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introduction.tex in NEMO/trunk/doc/latex/NEMO/main – NEMO

# source:NEMO/trunk/doc/latex/NEMO/main/introduction.tex@11522

Last change on this file since 11522 was 11522, checked in by nicolasmartin, 3 years ago

Review the beginning of the manual
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2\chapter*{Introduction}
3
4%\chaptertoc
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6%\paragraph{Changes record} ~\\
7
8%\thispagestyle{plain}
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10%{\footnotesize
11%  \begin{tabularx}{\textwidth}{l||X|X}
12%    Release & Author(s) & Modifications \\
13%    \hline
14%    {\em x.x} & {\em ...} & {\em ...}   \\
15%    {\em ...} & {\em ...} & {\em ...}   \\
16%  \end{tabularx}
17%}
18
19%\clearpage
20
21The \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean (\NEMO) is
22a framework of ocean related engines, namely the aforementioned for
23the ocean dynamics and thermodynamics,
24\SIcube \footnote{\textbf{S}ea-\textbf{I}ce modelling \textbf{I}ntegrated \textbf{I}nitiative}
25for the sea-ice dynamics and thermodynamics,
26\TOP \footnote{\textbf{T}racer in the \textbf{O}cean \textbf{P}aradigm} for
27the biogeochemistry (both transport and sources minus sinks
28(\PISCES \footnote{
29  \textbf{P}elagic \textbf{I}nteractions \textbf{S}cheme for
30  \textbf{C}arbon and \textbf{E}cosystem \textbf{S}tudies
31}
32)).
33The ocean component has been developed from the legacy of
34the \OPA \footnote{\textbf{O}c\'{e}an \textbf{PA}rall\'{e}lis\'{e} (French)}
36This model has been used for a wide range of applications, both regional or global,
37as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere.
38
39This manual provides information about the physics represented by the ocean component of \NEMO\ and
40the rationale for the choice of numerical schemes and the model design.
41For the use of framework,
42a guide which gathers the \texttt{README} files spread out in the source code can be build and
43exported in a web or printable format (see \path{./doc/rst}).
44Also a online copy is available on the \href{http://forge.ipsl.jussieu.fr/nemo}{forge platform}.
45
46%% =================================================================================================
47\section*{Manual outline}
48
49\subsection*{Chapters}
50
51The manual mirrors the organization of the model and it is organised in as follows:
52after the presentation of the continuous equations
53(primitive equations with temperature and salinity, and an equation of seawater) in the next chapter,
54the following chapters refer to specific terms of the equations each associated with
55a group of modules.
56
57\begin{description}
58\item [\nameref{chap:PE}] presents the equations and their assumptions, the vertical coordinates used,
59and the subgrid scale physics.
60The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates
61($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mix of them).
62Momentum equations are formulated in vector invariant or flux form.
63Dimensional units in the meter, kilogram, second (MKS) international system are used throughout.
64The following chapters deal with the discrete equations.
65\item [\nameref{chap:STP}] presents the model time stepping environment.
66it is a three level scheme in which the tendency terms of the equations are evaluated either
67centered in time, or forward, or backward depending of the nature of the term.
68\item [\nameref{chap:DOM}] presents the model \textbf{DOM}ain.
69It is discretised on a staggered grid (Arakawa C grid) with masking of land areas.
70Vertical discretisation used depends on both how the bottom topography is represented and whether
71the free surface is linear or not.
72Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with
73linear free surface (level position are then fixed in time).
74In non-linear free surface, the corresponding rescaled height coordinate formulation
75(\zstar or \sstar) is used
76(the level position then vary in time as a function of the sea surface heigh).
77\item [\nameref{chap:TRA} and \nameref{chap:DYN}] describe the discretisation of
78the prognostic equations for the active \textbf{TRA}cers (potential temperature and salinity) and
79the momentum (\textbf{DYN}amic).
80Explicit, split-explicit and filtered free surface formulations are implemented.
81A number of numerical schemes are available for momentum advection,
82for the computation of the pressure gradients, as well as for the advection of tracers
83(second or higher order advection schemes, including positive ones).
84\item [\nameref{chap:SBC}] can be implemented as prescribed fluxes,
85or bulk formulations for the surface fluxes (wind stress, heat, freshwater).
86The model allows penetration of solar radiation.
87There is an optional geothermal heating at the ocean bottom.
88Within the \NEMO\ system the ocean model is interactively coupled with
89a sea ice model (\SIcube) and a biogeochemistry model (\PISCES).
90Interactive coupling to Atmospheric models is possible via the \OASIS\ coupler.
91Two-way nesting is also available through an interface to the \AGRIF\ package,
92\ie\ \textbf{A}daptative \textbf{G}rid \textbf{R}efinement in \textbf{F}ortran
93\citep{debreu.vouland.ea_CG08}.
94The interface code for coupling to an alternative sea ice model (\CICE) has now been upgraded so that
95it works for both global and regional domains.
96\item [\nameref{chap:LBC}] presents the \textbf{L}ateral
97\textbf{B}oun\textbf{D}ar\textbf{Y} \textbf{C}onditions.
98Global configurations of the model make use of the ORCA tripolar grid,
99with special north fold boundary condition.
100Free-slip or no-slip boundary conditions are allowed at land boundaries.
101Closed basin geometries as well as periodic domains and open boundary conditions are possible.
102\item [\nameref{chap:LDF} and \nameref{chap:ZDF}] describe the physical parameterisations
103(\textbf{L}ateral \textbf{D}i\textbf{F}fusion and vertical \textbf{Z} \textbf{D}i\textbf{F}fusion)
104The model includes an implicit treatment of vertical viscosity and diffusivity.
105The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following
106a geopotential or neutral direction.
107There is an optional eddy induced velocity \citep{gent.mcwilliams_JPO90} with
108a space and time variable coefficient \citet{treguier.held.ea_JPO97}.
109The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient,
110with options to compute the coefficients with \citet{blanke.delecluse_JPO93},
111\citet{pacanowski.philander_JPO81}, or \citet{umlauf.burchard_JMR03} mixing schemes.
112\item [\nameref{chap:DIA}] describes model \textbf{I}n-\textbf{O}utputs \textbf{M}anagement and
113specific online \textbf{DIA}gnostics.
114The diagnostics includes the output of all the tendencies of the momentum and tracers equations,
115the output of tracers \textbf{TR}en\textbf{D}s averaged over the time evolving mixed layer,
116the output of the tendencies of the barotropic vorticity equation,
117the computation of on-line \textbf{FLO}ats trajectories...
118\item [\nameref{chap:OBS}] describes a tool which reads in \textbf{OBS}ervation files
119(profile temperature and salinity, sea surface temperature, sea level anomaly and
120sea ice concentration) and calculates an interpolated model equivalent value at
121the observation location and nearest model timestep.
122Originally developed of data assimilation, it is a fantastic tool for model and data comparison.
123\item [\nameref{chap:ASM}] describes how increments produced by
124data \textbf{A}s\textbf{S}i\textbf{M}ilation may be applied to the model equations.
125\item [\nameref{chap:MISC}] (including solvers)
126\item [\nameref{chap:CFG}] provides finally a brief introduction to
127the pre-defined model configurations
128(water column model \texttt{C1D}, ORCA and GYRE families of configurations).
129\end{description}
130
131%% =================================================================================================
132\subsection*{Appendices}
133
134\begin{description}
135\item [\nameref{apdx:s_coord}]
136\item [\nameref{apdx:diff_oper}]
137\item [\nameref{apdx:invariants}]