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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 grid
44(Arakawa C grid) with masking of land areas and uses a Leap-frog environment for time-stepping.
45Vertical discretisation used depends on both how the bottom topography is represented and
46whether the free surface is linear or not. Full step or partial step $z$-coordinate or
47$s$- (terrain-following) coordinate is used with linear free surface (level position are then
48fixed in time). In non-linear free surface, the corresponding rescaled height coordinate
49formulation (\textit{z*} or \textit{s*}) is used (the level position then vary in time as a
50function of the sea surface heigh). The following two chapters (\ref{TRA} and \ref{DYN})
51describe the discretisation of the prognostic equations for the active tracers and the
52momentum. Explicit, split-explicit and 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.
81Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature and salinity,
82sea surface temperature, sea level anomaly and sea ice concentration) and calculates an interpolated
83model equivalent value at the observation location and nearest model timestep. Originally
84developed of data assimilation, it is a fantastic tool for model and data comparison.
85Other Specific online diagnostics (not documented yet) are available in the model: output of all
86the tendencies of the momentum and tracers equations, output of tracers tendencies
87averaged over the time evolving mixed layer, output of the tendencies of the barotropic
88vorticity equation, on-line floats trajectories...
90The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor).
91It runs under UNIX. It is optimized for vector computers and parallelised by domain 
92decomposition with MPI. All input and output is done in NetCDF (Network Common Data
93Format) with a optional direct access format for output. To ensure the clarity and
94readability of the code it is necessary to follow coding rules. The coding rules for OPA
95include conventions for naming variables, with different starting letters for different types
96of variables (real, integer, parameter\ldots). Those rules are briefly presented in
97Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site.
99The model is organized with a high internal modularity based on physics. For example,
100each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and
101tracers is computed in a dedicated module.  To make it easier for the user to find his way
102around the code, the module names follow a three-letter rule. For example, \mdl{traldf} 
103is a module related to the TRAcers equation, computing the Lateral DiFfussion.
104The complete list of module names is presented in Appendix~\ref{Apdx_D}.
105Furthermore, modules are organized in a few directories that correspond to their category,
106as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}).
108The manual mirrors the organization of the model.
109After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters
110refer to specific terms of the equations each associated with a group of modules (Tab.~\ref{Tab_chap}).
115%\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline
116\begin{center}    \begin{tabular}{|l|l|l|}   \hline
117Chapter \ref{STP} & -                 & model time STePping environment \\    \hline
118Chapter \ref{DOM} & DOM    & model DOMain \\    \hline
119Chapter \ref{TRA} & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline
120Chapter \ref{DYN} & DYN    & DYNamic equations (momentum) \\      \hline
121Chapter \ref{SBC}    & SBC    & Surface Boundary Conditions \\       \hline
122Chapter \ref{LBC} & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline
123Chapter \ref{LDF} & LDF    & Lateral DiFfusion (parameterisations) \\   \hline
124Chapter \ref{ZDF} & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline
125Chapter \ref{OBS} & OBS    & OBServation and model comparison  \\    \hline
126Chapter \ref{ASM} & ASM    & ASsimilation increment  \\     \hline
127Chapter \ref{MISC}   & ...       & Miscellaneous  topics (DIA, DTA, IOM,   \\
128                  &              & SOL, TRD, FLO...)   \\       \hline
129Chapter \ref{CFG} &  -        & predefined configurations  \\     \hline
131\caption{    \label{Tab_chap}
132Organization of Chapters which miminc the one of the model directories. }
133\end{center}   \end{table}
137\subsubsection{Changes between releases}
138NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes
139the OPA version include in the release 3.3 of NEMO.  This release differs significantly
140from version 8, documented in \citet{Madec1998}.\\
142$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
144(1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic
145reduction of CPP keys; \\
146(2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; \\
147(3) partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$)
148with the addition of several options for pressure gradient computation \footnote{Partial
149support of $s$-coordinate: there is presently no support for neutral physics in $s$-
150coordinate and for the new options for horizontal pressure gradient computation with
151a non-linear equation of state.}; \\ 
152(4) more choices for the treatment of the free surface: full explicit, split-explicit and filtered. \\
153(5) suppression of the rigid-lid option;\\
154(6) non linear free surface option (associated with the rescaled height coordinate 
155\textit{z*} or  \textit{s}); \\
156(6) additional schemes for vector and flux forms of the momentum  advection; \\
157(7) additional advection schemes for tracers; \\
158(8) implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; \\
159(9) online diagnostics : tracers trend in the mixed layer and vorticity balance; \\
160(10) rewriting of the I/O management with the use of an I/O server; \\
161(11) generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler. \\
162(12) surface module (SBC) that simplify the way the ocean is forced and include two
163bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields\\
164(13) introduction of LIM 3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
165new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
167 \vspace{1cm}
168$\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.2 are :\\
170(1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\
171(2) additional scheme for  iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\
172(3) a rewriting of the bottom boundary scheme, following \citet{Campin_Goosse_Tel99}; \\
173(4) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\
174(5) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\
175(6) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\
176(7) optional application of an assimilation increment (thanks to NEMOVAR project); \\
177(8) introduction of .....   
179 \vspace{1cm}
180In addition, several minor modifications in the coding have been introduced with the constant
181concern of improving the model performance.
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