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

source: NEMO/trunk/doc/latex/NEMO/subfiles/introduction.tex @ 10442

Last change on this file since 10442 was 10442, checked in by nicolasmartin, 4 years ago

Front page edition, cleaning in custom LaTeX commands and add index for single subfile compilation

  • Use \thanks storing cmd to refer to the ST members list for 2018 in an footnote on the cover page
  • NEMO and Fortran in small capitals
  • Removing of unused or underused custom cmds, move local cmds to their respective .tex file
  • Addition of new ones (\zstar, \ztilde, \sstar, \stilde, \ie, \eg, \fortran, \fninety)
  • Fonts for indexed items: italic font for files (modules and .nc files), preformat for code (CPP keys, routines names and namelists content)
File size: 16.9 KB
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11The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines,
12namely OPA \footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics,
13LIM \footnote{LIM = Louvain la-neuve Ice Model} for the sea-ice dynamics and thermodynamics,
14TOP \footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources
15minus sinks (LOBSTER \footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for Ecosystem and Resources},
16PISCES \footnote{PISCES = Pelagic Interactions Scheme for Carbon and Ecosystem Studies})).
17It is intended to be a flexible tool for studying the ocean and its interactions with the other components of
18the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over
19a wide range of space and time scales.
20This documentation provides information about the physics represented by the ocean component of \NEMO and
21the rationale for the choice of numerical schemes and the model design.
22More specific information about running the model on different computers, or how to set up a configuration,
23are found on the \NEMO web site (
25The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}.
26This model has been used for a wide range of applications, both regional or global,
27as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere. 
29This manual is organised in as follows.
30\autoref{chap:PE} presents the model basics, \ie the equations and their assumptions,
31the vertical coordinates used, and the subgrid scale physics.
32This 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 coordinates
35($z$, $s$, \zstar, \sstar, \ztilde, \stilde, 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 are used throughout.
39The following chapters deal with the discrete equations.
40\autoref{chap:STP} presents the time domain.
41The model time stepping environment is a three level scheme in which the tendency terms of
42the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term.
43\autoref{chap:DOM} presents the space domain.
44The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas.
45Vertical discretisation used depends on both how the bottom topography is represented and
46whether the free surface is linear or not.
47Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with
48linear free surface (level position are then fixed in time).
49In non-linear free surface,
50the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used
51(the level position then vary in time as a function of the sea surface heigh).
52The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of
53the prognostic equations for the active tracers and the momentum.
54Explicit, split-explicit and filtered free surface formulations are implemented.
55A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients,
56as well as for the advection of tracers (second or higher order advection schemes, including positive ones).
58Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes,
59or bulk formulations for the surface fluxes (wind stress, heat, freshwater).
60The model allows penetration of solar radiation.
61There is an optional geothermal heating at the ocean bottom.
62Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and
63with biogeochemistry models (PISCES, LOBSTER).
64Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}.
65Two-way nesting is also available through an interface to the AGRIF package
66(Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}.
67The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so
68that it works for both global and regional domains, although AGRIF is still not available.
70Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}).
71Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition.
72Free-slip or no-slip boundary conditions are allowed at land boundaries.
73Closed basin geometries as well as periodic domains and open boundary conditions are possible.
75Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}.
76The model includes an implicit treatment of vertical viscosity and diffusivity.
77The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following
78a geopotential or neutral direction.
79There is an optional eddy induced velocity \citep{Gent1990} with a space and time variable coefficient
81The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient,
82with options to compute the 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.
92This selection of code at compilation time reduces the reliability of the whole platform since
93it changes the code from one set of CPP keys to the other.
94It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time.
95Usual coding looks like :
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
103\noindent \index{Namelist} Namelists
105The namelist allows to input variables (character, logical, real and integer) into the code.
106There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...)
107containing all the FOTRAN namelists needed.
108The implementation in NEMO uses a two step process. For each \fortran namelist, two files are read:
111  A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first.
112  This file contains all the namelist variables which are initialised to default values
114  A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards.
115  This file contains only the namelist variables which are changed from default values, and overwrites those.
117A template can be found in \path{NEMO/OPA_SRC/module.example}.
118The effective namelist, taken in account during the run, is stored at execution time in
119an output\_namelist\_dyn (or \_ice or \_top) file.
122%%gm  end
124Model outputs management and specific online diagnostics are described in \autoref{chap:DIA}.
125The diagnostics includes the output of all the tendencies of the momentum and tracers equations,
126the output of tracers tendencies averaged over the time evolving mixed layer,
127the output of the tendencies of the barotropic vorticity equation,
128the computation of on-line floats trajectories...
129\autoref{chap:OBS} describes a tool which reads in observation files
130(profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration)
131and calculates an interpolated model equivalent value at the observation location and nearest model timestep.
132Originally developed of data assimilation, it is a fantastic tool for model and data comparison.
133\autoref{chap:ASM} describes how increments produced by data assimilation may be applied to the model equations.
134Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model configurations
135(water column model, ORCA and GYRE families of configurations).
137The model is implemented in \fninety, with preprocessing (C-pre-processor).
138It runs under UNIX.
139It is optimized for vector computers and parallelised by domain decomposition with MPI.
140All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output.
141To ensure the clarity and readability of the code it is necessary to follow coding rules.
142The coding rules for OPA include conventions for naming variables,
143with different starting letters for different types of variables (real, integer, parameter\ldots).
144Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available on
145the \NEMO web site.
147The model is organized with a high internal modularity based on physics.
148For example, each trend (\ie, a term in the RHS of the prognostic equation) for momentum and tracers
149is computed in a dedicated module.
150To make it easier for the user to find his way around the code, the module names follow a three-letter rule.
151For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion.
152%The complete list of module names is presented in \autoref{apdx:D}.      %====>>>> to be done !
153Furthermore, modules are organized in a few directories that correspond to their category,
154as indicated by the first three letters of their name (\autoref{tab:chap}).
156The manual mirrors the organization of the model.
157After the presentation of the continuous equations (\autoref{chap:PE}),
158the following chapters refer to specific terms of the equations each associated with
159a group of modules (\autoref{tab:chap}).
164  % \begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline
165  \caption{ \protect\label{tab:chap}   Organization of Chapters mimicking the one of the model directories. }
166  \begin{center}
167    \begin{tabular}{|l|l|l|}  \hline
168      \autoref{chap:STP}   & -                 & model time STePping environment \\    \hline
169      \autoref{chap:DOM}   & DOM    & model DOMain \\    \hline
170      \autoref{chap:TRA}   & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline
171      \autoref{chap:DYN}   & DYN    & DYNamic equations (momentum) \\      \hline
172      \autoref{chap:SBC}   & SBC    & Surface Boundary Conditions \\       \hline
173      \autoref{chap:LBC}   & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline
174      \autoref{chap:LDF}   & LDF    & Lateral DiFfusion (parameterisations) \\   \hline
175      \autoref{chap:ZDF}   & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline
176      \autoref{chap:DIA}   & DIA    & I/O and DIAgnostics (also IOM, FLO and TRD) \\      \hline
177      \autoref{chap:OBS}   & OBS    & OBServation and model comparison  \\    \hline
178      \autoref{chap:ASM}   & ASM    & ASsiMilation increment  \\     \hline
179      \autoref{chap:MISC}  & SOL    & Miscellaneous  topics (including solvers)  \\       \hline
180      \autoref{chap:CFG}   &  -        & predefined configurations (including C1D) \\     \hline
181    \end{tabular}
182  \end{center}
187\subsubsection{Changes between releases}
188NEMO/OPA, like all research tools, is in perpetual evolution.
189The present document describes the OPA version include in the release 3.4 of NEMO.
190This release differs significantly from version 8, documented in \citet{Madec1998}.\\
192$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
195  transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys;
197  introduction of partial step representation of bottom topography
198  \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07};
200  partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with
201  the addition of several options for pressure gradient computation
202  \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in
203    $s$-coordinate and for the new options for horizontal pressure gradient computation with
204    a non-linear equation of state.
205  };
207  more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes,
208  and suppression of the rigid-lid option;
210  non linear free surface associated with the rescaled height coordinate \zstar or \textit{s};
212  additional schemes for vector and flux forms of the momentum advection;
214  additional advection schemes for tracers;
216  implementation of the AGRIF package (Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008};
218  online diagnostics : tracers trend in the mixed layer and vorticity balance;
220  rewriting of the I/O management with the use of an I/O server;
222  generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler;
224  surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and
225  which includes an on-the-fly interpolation of input forcing fields;
227  RGB light penetration and optional use of ocean color
229  major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02},
230  the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization which
231  is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08};
233  tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing
234  \citep{Koch-Larrouy_al_GRL07};
236  introduction of LIM-3, the new Louvain-la-Neuve sea-ice model
237  (C-grid rheology and new thermodynamics including bulk ice salinity)
238  \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
241 \vspace{1cm}
242$\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\
245  introduction of a modified leapfrog-Asselin filter time stepping scheme
246  \citep{Leclair_Madec_OM09};
248  additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress";
250  a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99};
252  addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03};
254  addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics;
256  addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07};
258  river runoffs added through a non-zero depth, and having its own temperature and salinity;
260  CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration;
262  generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...);
264  addition of an on-line observation and model comparison (thanks to NEMOVAR project);
266  optional application of an assimilation increment (thanks to NEMOVAR project);
268  coupling interface adjusted for WRF atmospheric model;
270  C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09};
272  LIM-3 ice-ocean momentum coupling applied to LIM-2;
274  a deep re-writting and simplification of the off-line tracer component (OFF\_SRC);
276  the merge of passive and active advection and diffusion modules;
278  Use of the Flexible Configuration Manager (FCM) to build configurations,
279  generate the Makefile and produce the executable;
281  Linear-tangent and Adjoint component (TAM) added, phased with v3.0
284In addition, several minor modifications in the coding have been introduced with the constant concern of
285improving the model performance.
288$\bullet$ The main modifications from NEMO/OPA v3.3 and  v3.4 are :\\
290\item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}";
291\item "Neptune effect" parametrisation;
292\item horizontal pressure gradient suitable for s-coordinate;
293\item semi-implicit bottom friction;
294\item finalisation of the merge of passive and active tracers advection-diffusion modules;
295\item a new bulk formulae (so-called MFS);
296\item use fldread for the off-line tracer component (OFF\_SRC);
297\item use MPI point to point communications  for north fold;
298\item diagnostic of transport;
302 \vspace{1cm}
303$\bullet$ The main modifications from NEMO/OPA v3.4 and  v3.6 are :\\
305 \item ... ;
309 \vspace{1cm}
310$\bullet$ The main modifications from NEMO/OPA v3.6 and  v4.0 are :\\
312\item new definition of configurations ;
313\item bulk formulation ;
314\item NEMO-wave large scale interactions ;
315\item ... ;
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