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10The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean
11related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the
12ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice
13Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer
14in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources
15minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not
16acronyms just name}. It is intended to be a flexible tool for studying the ocean and
17its interactions with the other components of the earth climate system (atmosphere,
18sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.
19This documentation provides information about the physics represented by the ocean
20component of \NEMO and the rationale for the choice of numerical schemes and
21the model design. More specific information about running the model on different
22computers, or how to set up a configuration, are found on the \NEMO web site
25The ocean component of \NEMO has been developed from the OPA model,
26release 8.2, described in \citet{Madec1998}. This model has been used for a wide
27range of applications, both regional or global, as a forced ocean model and as a
28model coupled with the sea-ice and/or the atmosphere. 
30This manual is organised in as follows. Chapter~\ref{PE} presents the model basics,
31$i.e.$ the equations and their assumptions, the vertical coordinates used, and the
32subgrid scale physics. This part deals with the continuous equations of the model
33(primitive equations, with temperature, salinity and an equation of seawater).
34The equations are written in a curvilinear coordinate system, with a choice of vertical
35coordinates ($z$, $s$, \textit{z*}, \textit{s*}, $\tilde{z}$, $\tilde{s}$, and a mixture of them).
36Momentum equations are formulated in vector invariant or flux form.
37Dimensional units in the meter, kilogram, second (MKS) international system
38are used throughout.
40The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the
41time domain. The model time stepping environment is a three level scheme in which
42the tendency terms of the equations are evaluated either centered  in time, or forward,
43or backward depending of the nature of the term.
44Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered
45grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends
46on both how the bottom topography is represented and whether the free surface is linear or not.
47Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used
48with linear free surface (level position are then fixed in time). In non-linear free surface,
49the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used
50(the level position then vary in time as a function of the sea surface heigh).
51The following two chapters (\ref{TRA} and \ref{DYN}) describe the discretisation of the
52prognostic equations for the active tracers and the momentum. Explicit, split-explicit
53and filtered free surface formulations are implemented.
54A number of numerical schemes are available for momentum advection, for the computation
55of the pressure gradients, as well as for the advection of tracers (second or higher
56order advection schemes, including positive ones).
58Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed
59fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The
60model allows penetration of solar radiation  There is an optional geothermal heating at
61the ocean bottom. Within the \NEMO system the ocean model is interactively coupled
62with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER).
63Interactive coupling to Atmospheric models is possible via the OASIS coupler
64\citep{OASIS2006}. Two-way nesting is also available through an interface to the
65AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}.
66The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008})
67has now been upgraded so that it works for both global and regional domains, although AGRIF
68is still not available.
70Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}). 
71Global configurations of the model make use of the ORCA tripolar grid, with special north
72fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land
73boundaries. Closed basin geometries as well as periodic domains and open boundary
74conditions are possible.
76Physical parameterisations are described in chapters~\ref{LDF} and \ref{ZDF}. The
77model includes an implicit treatment of vertical viscosity and diffusivity. The lateral
78Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential
79or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a
80space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic
81viscosity and diffusion with a space and time variable coefficient, with options to compute
82the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81},
83or \citet{Umlauf_Burchard_JMS03} mixing schemes.
84 \vspace{1cm}
86%%gm    To be put somewhere else ....
88\noindent CPP keys and namelists are used for inputs to the code.  \newline
90\noindent \index{CPP keys} CPP keys \newline
91Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time.
92Usual coding looks like :
93 \vspace{-10pt}
97#if defined key_option1   
98             This part of the FORTRAN code will be active   
99             only if key_option1 is activated at compiling step
105\noindent \index{Namelist} Namelists
107The namelist allows to input variables (character, logical, real and integer) into the code. There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) containing all the FOTRAN namelists needed. The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read:
109\item A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. This file contains all the namelist variables which are initialised to default values 
110\item A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. This file contains only the namelist variables which are changed from default values, and overwrites those.
112A template can be found in \path{NEMO/OPA_SRC/module.example}.
113The effective namelist, taken in account during the run, is stored at execution time in an output\_namelist\_dyn (or \_ice or \_top) file.
114 \vspace{1cm}
116%%gm  end
118Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}.
119The diagnostics includes the output of all the tendencies of the momentum and tracers equations,
120the output of tracers tendencies averaged over the time evolving mixed layer, the output of
121the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories...
122Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature
123and salinity, sea surface temperature, sea level anomaly and sea ice concentration)
124and calculates an interpolated model equivalent value at the observation location
125and nearest model timestep. Originally developed of data assimilation, it is a fantastic
126tool for model and data comparison. Chapter~\ref{ASM} describes how increments
127produced by data assimilation may be applied to the model equations.
128Finally, Chapter~\ref{CFG} provides a brief introduction to the pre-defined model
129configurations (water column model, ORCA and GYRE families of configurations).
131The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor).
132It runs under UNIX. It is optimized for vector computers and parallelised by domain 
133decomposition with MPI. All input and output is done in NetCDF (Network Common Data
134Format) with a optional direct access format for output. To ensure the clarity and
135readability of the code it is necessary to follow coding rules. The coding rules for OPA
136include conventions for naming variables, with different starting letters for different types
137of variables (real, integer, parameter\ldots). Those rules are briefly presented in
138Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site.
140The model is organized with a high internal modularity based on physics. For example,
141each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and
142tracers is computed in a dedicated module.  To make it easier for the user to find his way
143around the code, the module names follow a three-letter rule. For example, \mdl{traldf} 
144is a module related to the TRAcers equation, computing the Lateral DiFfussion.
145%The complete list of module names is presented in Appendix~\ref{Apdx_D}.      %====>>>> to be done !
146Furthermore, modules are organized in a few directories that correspond to their category,
147as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}).
149The manual mirrors the organization of the model.
150After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters
151refer to specific terms of the equations each associated with a group of modules (Tab.~\ref{Tab_chap}).
156%\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline
157\caption{ \label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. }
158\begin{center}    \begin{tabular}{|l|l|l|}   \hline
159Chapter \ref{STP} & -                 & model time STePping environment \\    \hline
160Chapter \ref{DOM} & DOM    & model DOMain \\    \hline
161Chapter \ref{TRA} & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline
162Chapter \ref{DYN} & DYN    & DYNamic equations (momentum) \\      \hline
163Chapter \ref{SBC}    & SBC    & Surface Boundary Conditions \\       \hline
164Chapter \ref{LBC} & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline
165Chapter \ref{LDF} & LDF    & Lateral DiFfusion (parameterisations) \\   \hline
166Chapter \ref{ZDF} & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline
167Chapter \ref{DIA} & DIA    & I/O and DIAgnostics (also IOM, FLO and TRD) \\      \hline
168Chapter \ref{OBS} & OBS    & OBServation and model comparison  \\    \hline
169Chapter \ref{ASM} & ASM    & ASsiMilation increment  \\     \hline
170Chapter \ref{MISC}   & SOL    & Miscellaneous  topics (including solvers)  \\       \hline
171Chapter \ref{CFG} &  -        & predefined configurations (including C1D) \\     \hline
173\end{center}   \end{table}
177\subsubsection{Changes between releases}
178NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes
179the OPA version include in the release 3.4 of NEMO.  This release differs significantly
180from version 8, documented in \citet{Madec1998}.\\
182$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
184\item transition to full native \textsc{Fortran} 90, deep code restructuring and drastic
185reduction of CPP keys;
186\item introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07};
187\item partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$)
188with the addition of several options for pressure gradient computation \footnote{Partial
189support of $s$-coordinate: there is presently no support for neutral physics in $s$-
190coordinate and for the new options for horizontal pressure gradient computation with
191a non-linear equation of state.};
192\item more choices for the treatment of the free surface: full explicit, split-explicit or filtered
193schemes, and suppression of the rigid-lid option;
194\item non linear free surface associated with the rescaled height coordinate 
195\textit{z*} or  \textit{s};
196\item additional schemes for vector and flux forms of the momentum  advection;
197\item additional advection schemes for tracers;
198\item implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008};
199\item online diagnostics : tracers trend in the mixed layer and vorticity balance;
200\item rewriting of the I/O management with the use of an I/O server;
201\item generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler ;
202\item surface module (SBC) that simplify the way the ocean is forced and include two
203bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields ;
204\item RGB light penetration and optional use of ocean color
205\item major changes in the TKE schemes: it now includes a Langmuir cell parameterization  \citep{Axell_JGR02},
206the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization
207which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08};
208\item tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07};
209\item introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
210new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
213 \vspace{1cm}
214$\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.3 are :\\
216\item introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09};
217\item additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress";
218\item a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99};
219\item addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03};
220\item addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics;
221\item addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07};
222\item river runoffs added through a non-zero depth, and having its own temperature and salinity;
223\item CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ;
224\item generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...) ;
225\item addition of an on-line observation and model comparison (thanks to NEMOVAR project);
226\item optional application of an assimilation increment (thanks to NEMOVAR project);
227\item coupling interface adjusted for WRF atmospheric model;
228\item C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09};
229\item LIM-3 ice-ocean momentum coupling applied to LIM-2 ;
230\item a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ;
231\item the merge of passive and active advection and diffusion modules ;
232\item  Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ;
233\item Linear-tangent and Adjoint component (TAM) added, phased with v3.0
235 \vspace{1cm}
236In addition, several minor modifications in the coding have been introduced with the constant
237concern of improving the model performance.
239 \vspace{1cm}
240$\bullet$ The main modifications from NEMO/OPA v3.3 and  v3.4 are :\\
242\item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}";
243\item "Neptune effect" parametrisation;
244\item horizontal pressure gradient suitable for s-coordinate;
245\item semi-implicit bottom friction;
246\item finalisation of the merge of passive and active tracers advection-diffusion modules;
247\item a new bulk formulae (so-called MFS);
248\item use fldread for the off-line tracer component (OFF\_SRC) ;
249\item use MPI point to point communications  for north fold;
250\item diagnostic of transport ;
254 \vspace{1cm}
255$\bullet$ The main modifications from NEMO/OPA v3.4 and  v3.6 are :\\
257 \item ... ;
261 \vspace{1cm}
262$\bullet$ The main modifications from NEMO/OPA v3.6 and  v4.0 are :\\
264\item new definition of configurations ;
265\item bulk formulation ;
266\item ... ;
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