[11522] | 1 | \chapter*{Introduction} |
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[11435] | 2 | |
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[11522] | 3 | The \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean (\NEMO) is |
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| 4 | a framework of ocean related engines, namely the aforementioned for |
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| 5 | the ocean dynamics and thermodynamics, |
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| 6 | \SIcube \footnote{\textbf{S}ea-\textbf{I}ce modelling \textbf{I}ntegrated \textbf{I}nitiative} |
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| 7 | for the sea-ice dynamics and thermodynamics, |
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| 8 | \TOP \footnote{\textbf{T}racer in the \textbf{O}cean \textbf{P}aradigm} for |
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| 9 | the biogeochemistry (both transport and sources minus sinks |
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| 10 | (\PISCES \footnote{ |
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| 11 | \textbf{P}elagic \textbf{I}nteractions \textbf{S}cheme for |
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| 12 | \textbf{C}arbon and \textbf{E}cosystem \textbf{S}tudies |
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| 13 | } |
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| 14 | )). |
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| 15 | The ocean component has been developed from the legacy of |
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| 16 | the \OPA \footnote{\textbf{O}c\'{e}an \textbf{PA}rall\'{e}lis\'{e} (French)} |
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| 17 | model, described in \citet{madec.delecluse.ea_NPM98}. |
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| 18 | This model has been used for a wide range of applications, both regional or global, |
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| 19 | as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere. |
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| 20 | |
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[11435] | 21 | This manual provides information about the physics represented by the ocean component of \NEMO\ and |
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[10354] | 22 | the rationale for the choice of numerical schemes and the model design. |
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[11435] | 23 | For the use of framework, |
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| 24 | a guide which gathers the \texttt{README} files spread out in the source code can be build and |
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[11522] | 25 | exported in a web or printable format (see \path{./doc/rst}). |
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| 26 | Also a online copy is available on the \href{http://forge.ipsl.jussieu.fr/nemo}{forge platform}. |
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[707] | 27 | |
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[11522] | 28 | %% ================================================================================================= |
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| 29 | \section*{Manual outline} |
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[707] | 30 | |
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[11522] | 31 | \subsection*{Chapters} |
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| 32 | |
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| 33 | The manual mirrors the organization of the model and it is organised in as follows: |
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| 34 | after the presentation of the continuous equations |
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| 35 | (primitive equations with temperature and salinity, and an equation of seawater) in the next chapter, |
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| 36 | the following chapters refer to specific terms of the equations each associated with |
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| 37 | a group of modules. |
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| 38 | |
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| 39 | \begin{description} |
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[11543] | 40 | \item [\nameref{chap:MB}] presents the equations and their assumptions, the vertical coordinates used, |
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[11522] | 41 | and the subgrid scale physics. |
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[10354] | 42 | The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates |
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[10496] | 43 | ($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mix of them). |
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[10354] | 44 | Momentum equations are formulated in vector invariant or flux form. |
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| 45 | Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. |
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| 46 | The following chapters deal with the discrete equations. |
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[11543] | 47 | \item [\nameref{chap:TD}] presents the model time stepping environment. |
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[11522] | 48 | it is a three level scheme in which the tendency terms of the equations are evaluated either |
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| 49 | centered in time, or forward, or backward depending of the nature of the term. |
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| 50 | \item [\nameref{chap:DOM}] presents the model \textbf{DOM}ain. |
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| 51 | It is discretised on a staggered grid (Arakawa C grid) with masking of land areas. |
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[11435] | 52 | Vertical discretisation used depends on both how the bottom topography is represented and whether |
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[10496] | 53 | the free surface is linear or not. |
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[11522] | 54 | Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with |
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| 55 | linear free surface (level position are then fixed in time). |
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| 56 | In non-linear free surface, the corresponding rescaled height coordinate formulation |
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| 57 | (\zstar or \sstar) is used |
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[10354] | 58 | (the level position then vary in time as a function of the sea surface heigh). |
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[11522] | 59 | \item [\nameref{chap:TRA} and \nameref{chap:DYN}] describe the discretisation of |
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| 60 | the prognostic equations for the active \textbf{TRA}cers (potential temperature and salinity) and |
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| 61 | the momentum (\textbf{DYN}amic). |
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[10354] | 62 | Explicit, split-explicit and filtered free surface formulations are implemented. |
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[11435] | 63 | A number of numerical schemes are available for momentum advection, |
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| 64 | for the computation of the pressure gradients, as well as for the advection of tracers |
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[10496] | 65 | (second or higher order advection schemes, including positive ones). |
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[11522] | 66 | \item [\nameref{chap:SBC}] can be implemented as prescribed fluxes, |
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| 67 | or bulk formulations for the surface fluxes (wind stress, heat, freshwater). |
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[10354] | 68 | The model allows penetration of solar radiation. |
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| 69 | There is an optional geothermal heating at the ocean bottom. |
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[11522] | 70 | Within the \NEMO\ system the ocean model is interactively coupled with |
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| 71 | a sea ice model (\SIcube) and a biogeochemistry model (\PISCES). |
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| 72 | Interactive coupling to Atmospheric models is possible via the \OASIS\ coupler. |
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| 73 | Two-way nesting is also available through an interface to the \AGRIF\ package, |
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| 74 | \ie\ \textbf{A}daptative \textbf{G}rid \textbf{R}efinement in \textbf{F}ortran |
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| 75 | \citep{debreu.vouland.ea_CG08}. |
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| 76 | The interface code for coupling to an alternative sea ice model (\CICE) has now been upgraded so that |
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| 77 | it works for both global and regional domains. |
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| 78 | \item [\nameref{chap:LBC}] presents the \textbf{L}ateral |
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| 79 | \textbf{B}oun\textbf{D}ar\textbf{Y} \textbf{C}onditions. |
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| 80 | Global configurations of the model make use of the ORCA tripolar grid, |
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| 81 | with special north fold boundary condition. |
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[10354] | 82 | Free-slip or no-slip boundary conditions are allowed at land boundaries. |
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[10496] | 83 | Closed basin geometries as well as periodic domains and open boundary conditions are possible. |
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[11522] | 84 | \item [\nameref{chap:LDF} and \nameref{chap:ZDF}] describe the physical parameterisations |
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| 85 | (\textbf{L}ateral \textbf{D}i\textbf{F}fusion and vertical \textbf{Z} \textbf{D}i\textbf{F}fusion) |
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[10354] | 86 | The model includes an implicit treatment of vertical viscosity and diffusivity. |
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| 87 | The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following |
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| 88 | a geopotential or neutral direction. |
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[11522] | 89 | There is an optional eddy induced velocity \citep{gent.mcwilliams_JPO90} with |
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| 90 | a space and time variable coefficient \citet{treguier.held.ea_JPO97}. |
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[10354] | 91 | The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, |
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[11522] | 92 | with options to compute the coefficients with \citet{blanke.delecluse_JPO93}, |
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| 93 | \citet{pacanowski.philander_JPO81}, or \citet{umlauf.burchard_JMR03} mixing schemes. |
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| 94 | \item [\nameref{chap:DIA}] describes model \textbf{I}n-\textbf{O}utputs \textbf{M}anagement and |
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| 95 | specific online \textbf{DIA}gnostics. |
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[10354] | 96 | The diagnostics includes the output of all the tendencies of the momentum and tracers equations, |
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[11522] | 97 | the output of tracers \textbf{TR}en\textbf{D}s averaged over the time evolving mixed layer, |
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[10354] | 98 | the output of the tendencies of the barotropic vorticity equation, |
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[11522] | 99 | the computation of on-line \textbf{FLO}ats trajectories... |
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| 100 | \item [\nameref{chap:OBS}] describes a tool which reads in \textbf{OBS}ervation files |
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| 101 | (profile temperature and salinity, sea surface temperature, sea level anomaly and |
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| 102 | sea ice concentration) and calculates an interpolated model equivalent value at |
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| 103 | the observation location and nearest model timestep. |
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[10354] | 104 | Originally developed of data assimilation, it is a fantastic tool for model and data comparison. |
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[11522] | 105 | \item [\nameref{chap:ASM}] describes how increments produced by |
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| 106 | data \textbf{A}s\textbf{S}i\textbf{M}ilation may be applied to the model equations. |
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[11543] | 107 | \item [\nameref{chap:STO}] |
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[11522] | 108 | \item [\nameref{chap:MISC}] (including solvers) |
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[11543] | 109 | \item [\nameref{chap:CFGS}] provides finally a brief introduction to |
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[11522] | 110 | the pre-defined model configurations |
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| 111 | (water column model \texttt{C1D}, ORCA and GYRE families of configurations). |
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| 112 | \end{description} |
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[707] | 113 | |
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[11522] | 114 | %% ================================================================================================= |
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| 115 | \subsection*{Appendices} |
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[707] | 116 | |
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[11522] | 117 | \begin{description} |
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[11543] | 118 | \item [\nameref{apdx:SCOORD}] |
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| 119 | \item [\nameref{apdx:DIFFOPERS}] |
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| 120 | \item [\nameref{apdx:INVARIANTS}] |
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| 121 | \item [\nameref{apdx:TRIADS}] |
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| 122 | \item [\nameref{apdx:DOMCFG}] |
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| 123 | \item [\nameref{apdx:CODING}] |
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[11522] | 124 | \end{description} |
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