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8The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean
9related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the
10ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice
11Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer
12in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources
13minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not
14acronyms just name}. It is intended to be a flexible tool for studying the ocean and
15its interactions with the other components of the earth climate system (atmosphere,
16sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.
17This documentation provides information about the physics represented by the ocean
18component of \NEMO and the rationale for the choice of numerical schemes and
19the model design. More specific information about running the model on different
20computers, or how to set up a configuration, are found on the \NEMO web site
23The ocean component of \NEMO has been developed from the OPA model,
24release 8.2, described in \citet{Madec1998}. This model has been used for a wide
25range of applications, both regional or global, as a forced ocean model and as a
26model coupled with the atmosphere. A complete list of references is found on the
27\NEMO web site.
29This manual is organised in as follows. Chapter~\ref{PE} presents the model basics,
30$i.e.$ the equations and their assumptions, the vertical coordinates used, and the
31subgrid scale physics. This part deals with the continuous equations of the model
32(primitive equations, with potential temperature, salinity and an equation of state).
33The equations are written in a curvilinear coordinate system, with a choice of vertical
34coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or 
35\textit{s*}). Momentum equations are formulated in the vector invariant form or in the
36flux form. Dimensional units in the meter, kilogram, second (MKS) international system
37are used throughout.
39The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the
40time domain. The model time stepping environment is a three level scheme in which
41the tendency terms of the equations are evaluated either centered  in time, or forward,
42or backward depending of the nature of the term.
43Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered
44grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends
45on both how the bottom topography is represented and whether the free surface is linear or not.
46Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used
47with linear free surface (level position are then fixed in time). In non-linear free surface,
48the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used
49(the level position then vary in time as a function of the sea surface heigh).
50The following two chapters (\ref{TRA} and \ref{DYN}) describe the discretisation of the
51prognostic equations for the active tracers and the momentum. Explicit, split-explicit
52and filtered free surface formulations are implemented.
53A number of numerical schemes are available for momentum advection, for the computation
54of the pressure gradients, as well as for the advection of tracers (second or higher
55order advection schemes, including positive ones).
57Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed
58fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The
59model allows penetration of solar radiation  There is an optional geothermal heating at
60the ocean bottom. Within the \NEMO system the ocean model is interactively coupled
61with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER).
62Interactive coupling to Atmospheric models is possible via the OASIS coupler
63\citep{OASIS2006}. Two-way nesting is also available through an interface to the
64AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}.
66Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}). 
67Global configurations of the model make use of the ORCA tripolar grid, with special north
68fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land
69boundaries. Closed basin geometries as well as periodic domains and open boundary
70conditions are possible.
72Physical parameterisations are described in chapters~\ref{LDF} and \ref{ZDF}. The
73model includes an implicit treatment of vertical viscosity and diffusivity. The lateral
74Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential
75or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a
76space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic
77viscosity and diffusion with a space and time variable coefficient, with options to compute
78the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81},
79or \citet{Umlauf_Burchard_JMS03} mixing schemes.
81Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}.
82The diagnostics includes the output of all the tendencies of the momentum and tracers equations,
83the output of tracers tendencies averaged over the time evolving mixed layer, the output of
84the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories...
85Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature
86and salinity, sea surface temperature, sea level anomaly and sea ice concentration)
87and calculates an interpolated model equivalent value at the observation location
88and nearest model timestep. Originally developed of data assimilation, it is a fantastic
89tool for model and data comparison. Chapter~\ref{ASM} describes how increments
90produced by data assimilation may be applied to the model equations.
91Finally, Chapter~\ref{CFG} provides a brief introduction to the pre-defined model
92configurations (water column model, ORCA and GYRE families of configurations).
94The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor).
95It runs under UNIX. It is optimized for vector computers and parallelised by domain 
96decomposition with MPI. All input and output is done in NetCDF (Network Common Data
97Format) with a optional direct access format for output. To ensure the clarity and
98readability of the code it is necessary to follow coding rules. The coding rules for OPA
99include conventions for naming variables, with different starting letters for different types
100of variables (real, integer, parameter\ldots). Those rules are briefly presented in
101Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site.
103The model is organized with a high internal modularity based on physics. For example,
104each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and
105tracers is computed in a dedicated module.  To make it easier for the user to find his way
106around the code, the module names follow a three-letter rule. For example, \mdl{traldf} 
107is a module related to the TRAcers equation, computing the Lateral DiFfussion.
108%The complete list of module names is presented in Appendix~\ref{Apdx_D}.      %====>>>> to be done !
109Furthermore, modules are organized in a few directories that correspond to their category,
110as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}).
112The manual mirrors the organization of the model.
113After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters
114refer to specific terms of the equations each associated with a group of modules (Tab.~\ref{Tab_chap}).
119%\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline
120\caption{ \label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. }
121\begin{center}    \begin{tabular}{|l|l|l|}   \hline
122Chapter \ref{STP} & -                 & model time STePping environment \\    \hline
123Chapter \ref{DOM} & DOM    & model DOMain \\    \hline
124Chapter \ref{TRA} & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline
125Chapter \ref{DYN} & DYN    & DYNamic equations (momentum) \\      \hline
126Chapter \ref{SBC}    & SBC    & Surface Boundary Conditions \\       \hline
127Chapter \ref{LBC} & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline
128Chapter \ref{LDF} & LDF    & Lateral DiFfusion (parameterisations) \\   \hline
129Chapter \ref{ZDF} & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline
130Chapter \ref{DIA} & DIA    & I/O and DIAgnostics (also IOM, FLO and TRD) \\      \hline
131Chapter \ref{OBS} & OBS    & OBServation and model comparison  \\    \hline
132Chapter \ref{ASM} & ASM    & ASsiMilation increment  \\     \hline
133Chapter \ref{MISC}   & SOL    & Miscellaneous  topics (including solvers)  \\       \hline
134Chapter \ref{CFG} &  -        & predefined configurations (including C1D) \\     \hline
136\end{center}   \end{table}
140\subsubsection{Changes between releases}
141NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes
142the OPA version include in the release 3.3 of NEMO.  This release differs significantly
143from version 8, documented in \citet{Madec1998}.\\
145$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
146(1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic
147reduction of CPP keys; \\
148(2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; \\
149(3) partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$)
150with the addition of several options for pressure gradient computation \footnote{Partial
151support of $s$-coordinate: there is presently no support for neutral physics in $s$-
152coordinate and for the new options for horizontal pressure gradient computation with
153a non-linear equation of state.}; \\ 
154(4) more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes. \\
155(5) suppression of the rigid-lid option;\\
156(6) non linear free surface option (associated with the rescaled height coordinate 
157\textit{z*} or  \textit{s}); \\
158(6) additional schemes for vector and flux forms of the momentum  advection; \\
159(7) additional advection schemes for tracers; \\
160(8) implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; \\
161(9) online diagnostics : tracers trend in the mixed layer and vorticity balance; \\
162(10) rewriting of the I/O management with the use of an I/O server; \\
163(11) generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler. \\
164(12) surface module (SBC) that simplify the way the ocean is forced and include two
165bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields\\
166(13) RGB light penetration and optional use of ocean color
167(14) major changes in the TKE schemes: it now includes a Langmuir cell parameterization  \citep{Axell_JGR02},
168the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization
169which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; \\
170(15) tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07}; \\
171(16) introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
172new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
174 \vspace{1cm}
175$\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.3 are :\\
176(1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\
177(2) additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\
178(3) a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; \\
179(4) addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03};
180(5) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\
181(6) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\
182(7) river runoffs added through a non-zero depth, and having its own temperature and salinity; \\
183(8) CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ; \\
184(9) generalisation of the use of \mdl{fldread} for all input fields (ocean, climatology, sea-ice damping...)
185(10) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\
186(11) optional application of an assimilation increment (thanks to NEMOVAR project); \\
187(12) coupling interface adjusted for WRF atmospheric model
188(13) C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; \\
189(14) a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ;  \\
190(15) the merge of passive and active advection and diffusion modules \\
191(16)  Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; \\
192(17) Linear-tangent and Adjoint component (TAM) added, phased with v3.0
194 \vspace{1cm}
195In addition, several minor modifications in the coding have been introduced with the constant
196concern of improving the model performance.
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