of the injection of mantle helium-3 into the
   deep ocean from six global coarse resolution models which participated
   in the Ocean Carbon Model Intercomparison Project (OCMIP). We also
   discuss the results of a study carried out with one of the models,
   which examines the effect of the subgrid-scale mixing parameterization.
   These sensitivity tests provide useful information to interpret the
   differences among the OCMIP models and between model simulations
   and the data.
   
   We find that the OCMIP models, which parameterize subgrid-scale mixing
   using an eddy-induced velocity, tend to
   
   underestimate the ventilation of the deep ocean, based on diagnostics
   with d3He. In these models, this parameterization is implemented
   with a constant thickness diffusivity coefficient. In future simulations,
   we recommend using such a parameterization with spatially and temporally
   varying coefficients in order to moderate its effect on stratification.
   
   The performance of the models with regard to the formation of AABW
   confirms the conclusion from a previous evaluation with CFC-11. Models
   coupled with a sea-ice model produce a substantial bottom water formation
   in the Southern Ocean that tends to overestimate AABW ventilation,
   while models that are not coupled with a sea-ice model systematically
   underestimate the formation of AABW.
   
   We also analyze specific features of the deep 3He distribution (3He
   plumes) that are particularly well depicted in the data and which
   put severe constraints on the deep circulation. We show that all
   the models fail to reproduce a correct propagation of these plumes
   in the deep ocean. The resolution of the models may be too coarse
   to reproduce the strong and narrow currents in the deep ocean, and
   the models do not incorporate the geothermal heating that may also
   contribute to the generation of these currents. We also use the context
   of OCMIP-2 to explore the potential of mantle helium-3 as a tool
   to compare and evaluate modeled deep-ocean circulations. Although
   the source function of mantle helium is known with a rather large
   uncertainty, we find that the parameterization used for the injection
   of mantle helium-3 is sufficient to generate realistic results, even
   in the Atlantic Ocean where a previous pioneering study [J. Geophys.
   Res. 100 (1995) 3829] claimed this parameterization generates
   
   inadequate results. These results are supported by a multi-tracer
   evaluation performed by considering the simulated distributions of
   both helium-3 and natural 14C, and comparing the simulated tracer
   fields with available data.},
  owner = {sandra},
  pdf = {Dutay_etal_OCMIP_JMS04.pdf},
  timestamp = {2006.10.17}
}

@ARTICLE{Eiseman1980,
  author = {P. R. Eiseman and A. P. Stone},
  title = {Conservation lows of fluid dynamics -- A survey},
  journal = {SIAM Review},
  year = {1980},
  volume = {22},
  pages = {12-27},
  owner = {gm},
  timestamp = {2007.08.03}
}

@PHDTHESIS{Farge1987,
  author = {M. Farge},
  title = {Dynamique non lineaire des ondes et des tourbillons dans les equations
   de Saint Venant},
  school = {Doctorat es Mathematiques, Paris VI University, 401 pp.},
  year = {1987},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Farrow1995,
  author = {D. E. Farrow and D. P. Stevens},
  title = {A new tracer advection scheme for Bryan--Cox type ocean general circulation
   models},
  journal = JPO,
  year = {1995},
  volume = {25},
  pages = {1731-1741.},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Fujio1991,
  author = {S. Fujio and N. Imasato},
  title = {Diagnostic calculation for circulation and water mass movement in
   the deep Pacific},
  journal = JGR,
  year = {1991},
  volume = {96},
  pages = {759-774},
  month = jan,
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Gargett1984,
  author = {A. E. Gargett},
  title = {Vertical eddy diffusivity in the ocean interior},
  journal = JMR,
  year = {1984},
  volume = {42},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Gaspar1990,
  author = {P. Gaspar and Y. Gr{\'e}goris and J.-M. Lefevre},
  title = {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 = JGR,
  year = {1990},
  volume = {95(C9)},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Gent1990,
  author = {P. R. Gent and J. C. Mcwilliams},
  title = {Isopycnal Mixing in Ocean Circulation Models},
  journal = JPO,
  year = {1990},
  volume = {20},
  pages = {150-155},
  number = {1},
  abstract = {A subgrid-scale form for mesoscale eddy mixing on isopycnal surfaces
   is proposed for use in non-eddy-resolving ocean circulation models.
   The mixing is applied in isopycnal coordinates to isopycnal layer
   thickness, or inverse density gradient, as well as to passive scalars,
   temperature and salinity. The transformation of these mixing forms
   to physical coordinates is also presented.},
  date = {January 01, 1990},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Gerdes1993a,
  author = {R. Gerdes},
  title = {A primitive equation ocean circulation model using a general vertical
   coordinate transformation 1. Description and testing of the model},
  journal = JGR,
  year = {1993},
  volume = {98},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Gerdes1993b,
  author = {R. Gerdes},
  title = {A primitive equation ocean circulation model using a general vertical
   coordinate transformation 2. Application to an overflow problem},
  journal = JGR,
  year = {1993},
  volume = {98},
  pages = {14703-14726},
  owner = {gm},
  timestamp = {2007.08.03}
}

@BOOK{Gill1982,
  title = {Atmosphere-Ocean Dynamics},
  publisher = {International Geophysics Series, Academic Press, New-York},
  year = {1982},
  author = {A. E. Gill}
}

@ARTICLE{Griffes2005,
  author = {S. M. Griffes and A. Gnanadesikan and K. W. Dixon and J. P. Dunne
   and R. Gerdes and M. J. Harrison and A. Rosati and J. L. Russell
   and B. L. Samuels and M. J. Spelman and M. Winton and R. Zhang},
  title = {Formulation of an ocean model for global climate simulations},
  journal = OS,
  year = {2005},
  pages = {165–246},
  abstract = {This paper summarizes the formulation of the ocean component to the
   Geophysical
   
   Fluid Dynamics Laboratory’s (GFDL) coupled climate model used for
   the 4th IPCC As- Assessment
   
   (AR4) of global climate change. In particular, it reviews elements
   of ocean
   
   sessment climate models and how they are pieced together for use in
   a state-of-the-art coupled 5
   
   model. Novel issues are also highlighted, with particular attention
   given to sensitivity of
   
   the coupled simulation to physical parameterizations and numerical
   methods. Features
   
   of the model described here include the following: (1) tripolar grid
   to resolve the Arctic
   
   Ocean without polar filtering, (2) partial bottom step representation
   of topography to
   
   better represent topographically influenced advective and wave processes,
   (3) more 10
   
   accurate equation of state, (4) three-dimensional flux limited tracer
   advection to reduce
   
   overshoots and undershoots, (5) incorporation of regional climatological
   variability in
   
   shortwave penetration, (6) neutral physics parameterization for representation
   of the
   
   pathways of tracer transport, (7) staggered time stepping for tracer
   conservation and
   
   numerical eciency, (8) anisotropic horizontal viscosities for representation
   of equato- 15
   
   rial currents, (9) parameterization of exchange with marginal seas,
   (10) incorporation
   
   of a free surface that accomodates a dynamic ice model and wave propagation,
   (11)
   
   transport of water across the ocean free surface to eliminate unphysical
   “virtual tracer
   
   flux” methods, (12) parameterization of tidal mixing on continental
   shelves.},
  owner = {sandra},
  pdf = {Griffies_al_OSD05.pdf},
  timestamp = {2007.01.25}
}

@BOOK{Griffies2004,
  title = {Fundamentals of ocean climate models},
  publisher = {Princeton University Press, 434pp},
  year = {2004},
  author = {S. M. Griffies},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Griffies1998,
  author = {S. M. Griffies and A. Gnanadesikan and R. C. Pacanowski and V. D.
   Larichev and J. K. Dukowicz and R. D. Smith},
  title = {Isoneutral Diffusion in a z-Coordinate Ocean Model},
  journal = JPO,
  year = {1998},
  volume = {28},
  pages = {805-830},
  number = {5},
  abstract = {This paper considers the requirements that must be satisfied in order
   to provide a stable and physically based isoneutral tracer diffusion
   scheme in a z-coordinate ocean model. Two properties are emphasized:
   1) downgradient orientation of the diffusive fluxes along the neutral
   directions and 2) zero isoneutral diffusive flux of locally referenced
   potential density. It is shown that the Cox diffusion scheme does
   not respect either of these properties, which provides an explanation
   for the necessity to add a nontrivial background horizontal diffusion
   to that scheme. A new isoneutral diffusion scheme is proposed that
   aims to satisfy the stated properties and is found to require no
   horizontal background diffusion.},
  date = {May 01, 1998},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Griffies2001,
  author = {S. M. Griffies and R. C. Pacanowski and M. Schmidt and V. Balaji},
  title = {Tracer Conservation with an Explicit Free Surface Method for z-Coordinate
   Ocean Models},
  journal = MWR,
  year = {2001},
  volume = {129},
  pages = {1081-1098},
  number = {5},
  abstract = {This paper details a free surface method using an explicit time stepping
   scheme for use in z-coordinate ocean models. One key property that
   makes the method especially suitable for climate simulations is its
   very stable numerical time stepping scheme, which allows for the
   use of a long density time step, as commonly employed with coarse-resolution
   rigid-lid models. Additionally, the effects of the undulating free
   surface height are directly incorporated into the baroclinic momentum
   and tracer equations. The novel issues related to local and global
   tracer conservation when allowing for the top cell to undulate are
   the focus of this work. The method presented here is quasi-conservative
   locally and globally of tracer when the baroclinic and tracer time
   steps are equal. Important issues relevant for using this method
   in regional as well as large-scale climate models are discussed and
   illustrated, and examples of scaling achieved on parallel computers
   provided.},
  date = {May 01, 2001},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Guily2001,
  author = {E. Guilyardi and G. Madec and L. Terray},
  title = {The role of lateral ocean physics in the upper ocean thermal balance
   of a coupled ocean-atmosphere GCM},
  journal = CD,
  year = {2001},
  volume = {17},
  pages = {589-599},
  number = {8},
  pdf = {/home/ericg/TeX/Papers/Published_pdfs/Guilyardi_al_CD01.pdf}
}

@BOOK{Haltiner1980,
  title = {Numerical prediction and dynamic meteorology},
  publisher = {John Wiley {\&} Sons Eds., second edition, 477pp},
  year = {1980},
  author = {G. J. Haltiner and R. T. Williams},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Haney1991,
  author = {R. L. Haney},
  title = {On the Pressure Gradient Force over Steep Topography in Sigma Coordinate
   Ocean Models},
  journal = JPO,
  year = {1991},
  volume = {21},
  pages = {610--619
   
   },
  number = {4},
  abstract = {The error in computing the pressure gradient force near steep topography
   using terms following (σ) coordinates is investigated in an
   ocean model using the family of vertical differencing schemes proposed
   by Arakawa and Suarez. The truncation error is estimated by substituting
   known buoyancy profiles into the finite difference hydrostatic and
   pressure gradient terms. The error due to “hydrostatic inconsistency,”
   which is not simply a space truncation error, is also documented.
   The results show that the pressure gradient error is spread throughout
   the water column, and it is sensitive to the vertical resolution
   and to the placement of the grid points relative to the vertical
   structure of the buoyancy field being modeled. Removing a reference
   state, as suggested for the atmosphere by Gary, reduces the truncation
   error associated with the two lowest vertical modes by a factor of
   2 to 3. As an example, the error in computing the pressure gradient
   using a standard 10-level primitive equation model applied to buoyancy
   profiles and topographic slopes typical of the California Current
   region corresponds to a false geostrophic current of the order of
   10–12 cm s−1. The analogous error in a hydrostatically
   consistent 30-level model with the reference state removed is about
   an order of magnitude smaller.},
  date = {April 01, 1991},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Hsu1990,
  author = {Hsu, Yueh-Jiuan G. and Arakawa, Akio},
  title = {Numerical Modeling of the Atmosphere with an Isentropic Vertical
   Coordinate},
  journal = MWR,
  year = {1990},
  volume = {118},
  pages = {1933--1959
   
   },
  number = {10},
  abstract = {In constructing a numerical model of the atmosphere, we must choose
   an appropriate vertical coordinate. Among the various possibilities,
   isentropic vertical coordinates such as the θ-coordinate seem
   to have the greatest potential, in spite of the technical difficulties
   in treating the intersections of coordinate surfaces with the lower
   boundary. The purpose of this paper is to describe the θ-coordinate
   model we have developed and to demonstrate its potential through
   simulating the nonlinear evolution of a baroclinic wave.In the model
   we have developed, vertical discretization maintains important integral
   constraints, such as conservation of the angular momentum and total
   energy. In treating the intersections of coordinate surfaces with
   the lower boundary, we have followed the massless-layer approach
   in which the intersecting coordinate surfaces are extended along
   the boundary by introducing massless layers. Although this approach
   formally eliminates the intersection problem, it raises other computational
   problems. Horizontal discretization of the continuity and momentum
   equations in the model has been carefully designed to overcome these
   problems.Selected results from a 10-day integration with the 25-layer,
   β-plane version of the model are presented. It seems that the
   model can simulate the nonlinear evolution of a baroclinic wave and
   associated dynamical processes without major computational difficulties.},
  date = {October 01, 1990},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{JackMcD1995,
  author = {D. R. Jackett and T. J. McDougall},
  title = {Minimal adjustment of hydrographic data to achieve static stability},
  journal = JAOT,
  year = {1995},
  volume = {12},
  pages = {381-389},
  owner = {gm},
  timestamp = {2007.08.04}
}

@BOOK{Jerlov1968,
  title = {Optical Oceanography},
  publisher = {194pp},
  year = {1968},
  author = {N. G. Jerlov},
  owner = {gm},
  timestamp = {2007.08.04}
}

@INPROCEEDINGS{Killworth1989,
  author = {P. D. Killworth},
  title = {On the parameterization of deep convection in ocean models},
  booktitle = {Parameterization of small-scale processes},
  year = {1989},
  editor = {Hawaiian winter workshop},
  month = {January 17-20},
  organization = {University of Hawaii at Manoa},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Killworth1991,
  author = {Killworth, P. D. and Stainforth, D. and Webb, D. J. and Paterson,
   S. M.},
  title = {The Development of a Free-Surface Bryan-Cox-Semtner Ocean Model},
  journal = JPO,
  year = {1991},
  volume = {21},
  pages = {1333--1348},
  number = {9},
  abstract = {A version of the Bryan–Cox–Semtner numerical ocean general
   circulation model, adapted to include a free surface, is described.
   The model is designed for the following uses: tidal studies
   (a tidal option is explicitly included); assimilation of altimetric
   data (since the surface elevation is now a prognostic variable);
   and in situations where accurate relaxation to obtain the streamfunction
   in the original model is too time consuming. Comparison is made between
   a 300-year run of the original model and the free-surface version,
   using a very coarse North Atlantic calculation as the basis. The
   results are very similar, differing only in the streamfunction over
   topography; this is to be expected, since the treatment of topographic
   torques on the barotropic flow differs because of the nature of the
   modifications.},
  date = {September 01, 1991},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Kolmogorov1942,
  author = {A. N. Kolmogorov},
  title = {The equation of turbulent motion in an incompressible fluid},
  journal = {Izv. Akad. Nauk SSSR, Ser. Fiz.},
  year = {1942},
  volume = {6},
  pages = {56-58},
  owner = {gm},
  timestamp = {2007.08.06}
}

@PHDTHESIS{Levy1996,
  author = {M. L\'{e}vy},
  title = {Mod\'{e}lisation des processus biog\'{e}ochimiques en M\'{e}diterran\'{e}e
   nord-occidentale. Cycle saisonnier et variabilit\'{e} m\'{e}so\'{e}chelle},
  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 207pp},
  year = {1996},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Levy2001,
  author = {M. L\'{e}vy and A. Estubier and G Madec},
  title = {Choice of an advection scheme for biogeochemical models},
  journal = GRL,
  year = {2001},
  volume = {28},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Levy1998,
  author = {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
  title = {The onset of a bloom after deep winter convection in the Northwestern
   Mediterranean Sea: mesoscale 
   
   process study with a primitive equation model},
  journal = JMS,
  year = {1998},
  volume = {16/1-2},
  owner = {gm},
  timestamp = {2007.08.10}
}

@BOOK{LargeYeager2004,
  title = {Diurnal to decadal global forcing for ocean and sea-ice models: the
   data sets and flux climatologies},
  publisher = {NCAR Technical Note, NCAR/TN-460+STR, CGD Division of the National
   Center for Atmospheric Research},
  year = {2004},
  author = {W. Large and S. Yeager},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{large1994,
  author = {W. G. Large and J. C. McWilliams and S. C. Doney},
  title = {Oceanic vertical mixing - a review and a model with a nonlocal boundary
   layer parameterization},
  journal = {Reviews of Geophysics},
  year = {1994},
  volume = {32},
  pages = {363-404},
  doi = {10.1029/94RG01872},
  owner = {gm},
  timestamp = {2007.08.03}
}

@PHDTHESIS{Lazar1997,
  author = {A. Lazar},
  title = {La branche froide de la circulation thermohaline - sensibilit\'{e}
   \`{a} la diffusion turbulente dans un mod\`{e}le de circulation g\'{e}n\'{e}rale
   id\'{e}alis\'{e}e},
  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 200pp},
  year = {1997},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Lazar1999,
  author = {A. Lazar and G. Madec and P. Delecluse},
  title = {The Deep Interior Downwelling, the Veronis Effect, and Mesoscale
   Tracer Transport Parameterizations in an OGCM},
  journal = JPO,
  year = {1999},
  volume = {29},
  pages = {2945-2961},
  number = {11},
  abstract = {Numerous numerical simulations of basin-scale ocean circulation display
   a vast interior downwelling and a companion intense western boundary
   layer upwelling at midlatitude below the thermocline. These features,
   related to the so-called Veronis effect, are poorly rationalized
   and depart strongly from the classical vision of the deep circulation
   where upwelling is considered to occur in the interior. Furthermore,
   they significantly alter results of ocean general circulation models
   (OGCMs) using horizontal Laplacian diffusion. Recently, some studies
   showed that the parameterization for mesoscale eddy effects formulated
   by Gent and McWilliams allows integral quantities like the streamfunction
   and meridional heat transport to be free of these undesired effects.
   In this paper, an idealized OGCM is used to validate an analytical
   rationalization of the processes at work and help understand the
   physics. The results show that the features associated with the Veronis
   effect can be related quantitatively to three different width scales
   that characterize the baroclinic structure of the deep western boundary
   current. In addition, since one of these scales may be smaller than
   the Munk barotropic layer, usually considered to determine the minimum
   resolution and horizontal viscosity for numerical models, the authors
   recommend that it be taken into account. Regarding the introduction
   of the new parameterization, diagnostics in terms of heat balances
   underline some interesting similarities between local heat fluxes
   by eddy-induced velocities and horizontal diffusion at low and midlatitudes
   when a common large diffusivity (here 2000 m2 s−1) is used.
   The near-quasigeostrophic character of the flow explains these results.
   As a consequence, the response of the Eulerian-mean circulation is
   locally similar for runs using either of the two parameterizations.
   However, it is shown that the advective nature of the eddy-induced
   heat fluxes results in a very different effective circulation, which
   is the one felt by tracers.},
  date = {November 01, 1999},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Leonard1991,
  author = {B. P. Leonard},
  title = {The ULTIMATE conservative difference scheme applied to unsteady one--dimensional
   advection},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  year = {1991},
  pages = {17-74},
  owner = {gm},
  timestamp = {2007.08.04}
}

@TECHREPORT{Leonard1988,
  author = {B. P. Leonard},
  title = {Universal limiter for transient interpolation modelling of the advective
   transport equations},
  institution = {Technical Memorandum TM-100916 ICOMP-88-11, NASA},
  year = {1988},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Leonard1979,
  author = {B. P. Leonard},
  title = {A stable and accurate convective modelling procedure based on quadratic
   upstream interpolation},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  year = {1979},
  volume = {19},
  pages = {59-98},
  month = jun,
  owner = {gm},
  timestamp = {2007.08.04}
}

@TECHREPORT{Levier2007,
  author = {B. Levier and A.-M. Tr\'{e}guier and G. Madec and V. Garnier},
  title = {Free surface and variable volume in the NEMO code},
  institution = {MERSEA MERSEA IP report WP09-CNRS-STR-03-1A, 47pp, available on the
   NEMO web site},
  year = {2007},
  owner = {gm},
  timestamp = {2007.08.03}
}

@BOOK{levitus82,
  title = {Climatological Atlas of the world ocean},
  publisher = {NOAA professional paper No. 13, 174pp},
  year = {1982},
  author = {S Levitus },
  note = {173 p.}
}

@TECHREPORT{Lott1989,
  author = {F. Lott and G. Madec},
  title = {Implementation of bottom topography in the Ocean General Circulation
   Model OPA of the LODYC: formalism and experiments.},
  institution = {LODYC, France, 36pp.},
  year = {1989},
  number = {3},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Lott1990,
  author = {F. Lott and G. Madec and J. Verron},
  title = {Topographic experiments in an Ocean General Circulation Model},
  journal = {Ocean Modelling},
  year = {1990},
  volume = {88},
  pages = {1-4},
  owner = {gm},
  timestamp = {2007.08.03}
}

@PHDTHESIS{Madec1990,
  author = {G. Madec},
  title = {La formation d'eau profonde et son impact sur la circulation r\'{e}gionale
   en M\'{e}diterran\'{e}e Occidentale - une approche num\'{e}rique},
  school = {Universit\'{e}Pierre et Marie Curie, Paris,  France, 194pp.},
  year = {1990},
  owner = {gm},
  timestamp = {2007.08.10}
}

@ARTICLE{Madec1991a,
  author = {G. Madec and M. Chartier and M. Cr\'{e}pon},
  title = {Effect of thermohaline forcing variability on deep water formation
   in the Northwestern Mediterranean Sea - a high resulution three-dimensional
   study},
  journal = DAO,
  year = {1991},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Madec1991b,
  author = {G. Madec and M. Chartier and P. Delecluse and M. Cr\'{e}pon},
  title = {A three-dimensional numerical study of deep water formation in the
   
   
   Northwestern Mediterranean Sea .},
  journal = JPO,
  year = {1991},
  volume = {21},
  owner = {gm},
  timestamp = {2007.08.06}
}

@INBOOK{Madec1991c,
  chapter = {Thermohaline-driven deep water formation in the Northwestern Mediterranean
   Sea},
  title = {Deep convection and deep water formation in the oceans},
  publisher = {Elsevier Oceanographic Series},
  year = {1991},
  author = {G. Madec and M. Cr\'{e}pon},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Madec1997,
  author = {G. Madec and P. Delecluse},
  title = {The OPA/ARPEGE and OPA/LMD Global Ocean-Atmosphere Coupled Model},
  journal = {Int. WOCE Newsletter},
  year = {1997},
  volume = {26},
  pages = {12-15},
  owner = {gm},
  timestamp = {2007.08.06}
}

@TECHREPORT{Madec1998,
  author = {G. Madec and P. Delecluse and M. Imbard and C. Levy},
  title = {OPA 8 Ocean General Circulation Model - Reference Manual},
  institution = {LODYC/IPSL Note 11},
  year = {1998}
}

@ARTICLE{MadecImb1996,
  author = {G Madec and M Imbard},
  title = {A global ocean mesh to overcome the north pole singularity},
  journal = CD,
  year = {1996},
  volume = {12},
  pages = {381-388}
}

@ARTICLE{Madec1996,
  author = {G. Madec and F. Lott and P. Delecluse and M. Cr\'{e}pon},
  title = {Large-Scale Preconditioning of Deep-Water Formation in the Northwestern
   Mediterranean Sea},
  journal = JPO,
  year = {1996},
  volume = {26},
  pages = {1393-1408},
  number = {8},
  month = aug,
  abstract = {The large-scale processes preconditioning the winter deep-water formation
   in the northwestern Mediterranean Sea are investigated with a primitive
   equation numerical model where convection is parameterized by a non-penetrative
   convective adjustment algorithm. The ocean is forced by momentum
   and buoyancy fluxes that have the gross features of mean winter forcing
   found in the MEDOC area. The wind-driven barotropic circulation appears
   to be a major ingredient of the preconditioning phase of deep-water
   formation. After three months, the ocean response is dominated by
   a strong barotropic cyclonic vortex located under the forcing area,
   which fits the Sverdrup balance away from the northern coast. In
   the vortex center, the whole water column remains trapped under the
   forcing area all winter. This trapping enables the thermohaline forcing
   to drive deep-water formation efficiently. Sensitivity studies show
   that, β effect and bottom topography play a paramount role and
   confirm that deep convection occurs only in areas that combine a
   strong surface thermohaline forcing and a weak barotropic advection
   so that water masses are submitted to the negative buoyancy fluxes
   for a much longer time. In particular, the impact of the Rhône
   Deep Sea Fan on the barotropic circulation dominates the β effect:
   the barotropic flow is constrained to follow the bathymetric contours
   and the cyclonic vortex is shifted southward so that the fluid above
   the fan remains quiescent. Hence, buoyancy fluxes trigger deep convection
   above the fan in agreement with observations. The selection of the
   area of deep-water formation through the defection of the barotropic
   circulation by the topography seems a more efficient mechanism than
   those associated with the wind- driven barotropic vortex. This is
   due to its permanency, while the latter may be too sensitive to time
   and space variations of the forcing.},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Madec1988,
  author = {G. Madec and C. Rahier and M. Chartier},
  title = {A comparison of two-dimensional elliptic solvers for the barotropic
   streamfunction in a multilevel OGCM},
  journal = {Ocean Modelling},
  year = {1988},
  volume = {78},
  owner = {gm},
  timestamp = {2007.08.10}
}

@ARTICLE{Maltrud1998,
  author = {M. E. Maltrud and R. D. Smith and A. J. Semtner and R. C. Malone},
  title = {Global eddy-resolving ocean simulations driven by 1985-1995 atmospheric
   winds},
  journal = JGR,
  year = {1998},
  volume = {103(C13)},
  pages = {30,825-30,854},
  owner = {gm},
  timestamp = {2007.08.05}
}

@PHDTHESIS{MartiTh1992,
  author = {O. Marti},
  title = {Etude de l'oc\'{e}an mondial : mod\'{e}lisation de la circulation
   et du transport de traceurs anthropog\'{e}niques},
  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 201pp},
  year = {1992},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Marti1992,
  author = {O. Marti and G. Madec and P. Delecluse},
  title = {Comment on "Net diffusivity in ocean general circulation models with
   nonuniform grids" by F. L. Yin and I. Y. Fung},
  journal = JGR,
  year = {1992},
  volume = {97},
  pages = {12763-12766},
  month = aug,
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{McDougall1987,
  author = {T. J. McDougall},
  title = {Neutral Surfaces},
  journal = {Journal of Physical Oceanography},
  year = {1987},
  volume = {17},
  pages = {1950-1964},
  number = {11},
  abstract = {Scalar properties in the ocean are stirred (and subsequently mixed)
   rather efficiently by mesoscale eddies and two-dimensional turbulence
   along “neutral surfaces”, defined such that when water
   parcels are moved small distances in the neutral surface, they experience
   no buoyant restoring forces. By contrast, work would have to be done
   on a moving fluid parcel in order to keep it on a potential density
   surface. The differences between neutral surfaces and potential density
   surfaces are due to the variation of α/β with pressure
   (where α is the thermal expansion coefficient and β is
   the saline contraction coefficient). By regarding the equation of
   state of seawater as a function of salinity, potential temperature,
   and pressure, rather than in terms of salinity, temperature, and
   pressure, it is possible to quantify the differences between neutral
   surfaces and potential density surfaces. In particular, the spatial
   gradients of scalar properties (e.g., S, θ, tritium or potential
   vorticity) on a neutral surface can be quite different to the corresponding
   gradients in a potential density surface. For example, at a potential
   temperature of 4°C and a pressure of 1000 db, the lateral gradient
   of potential temperature in a potential density surface (referenced
   to sea level) is too large by between 50% and 350% (depending
   on the stability ratio Rp of the water column) compared with the
   physically relevant gradient of potential temperature on the neutral
   surface. Three-examples of neutral surfaces are presented, based
   on the Levitus atlas of the North Atlantic.},
  date = {November 01, 1987},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Merryfield1999,
  author = {W. J. Merryfield and G. Holloway and A. E. Gargett},
  title = {A Global Ocean Model with Double-Diffusive Mixing},
  journal = JPO,
  year = {1999},
  volume = {29},
  pages = {1124-1142},
  number = {6},
  abstract = {A global ocean model is described in which parameterizations of diapycnal
   mixing by double-diffusive fingering and layering are added to a
   stability-dependent background turbulent diffusivity. Model runs
   with and without double-diffusive mixing are compared for annual-mean
   and seasonally varying surface forcing. Sensitivity to different
   double-diffusive mixing parameterizations is considered. In all cases,
   the locales and extent of salt fingering (as diagnosed from buoyancy
   ratio Rρ) are grossly comparable to climatology, although fingering
   in the models tends to be less intense than observed. Double-diffusive
   mixing leads to relatively minor changes in circulation but exerts
   significant regional influences on temperature and salinity.},
  date = {June 01, 1999},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Murray1996,
  author = {R. J. Murray},
  title = {Explicit Generation of Orthogonal Grids for Ocean Models},
  journal = JCP,
  year = {1996},
  volume = {126},
  pages = {251-273},
  number = {2},
  month = {July},
  owner = {gm},
  timestamp = {2007.08.03}
}

@PHDTHESIS{OlivierPh2001,
  author = {F. Olivier},
  title = {Etude de l'activit\'{e} biologique et de la circulation oc\'{e}anique
   dans un jet g\'{e}ostrophique: le front Alm\'{e}ria-Oran},
  school = {Universit\'{e} Pierre et Marie Curie, Paris, France},
  year = {2001},
  owner = {gm},
  timestamp = {2007.08.14}
}

@ARTICLE{PacPhil1981,
  author = {R.C. Pacanowski and S.G.H. Philander},
  title = {Parameterization of Vertical Mixing in Numerical Models of Tropical
   Oceans},
  journal = JPO,
  year = {1981},
  volume = {11},
  pages = {1443-1451},
  number = {11},
  abstract = {Measurements indicate that mixing processes are intense in the surface
   layers of the ocean but weak below the thermocline, except for the
   region below the core of the Equatorial Undercurrent where vertical
   temperature gradients are small and the shear is large. Parameterization
   of these mixing processes by means of coefficients of eddy mixing
   that are Richardson-number dependent, leads to realistic simulations
   of the response of the equatorial oceans to different windstress
   patterns. In the case of eastward winds results agree well with measurements
   in the Indian Ocean. In the case of westward winds it is of paramount
   importance that the nonzero heat flux into the ocean be taken into
   account. This beat flux stabilizes the upper layers and reduces the
   intensity of the mixing, especially in the cast. With an appropriate
   surface boundary condition, the results are relatively insensitive
   to values assigned to constants in the parameterization formula.},
  date = {November 01, 1981},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Paulson1977,
  author = {C. A. Paulson and J. J. Simpson},
  title = {Irradiance Measurements in the Upper Ocean},
  journal = JPO,
  year = {1977},
  volume = {7},
  pages = {952-956},
  number = {6},
  abstract = {Observations were made of downward solar radiation as a function of
   depth during an experiment in the North Pacific (35°N, 155°W).
   The irradiance meter employed was sensitive to solar radiation of
   wavelength 400–1000 nm arriving from above at a horizontal
   surface. Because of selective absorption of the short and long wavelengths,
   the irradiance decreases much faster than exponential in the upper
   few meters, falling to one-third of the incident value between 2
   and 3 m depth. Below 10 m the decrease was exponential at a rate
   characteristic of moderately clear water of Type IA. Neglecting one
   case having low sun altitude, the observations are well represented
   by the expression I/I0=Rez/ζ1+(1−R)ezζ2,
   where I is the irradiance at depth −z, I0 is the irradiance
   at the surface less reflected solar radiation, R=0.62, ζ1
   and ζ2 are attenuation lengths equal to 1.5 and 20 m, respectively,
   and z is the vertical space coordinate, positive upward with the
   origin at mean sea level. The depth at which the irradiance falls
   to 10% of its surface value is nearly the same as observations
   of Secchi depth when cases with high wind speed or low solar altitude
   are neglected. Parameters R, ζ1, and ζ2 are computed for
   the entire range of oceanic water types.},
  date = {November 01, 1977},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Phillips1959,
  author = {R. S.  Phillips},
  title = {Dissipative Operators and Hyperbolic Systems of Partial Differential
   Equations},
  journal = {Transactions of the American Mathematical Society},
  year = {1959},
  volume = {90(2)},
  pages = {193-254},
  doi = {doi:10.2307/1993202},
  owner = {gm},
  timestamp = {2007.08.10}
}

@ARTICLE{Reverdin1991,
  author = {G. Reverdin and P. Delecluse and C. L\'{e}vy and P. Andrich and A.
   Morli\`{e}re and J. M. Verstraete},
  title = {The near surface tropical Atlantic in 1982-1984 : results from a
   numerical simulation and a data analysis},
  journal = PO,
  year = {1991},
  volume = {27},
  pages = {273-340},
  owner = {gm},
  timestamp = {2007.08.04}
}

@BOOK{Richtmyer1967,
  title = {Difference methods for initial-value problems},
  publisher = {Interscience Publisher, Second Edition, 405pp},
  year = {1967},
  author = {R. D. Richtmyer and K. W. Morton},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Robert1966,
  author = {A. J. Robert},
  title = {The integration of a Low order spectral form of the primitive meteorological
   equations},
  journal = {J. Meteo. Soc. Japan},
  year = {1966},
  volume = {44, 2},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Roullet2000,
  author = {G. Roullet and G. Madec},
  title = {salt conservation, free surface, and varying levels: a new formulation
   for ocean general circulation models},
  journal = JGR,
  year = {2000},
  volume = {105},
  pages = {23,927-23,942},
  owner = {sandra},
  pdf = {Roullet_Madec_JGR00.pdf},
  timestamp = {2007.03.22}
}

@ARTICLE{Sadourny1975,
  author = {R. Sadourny},
  title = {The Dynamics of Finite-Difference Models of the Shallow-Water Equations},
  journal = JAS,
  year = {1975},
  volume = {32},
  pages = {680-689},
  number = {4},
  abstract = {Two simple numerical models of the shallow-water equations identical
   in all respects but for their con-servation properties have been
   tested regarding their internal mixing processes. The experiments
   show that violation of enstrophy conservation results in a spurious
   accumulation of rotational energy in the smaller scales, reflected
   by an unrealistic increase of enstrophy, which ultimately produces
   a finite rate of energy dissipation in the zero viscosity limit,
   thus violating the well-known dynamics of two-dimensional flow. Further,
   the experiments show a tendency to equipartition of the kinetic energy
   of the divergent part of the flow in the inviscid limit, suggesting
   the possibility of a divergent energy cascade in the physical system,
   as well as a possible influence of the energy mixing on the process
   of adjustment toward balanced flow.},
  date = {April 01, 1975},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Sarmiento1982,
  author = {J. L. Sarmiento and K. Bryan},
  title = {Ocean transport model for the North Atlantic},
  journal = JGR,
  year = {1982},
  volume = {87},
  pages = {394-409},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Sacha2005,
  author = {A. F. Shchepetkin and J. C. McWilliams},
  title = {The regional oceanic modeling system (ROMS) - a split-explicit, free-surface,
   topography-following-coordinate oceanic modelr},
  journal = {Ocean Modelling},
  year = {2005},
  volume = {9, 4},
  pages = {347-404},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Sacha2003,
  author = {A. F. Shchepetkin and J. C. McWilliams},
  title = {A method for computing horizontal pressure-gradient force in an oceanic
   model with a nonaligned 
   
   vertical coordinate},
  journal = JGR,
  year = {2003},
  volume = {108(C3)},
  pages = {3090, doi:10.1029/2001JC001047},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Shchepetkin1996,
  author = {A. F. Shchepetkin and J. J. O'Brien},
  title = {A Physically Consistent Formulation of Lateral Friction in Shallow-Water
   Equation Ocean Models},
  journal = MWR,
  year = {1996},
  volume = {124},
  pages = {1285-1300},
  number = {6},
  abstract = {Dissipation in numerical ocean models has two purposes: to simulate
   processes in which the friction is physically relevant and to prevent
   numerical instability by suppressing accumulation of energy in the
   smallest resolved scales. This study shows that even for the latter
   case the form of the friction term should be chosen in a physically
   consistent way. Violation of fundamental physical principles reduces
   the fidelity of the numerical solution, even if the friction is small.
   Several forms of the lateral friction, commonly used in numerical
   ocean models, are discussed in the context of shallow-water equations
   with nonuniform layer thickness. It is shown that in a numerical
   model tuned for the minimal dissipation, the improper form of the
   friction term creates finite artificial vorticity sources that do
   not vanish with increased resolution, even if the viscous coefficient
   is reduced consistently with resolution. An alternative numerical
   implementation of the no-slip boundary conditions for an arbitrary
   coast line is considered. It was found that the quality of the numerical
   solution may be considerably improved by discretization of the viscous
   stress tensor in such a way that the numerical boundary scheme approximates
   not only the stress tensor to a certain order of accuracy but also
   simulates the truncation error of the numerical scheme used in the
   interior of the domain. This ensures error cancellation during subsequent
   use of the elements of the tensor in the discrete version of the
   momentum equations, allowing for approximation of them without decrease
   in the order of accuracy near the boundary.},
  date = {June 01, 1996},
  owner = {gm},
  timestamp = {2007.08.14}
}

@ARTICLE{Simmons2003,
  author = {H. L. Simmons and S. R. Jayne and L. C. St. Laurent and A. J. Weaver},
  title = {Tidally driven mixing in a numerical model of the
   
   ocean general circulation},
  journal = OM,
  year = {2003},
  pages = {1-19},
  abstract = {Astronomical data reveals that approximately 3.5 terawatts (TW) of
   tidal energy is dissipated in the
   
   ocean. Tidal models and satellite altimetry suggest that 1 TW of this
   energy is converted from the barotropic
   
   to internal tides in the deep ocean, predominantly around regions
   of rough topography such as midocean
   
   ridges. Aglobal tidal model is used to compute turbulent energy levels
   associated with the dissipation
   
   of internal tides, and the diapycnal mixing supported by this energy
   ?ux is computed using a simple parameterization.
   
   The mixing parameterization has been incorporated into a coarse resolution
   numerical model of the
   
   global ocean. This parameterization o?ers an energetically consistent
   and practical means of improving the
   
   representation of ocean mixing processes in climate models. Novel
   features of this implementation are that
   
   the model explicitly accounts for the tidal energy source for mixing,
   and that the mixing evolves both
   
   spatially and temporally with the model state. At equilibrium, the
   globally averaged di?usivity pro?le
   
   ranges from 0.3 cm2 s1 at thermocline depths to 7.7 cm2 s1 in the
   abyss with a depth average of 0.9
   
   cm2 s1, in close agreement with inferences from global balances.
   Water properties are strongly in?uenced
   
   by the combination of weak mixing in the main thermocline and enhanced
   mixing in the deep ocean.
   
   Climatological comparisons show that the parameterized mixing scheme
   results in a substantial reduction},
  owner = {sandra},
  pdf = {Simmons_mixing_OM2003.pdf},
  timestamp = {2007.03.22}
}

@ARTICLE{Song1994,
  author = {Y. Song and D. Haidvogel},
  title = {A Semi-implicit Ocean Circulation Model Using a Generalized Topography-Following
   Coordinate System
   
   Authors:},
  journal = JCP,
  year = {1994},
  volume = {115, 1},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Song1998,
  author = {Y. T. Song},
  title = {A General Pressure Gradient Formulation for Ocean Models. Part I:
   Scheme Design and Diagnostic Analysis},
  journal = MWR,
  year = {1998},
  volume = {126},
  pages = {3213-3230},
  number = {12},
  abstract = {A Jacobian formulation of the pressure gradient force for use in models
   with topography-following coordinates is proposed. It can be used
   in conjunction with any vertical coordinate system and is easily
   implemented. Vertical variations in the pressure gradient are expressed
   in terms of a vertical integral of the Jacobian of density and depth
   with respect to the vertical computational coordinate. Finite difference
   approximations are made on the density field, consistent with piecewise
   linear and continuous fields, and accurate pressure gradients are
   obtained by vertically integrating the discrete Jacobian from sea
   surface.Two discrete schemes are derived and examined in detail:
   the first using standard centered differencing in the generalized
   vertical coordinate and the second using a vertical weighting such
   that the finite differences are centered with respect to the Cartesian
   z coordinate. Both schemes achieve second-order accuracy for any
   vertical coordinate system and are significantly more accurate than
   conventional schemes based on estimating the pressure gradients by
   finite differencing a previously determined pressure field.The standard
   Jacobian formulation is constructed to give exact pressure gradient
   results, independent of the bottom topography, if the buoyancy field
   varies bilinearly with horizontal position, x, and the generalized
   vertical coordinate, s, over each grid cell. Similarly, the weighted
   Jacobian scheme is designed to achieve exact results, when the buoyancy
   field varies linearly with z and arbitrarily with x, that is, b(x,z)
   = b0(x) + b1(x)z.When horizontal resolution cannot be made
   fine enough to avoid hydrostatic inconsistency, errors can be substantially
   reduced by the choice of an appropriate vertical coordinate. Tests
   with horizontally uniform, vertically varying, and with horizontally
   and vertically varying buoyancy fields show that the standard Jacobian
   formulation achieves superior results when the condition for hydrostatic
   consistency is satisfied, but when coarse horizontal resolution causes
   this condition to be strongly violated, the weighted Jacobian may
   give superior results.},
  date = {December 01, 1998},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{SongWright1998,
  author = {Y. T. Song and D. G. Wright},
  title = {A General Pressure Gradient Formulation for Ocean Models. Part II
   - Energy, Momentum, and Bottom Torque Consistency},
  journal = MWR,
  year = {1998},
  volume = {126},
  pages = {3231-3247},
  number = {12},
  abstract = {A new formulation of the pressure gradient force for use in models
   with topography-following coordinates is proposed and diagnostically
   analyzed in Part I. Here, it is shown that important properties of
   the continuous equations are retained by the resulting numerical
   schemes, and their performance in prognostic simulations is examined.
   Numerical consistency is investigated with respect to global energy
   conservation, depth-integrated momentum changes, and the representation
   of the bottom pressure torque. The performances of the numerical
   schemes are tested in prognostic integrations of an ocean model to
   demonstrate numerical accuracy and long-term integral stability.
   Two typical geometries, an isolated tall seamount and an unforced
   basin with sloping boundaries, are considered for the special case
   of no external forcing and horizontal isopycnals to test numerical
   accuracy. These test problems confirm that the proposed schemes yield
   accurate approximations to the pressure gradient force. Integral
   consistency conditions are verified and the energetics of the “advective
   elimination” of the pressure gradient error (Mellor et al)
   is considered.A large-scale wind-driven basin with and without topography
   is used to test the model’s long-term integral performance
   and the effects of bottom pressure torque on the transport in western
   boundary currents. Integrations are carried out for 10 years in each
   case and results show that the schemes are stable, and the steep
   topography causes no obvious numerical problems. A realistic meandering
   western boundary current is well developed with detached cold cyclonic
   and warm anticyclonic eddies as it extends across the basin. In addition,
   the results with topography show earlier separation and enhanced
   transport in the western boundary currents due to the bottom pressure
   torque.},
  date = {December 01, 1998},
  owner = {gm},
  timestamp = {2007.08.05}
}

@PHDTHESIS{Speich1992,
  author = {S. Speich},
  title = {Etude du for\c{c}age de la circulation g\'{e}n\'{e}rale oc\'{e}anique
   par les d\'{e}troits - cas de la mer d'Alboran},
  school = {Universit\'{e} Pierre et Marie Curie, Paris, France},
  year = {1992},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Speich1996,
  author = {S. Speich and G. Madec and M. Cr\'{e}pon},
  title = {The circulation in the Alboran Sea - a sensitivity study},
  journal = JPO,
  year = {1996},
  volume = {26},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Steele2001,
  author = {M. Steele and R. Morley and W. Ermold},
  title = {PHC- A Global Ocean Hydrography with a High-Quality Arctic Ocean},
  journal = {Journal of Climate},
  year = {2001},
  volume = {14},
  pages = {2079--2087
   
   },
  number = {9},
  abstract = {A new gridded ocean climatology, the Polar Science Center Hydrographic
   Climatology (PHC), has been created that merges the 1998 version
   of the World Ocean Atlas with the new regional Arctic Ocean Atlas.
   The result is a global climatology for temperature and salinity that
   contains a good description of the Arctic Ocean and its environs.
   Monthly, seasonal, and annual average products have been generated.
   How the original datasets were prepared for merging, how the optimal
   interpolation procedure was performed, and characteristics of the
   resulting dataset are discussed, followed by a summary and discussion
   of future plans.},
  date = {May 01, 2001},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Stein1992,
  author = {C. A. Stein and S. Stein},
  title = {A model for the global variation in oceanic depth and heat flow with
   lithospheric age},
  journal = {Nature},
  year = {1992},
  volume = {359},
  pages = {123-129},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Thiem2006,
  author = {O. Thiem and J. Berntsen},
  title = {Internal pressure errors in sigma-coordinate ocean models due to
   anisotropy},
  journal = {Ocean Modelling},
  year = {2006},
  volume = {12, 1-2},
  owner = {gm},
  timestamp = {2007.08.05}
}

@ARTICLE{Treguier1996,
  author = {A.-M. Tr\'{e}guier and J. Dukowicz and K. Bryan},
  title = {Properties of nonuniform grids used in ocean general circulation
   models},
  journal = JGR,
  year = {1996},
  volume = {101},
  pages = {20877-20881},
  owner = {gm},
  timestamp = {2007.08.03}
}

@ARTICLE{Treguier1997,
  author = {A. M. Tr\'{e}guier and I. M. Held and V. D. Larichev},
  title = {Parameterization of Quasigeostrophic Eddies in Primitive Equation
   Ocean Models},
  journal = JPO,
  year = {1997},
  volume = {27},
  pages = {567-580},
  number = {4},
  abstract = {A parameterization of mesoscale eddy fluxes in the ocean should be
   consistent with the fact that the ocean interior is nearly adiabatic.
   Gent and McWilliams have described a framework in which this can
   be approximated in z-coordinate primitive equation models by incorporating
   the effects of eddies on the buoyancy field through an eddy-induced
   velocity. It is also natural to base a parameterization on the simple
   picture of the mixing of potential vorticity in the interior and
   the mixing of buoyancy at the surface. The authors discuss the various
   constraints imposed by these two requirements and attempt to clarify
   the appropriate boundary conditions on the eddy-induced velocities
   at the surface. Quasigeostrophic theory is used as a guide to the
   simplest way of satisfying these constraints.},
  date = {April 01, 1997},
  owner = {gm},
  timestamp = {2007.08.03}
}

@BOOK{UNESCO1983,
  title = {Algorithms for computation of fundamental property of sea water},
  publisher = {Techn. Paper in Mar. Sci, 44, UNESCO},
  year = {1983},
  author = {UNESCO},
  owner = {gm},
  timestamp = {2007.08.04}
}

@TECHREPORT{OASIS2006,
  author = {S. Valcke},
  title = {OASIS3 User Guide (prism\_2-5)},
  institution = {PRISM Support Initiative Report No 3, CERFACS, Toulouse, France,
   64 pp},
  year = {2006},
  owner = {gm},
  timestamp = {2007.08.05}
}

@TECHREPORT{valal00,
  author = {S. Valcke and L. Terray and A. Piacentini },
  title = {The OASIS Coupled User Guide Version 2.4},
  institution = {CERFACS},
  year = {2000},
  number = {TR/CMGC/00-10}
}

@ARTICLE{Weatherly1984,
  author = {G. L. Weatherly},
  title = {An estimate of bottom frictional dissipation by Gulf Stream fluctuations},
  journal = JMR,
  year = {1984},
  volume = {42, 2},
  pages = {289-301},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Weaver1997,
  author = {A. J. Weaver and M. Eby},
  title = {On the numerical implementation of advection schemes for use in conjuction
   with various mixing 
   
   parameterizations in the GFDL ocean model},
  journal = JPO,
  year = {1997},
  volume = {27},
  owner = {gm},
  timestamp = {2007.08.06}
}

@ARTICLE{Webb1998,
  author = {D. J. Webb and B. A. de Cuevas and C. S. Richmond},
  title = {Improved Advection Schemes for Ocean Models},
  journal = JAOT,
  year = {1998},
  volume = {15},
  pages = {1171-1187},
  number = {5},
  abstract = {Leonard’s widely used QUICK advection scheme is, like the Bryan–Cox–Semtner
   ocean model, based on a control volume form of the advection equation.
   Unfortunately, in its normal form it cannot be used with the leapfrog–Euler
   forward time-stepping schemes used by the ocean model. Farrow and
   Stevens overcame the problem by implementing a predictor–corrector
   time-stepping scheme, but this is computationally expensive to run.
   The present paper shows that the problem can be overcome by splitting
   the QUICK operator into an O(δx2) advective term and a velocity
   dependent biharmonic diffusion term. These can then be time-stepped
   using the combined leapfrog and Euler forward schemes of the Bryan–Cox–Semtner
   ocean model, leading to a significant increase in model efficiency.
   A small change in the advection operator coefficients may also be
   made leading to O(δx4) accuracy. Tests of the improved schemes
   are carried out making use of a global eddy-permitting ocean model.
   Results are presented from cases where the schemes were applied to
   only the tracer fields and also from cases where they were applied
   to both the tracer and velocity fields. It is found that the new
   schemes have the most effect in the western boundary current regions,
   where, for example, the warm core of the Agulhas Current is no longer
   broken up by numerical noise.},
  date = {October 01, 1998},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Willebrand2001,
  author = {J. Willebrand and B. Barnier and C. Boning and C. Dieterich and P.
   D. Killworth and C. Le Provost and Y. Jia and J.-M. Molines and A.
   L. New},
  title = {Circulation characteristics in three eddy-permitting models of the
   North Atlantic},
  journal = {Progress in Oceanography},
  year = {2001},
  volume = {48, 2},
  pages = {123-161},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Zalesak1979,
  author = {S. T. Zalesak},
  title = {Fully multidimensional flux corrected transport algorithms for fluids},
  journal = JCP,
  year = {1979},
  volume = {31},
  owner = {gm},
  timestamp = {2007.08.04}
}

@ARTICLE{Zhang1992,
  author = {Zhang, R.-H. and Endoh, M.},
  title = {A free surface general circulation model for the tropical Pacific
   Ocean},
  journal = JGR,
  year = {1992},
  volume = {97},
  pages = {11237-11255},
  month = jul,
  owner = {gm}
}

@INBOOK{Delecluse2000,
  chapter = {Ocean modelling and the role of the ocean in the climate system},
  pages = {237-313},
  title = {Modeling the Earth's Climate and its Variability, Les Houches, Session
   LXVII 1997},
  year = {2000},
  editor = {W. R. Holland and  S. Jaussaume and F. David},
  owner = {gm},
  timestamp = {2007.08.17}
}

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