1 | %\begin{figure}[htbp] |
---|
2 | %\centerline{\includegraphics[width=1.64in,height=11.72in]{OPA9_Chap_0_Introduction1.eps}} |
---|
3 | %\label{fig1} |
---|
4 | %\end{figure} |
---|
5 | |
---|
6 | \textbf{Institut Pierre Simon Laplace} |
---|
7 | |
---|
8 | \textbf{des Sciences de l'Environnement Global} |
---|
9 | |
---|
10 | \textit{Notes du P\^{o}le de Mod\'{e}lisation} |
---|
11 | |
---|
12 | NEMO : the OPA ocean engine |
---|
13 | |
---|
14 | (NEMO version 2.3) |
---|
15 | |
---|
16 | Gurvan Madec, {\ldots} |
---|
17 | |
---|
18 | Laboratoire d'Oc\'{e}anographie et du Climat: Exp\'{e}rimentation |
---|
19 | |
---|
20 | et Approches Num\'{e}riques |
---|
21 | |
---|
22 | %\begin{figure}[htbp] |
---|
23 | %\centerline{\includegraphics[width=4.58in,height=4.35in]{OPA9_Chap_0_Introduction2.eps}} |
---|
24 | %\label{fig2} |
---|
25 | %\end{figure} |
---|
26 | |
---|
27 | \newpage |
---|
28 | \begin{center} |
---|
29 | NEMO : the OPA ocean engine |
---|
30 | \end{center} |
---|
31 | |
---|
32 | Gurvan Madec |
---|
33 | |
---|
34 | Laboratoire d'Oc\'{e}anographie et du Climat: Exp\'{e}rimentation Approches |
---|
35 | Num\'{e}riques |
---|
36 | |
---|
37 | CNRS/IRD/UPMC, UMR 7617 |
---|
38 | |
---|
39 | \subsection{Abstract} |
---|
40 | \label{subsec:abstract} |
---|
41 | OPA is the ocean engine of NEMO, a framework of ocean related components |
---|
42 | developed for both research and operational purposes. It is a primitive |
---|
43 | equation model adapted to regional and global ocean circulation. It is |
---|
44 | intended to be a flexible tool for studying the ocean and its interactions |
---|
45 | with the others components of the earth climate system (atmosphere, sea-ice, |
---|
46 | biogeochemical tracers, ...) over a wide range of space and time scales. |
---|
47 | Prognostic variables are the three-dimensional velocity field, the sea |
---|
48 | surface height, the temperature and the salinity. In the horizontal |
---|
49 | direction, the model uses a curvilinear orthogonal grid and in the vertical |
---|
50 | direction, a $z$ full or partial step coordinate, or $s$-coordinate, or a mixture |
---|
51 | of the two. The distribution of variables is a three-dimensional Arakawa |
---|
52 | C-type grid. Various physical choices are available to describe ocean |
---|
53 | physics, including a 1.5 turbulent closure or a KPP scheme for the vertical |
---|
54 | mixing. Within NEMO, OPA is interfaced with a sea-ice model (LIM), passive |
---|
55 | tracer and biogeochemical models (TOP) and, via the OASIS coupler, with |
---|
56 | several atmospheric general circulation models. In addition, it can be run |
---|
57 | on many different computers, including shared and distributed memory |
---|
58 | multiprocessor computers. |
---|
59 | |
---|
60 | \textsc{\textbf{R\'{e}sum\'{e}}} |
---|
61 | |
---|
62 | OPA est le moteur oc\'{e}anique de NEMO, un syst\`{e}me de mod\'{e}lisation |
---|
63 | de l'oc\'{e}an d\'{e}velopp\'{e} \`{a} des fins de recherche et |
---|
64 | d'oc\'{e}anographie op\'{e}rationnelle. Ce moteur est un mod\`{e}le aux |
---|
65 | \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et |
---|
66 | globale. Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre |
---|
67 | spatiotemporel l'oc\'{e}an et ses interactions avec les autres composantes |
---|
68 | du syst\`{e}me climatique terrestre (atmosph\`{e}re, glace de mer, traceurs |
---|
69 | biog\'{e}ochimiques...). Les variables pronostiques sont le champ |
---|
70 | tridimensionnel de vitesse, la hauteur de la mer , la temperature et la |
---|
71 | salinit\'{e}. La distribution des variables se fait sur une grille $C$ |
---|
72 | d'Arakawa tridimensionnelle utilisant une coordonn\'{e}e verticale $z$ \`{a} |
---|
73 | niveaux entiers ou partiels, ou une coordonn\'{e}e$ s$, ou encore une |
---|
74 | combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour |
---|
75 | d\'{e}crire la physique oc\'{e}anique, incluant notamment une fermeture |
---|
76 | turbulente d'ordre 1.5 ou un sch\'{e}ma KPP pour le m\'{e}lange vertical. |
---|
77 | Via l'infrastructure NEMO, OPA est interfac\'{e} avec un mod\`{e}le de glace |
---|
78 | de mer, des mod\`{e}les biog\'{e}ochimiques et de traceur passif, et, via le |
---|
79 | coupleur OASIS, \`{a} plusieurs mod\`{e}les de circulation g\'{e}n\'{e}rale |
---|
80 | atmosph\'{e}rique. En outre, il peut \^{e}tre ex\'{e}cut\'{e} sur de |
---|
81 | nombreux calculateurs, y compris des calculateurs multiprocesseurs \`{a} |
---|
82 | m\'{e}moire partag\'{e}e ou distribu\'{e}e. |
---|
83 | |
---|
84 | \newpage |
---|
85 | \textbf{PLAN :} |
---|
86 | |
---|
87 | Put it here |
---|
88 | |
---|
89 | \textsc{\textbf{Disclaimer 1}} |
---|
90 | |
---|
91 | \textsc{\textbf{Foreword 3}} |
---|
92 | |
---|
93 | \textsc{\textbf{Introduction 4}} |
---|
94 | |
---|
95 | \textsc{\textbf{Disclaimer}} |
---|
96 | |
---|
97 | OPA (an acronym for Ocean PArall\'{e}lis\'{e}) is the ocean component of |
---|
98 | NEMO (Nucleus for European Modelling of the Ocean (\underline |
---|
99 | {www.locean-ipsl.upmc.fr/NEMO}). Like all components of NEMO, it is |
---|
100 | developed under the CECILL license, which is a french adaptation of the GNU |
---|
101 | \textbf{GPL} (General Public license). Anyone may use OPA freely for |
---|
102 | research purposes, and is encouraged to communicate back to the NEMO team |
---|
103 | its own developments and improvements. The model and the present document |
---|
104 | have been made available as a service to the community. We cannot certify |
---|
105 | that the code and its manual are free of errors. Bugs are inevitable and |
---|
106 | some have undoubtedly survived the testing phase. Users are encouraged to |
---|
107 | bring them to our attention. The author assumes no responsibility for |
---|
108 | problems, errors, or incorrect usage of OPA. |
---|
109 | |
---|
110 | The OPA OGCM reference in papers and other publications is as follows: |
---|
111 | |
---|
112 | Madec, G., 2007: NEMO: the OPA ocean engine. Note du P\^{o}le de |
---|
113 | mod\'{e}lisation, Institut Pierre-Simon Laplace (IPSL), France, N\r{ }XX, |
---|
114 | YYpp. |
---|
115 | |
---|
116 | Gurvan Madec: gm@locean-ipsl.upmc.fr |
---|
117 | |
---|
118 | {\ldots}. |
---|
119 | |
---|
120 | \textsc{\textbf{Foreword}} |
---|
121 | |
---|
122 | OPA is the ocean engine of the Nucleus of European Model of the Ocean |
---|
123 | (NEMO). This model, like all research tools, is in perpetual evolution. The |
---|
124 | present document describes the OPA model include in the release 2.3 of NEMO. |
---|
125 | This is the release 9 of OPA. This version differs significantly from |
---|
126 | version 8, documented in Madec \textit{et al.} (1998). The major modifications are |
---|
127 | |
---|
128 | (1) transition to full native Fortran 90, deep code restructuring and |
---|
129 | drastic reduction of CPP keys, |
---|
130 | |
---|
131 | (2) introduction of partial step representation of bottom topography |
---|
132 | |
---|
133 | (3) reactivation of a terrain-following vertical coordinate |
---|
134 | ($s-$coordinates) with the addition of several options for pressure gradient |
---|
135 | computation, |
---|
136 | |
---|
137 | (4) mixed $z-s$ coordinate |
---|
138 | |
---|
139 | (5) more choices for the treatment of the free surface: full explicit, |
---|
140 | split-explicit , filtered and rigid-lid |
---|
141 | |
---|
142 | (6) non linear free surface option (variable level thickness distributed on |
---|
143 | the whole water column) |
---|
144 | |
---|
145 | (7) additional schemes for vector and flux forms of the momentum advection |
---|
146 | |
---|
147 | (8) addition of several advection schemes on tracers |
---|
148 | |
---|
149 | (9) implementation of the AGRIF package (Adaptative Grid Refinement in |
---|
150 | Fortran) |
---|
151 | |
---|
152 | (10) online diagnostics : tracers trend in the mixed layer and vorticity |
---|
153 | balance |
---|
154 | |
---|
155 | (11) rewriting of the I/O management |
---|
156 | |
---|
157 | (12) OASIS 3 and 4 couplers interfacing with atmospheric global circulation |
---|
158 | models. |
---|
159 | |
---|
160 | In addition, several minor modifications in the coding have been introduced |
---|
161 | with the constant concern of improving performance on both scalar and vector |
---|
162 | computers. |
---|
163 | |
---|
164 | At the time of this writing, the current release is NEMO 2.3. The new |
---|
165 | surface module described in this document is not yet part of the current |
---|
166 | distribution. |
---|
167 | |
---|
168 | \newpage |
---|
169 | |
---|
170 | \textsc{\textbf{Introduction}} |
---|
171 | |
---|
172 | The Nucleus for European Modelling of the Ocean (NEMO) is a framework of |
---|
173 | ocean related engines, namely OPA for the Ocean dynamics and thermodynamics, |
---|
174 | LIM for the sea-ice dynamics and thermodynamics, TOP for the biogeochemistry |
---|
175 | (both transport (TRP) and sources minus sinks (LOBSTER, PISCES). It is |
---|
176 | intended to be a flexible tool for studying the ocean and its interactions |
---|
177 | with the others components of the earth climate system (atmosphere, sea-ice, |
---|
178 | biogeochemical tracers, ...) over a wide range of space and time scales. |
---|
179 | This documentation provides information about the physics represented by the |
---|
180 | OPA ocean model and the rationale for the choice of numerical schemes and |
---|
181 | the model design. More specific information about running the model on |
---|
182 | different computers, or how to set up a configuration, are found on the NEMO |
---|
183 | web site (\underline {www.locean-ipsl.upmc.fr/NEMO}). |
---|
184 | |
---|
185 | The ocean component of NEMO has been developed from the OPA8.2 model |
---|
186 | described in Madec \textit{et al.} (1998). This model has been used for a wide range of |
---|
187 | applications, either regional or global, as a forced ocean model or coupled |
---|
188 | with the atmosphere. A complete list of references is found on the NEMO web |
---|
189 | site. |
---|
190 | |
---|
191 | This manual is organised in four parts. The first part presents the model |
---|
192 | basics, i.e. the equations and their assumptions, the vertical coordinates |
---|
193 | used, and the subgrid scale physics. This part deals with the continuous |
---|
194 | equations of the model (primitive equations, with potential temperature, |
---|
195 | salinity and an equation of state). The equations are written in a |
---|
196 | curvilinear coordinate system, with a choice of vertical coordinates ($z$, $s$, |
---|
197 | and variable volumes). Momentum equations are formulated in the vector |
---|
198 | invariant form. The model equations are written in dimensional units in the |
---|
199 | meter, kilogram, second (MKS) international system |
---|
200 | |
---|
201 | The following chapters deal with the discrete equations. The second chapter |
---|
202 | presents the space and time domain. The model is discretised on a staggered |
---|
203 | grid (Arakawa C grid) with masking of land areas. Vertical discretisation |
---|
204 | uses $z$ coordinates (including partial step), $s$ (terrain-following) coordinate |
---|
205 | (fixed volume thickness and linear free surface), or$ s* $coordinate (variable |
---|
206 | volume thickness and nonlinear free surface). The following chapters |
---|
207 | describe the discretisation of the prognostic equations (momentum and |
---|
208 | tracers). Explicit, split-explicit or implicit free surface formulations are |
---|
209 | implemented as well as arid-lid approximation. A number of numerical schemes |
---|
210 | are available for momentum advection, for the computation of the pressure |
---|
211 | gradients, as well as for the advection of tracers (second or higher order |
---|
212 | advection schemes, including positive ones). |
---|
213 | |
---|
214 | Physical parameterisations are described in chapters The model includes an |
---|
215 | implicit treatment of vertical viscosity and diffusivity. The lateral |
---|
216 | Laplacian and biharmonic viscosity and diffusion can be rotated following a |
---|
217 | geopotential or neutral direction. There is an optional eddy induced |
---|
218 | velocity (Gent and McWilliams 1992) with a space and time variable |
---|
219 | coefficient, with options to compute the coefficients with Tr\'{e}guier et |
---|
220 | al. (199X), or Visbeck et al. XXX) schemes. The model has vertical harmonic |
---|
221 | viscosity and diffusion with a space and time variable coefficient, with |
---|
222 | options to compute the coefficients with Blanke and Delecluse (1992), Large |
---|
223 | et al. (1994), or Pacanowski and Philander (1981) mixing schemes. |
---|
224 | |
---|
225 | Optional tidal mixing parametrisation |
---|
226 | |
---|
227 | Other model characteristics (chapter {\ldots}) are the lateral boundary |
---|
228 | conditions. Global configurations of the model make use of the ORCA tripolar |
---|
229 | grid, with special north fold boundary condition. Free-slip or no-slip |
---|
230 | boundary conditions are allowed at land boundaries. Closed basin geometries |
---|
231 | as well as periodic domains and open boundary conditions are possible. |
---|
232 | |
---|
233 | Surface boundary conditions can be implemented as prescribed fluxes, or bulk |
---|
234 | formulations for the surface fluxes (wind stress, heat, freshwater). The |
---|
235 | model allows penetration of solar radiation There is an optional geothermal |
---|
236 | heating at the ocean bottom. Within the NEMO system the ocean model is |
---|
237 | interactively coupled with a sea ice model (LIM) and with biogeochemistry |
---|
238 | models (PISCES, LOBSTER).Interactive coupling to Atmospheric models is |
---|
239 | possible via the OASIS (ref!!!) coupler. |
---|
240 | |
---|
241 | Specific online diagnostics are available in the model: output of all the |
---|
242 | tendencies of the momentum and tracers equations, output of tracers |
---|
243 | tendencies averaged over the time evolving mixed layer. |
---|
244 | |
---|
245 | The model is implemented in Fortran 90, with preprocessing (C preprocessor). |
---|
246 | It runs under UNIX. It is optimized for vector computers and parallelised by |
---|
247 | domain decomposition with MPI. All input and output is done in NetCDF |
---|
248 | (Network Common Data Format) with a optional direct access format for |
---|
249 | output. To ensure the clarity and readability of the code it is necessary to |
---|
250 | follow \textit{coding rules}. The coding rules for OPA include conventions for naming variables, |
---|
251 | with different starting letters for different types of variables (real, |
---|
252 | integer, parameter{\ldots}) Those rules are presented in a document |
---|
253 | available on the NEMO web site.. |
---|
254 | |
---|
255 | The model is organized with a high internal modularity based on physics. In |
---|
256 | particular, each trend (e.g., a term in the rhs of the prognostic equation) |
---|
257 | for momentum and tracers is computed in a dedicated module. To make it |
---|
258 | easier for the user to find his way around the code, the module names follow |
---|
259 | the \textit{three-letter rule}. Each module name is made of three-letter sequences. For example, |
---|
260 | TRADMP.F90 is a module related to the TRAcers equation, computing the |
---|
261 | DaMPing. The complete list of module names is presented in annex. |
---|
262 | Furthermore, modules are organized in a few directories that correspond to |
---|
263 | their category, as indicated by the first three letters of their name. |
---|
264 | |
---|
265 | The manual follows this organization. After the presentation of the |
---|
266 | continuous equations (chapter 1), the following chapters refer to specific |
---|
267 | terms of the equations each associated with a group of modules . |
---|
268 | |
---|
269 | \begin{table}[htbp] |
---|
270 | \begin{center} |
---|
271 | \begin{tabular}{|p{143pt}|l|l|} |
---|
272 | \hline |
---|
273 | Chapter 2& |
---|
274 | DOM& |
---|
275 | Model DOMain \\ |
---|
276 | \hline |
---|
277 | Chapter 3& |
---|
278 | DYN& |
---|
279 | DYNamic equations (momentum) \\ |
---|
280 | \hline |
---|
281 | Chapter 4& |
---|
282 | TRA& |
---|
283 | TRAcer equations (potential temperature and salinity) \\ |
---|
284 | \hline |
---|
285 | Chapter 5 & |
---|
286 | SBC& |
---|
287 | Surface Boundary Conditions \\ |
---|
288 | \hline |
---|
289 | Chapter 6& |
---|
290 | LDF& |
---|
291 | Lateral DiFfusion (parameterisations) \\ |
---|
292 | \hline |
---|
293 | Chapter 7& |
---|
294 | ZDF& |
---|
295 | Vertical DiFfusion \\ |
---|
296 | \hline |
---|
297 | Chapter 8& |
---|
298 | OBC, lbclnk module& |
---|
299 | Lateral boundary conditions \\ |
---|
300 | \hline |
---|
301 | Chapter 9& |
---|
302 | miscellaneous& |
---|
303 | \\ |
---|
304 | \hline |
---|
305 | \end{tabular} |
---|
306 | \label{tab1} |
---|
307 | \end{center} |
---|
308 | \end{table} |
---|
309 | |
---|
310 | \textbf{Nota Bene :} |
---|
311 | |
---|
312 | Red color : not in the current reference version (v2.3beta) but expected |
---|
313 | soon |
---|
314 | |
---|
315 | Yellow : missing references, text to be updated{\ldots} |
---|
316 | |
---|
317 | \end{document} |
---|