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1\documentclass[../tex_main/NEMO_manual]{subfiles}
2\begin{document}
3% ================================================================
4% Chapter � Configurations
5% ================================================================
6\chapter{Configurations}
7\label{chap:CFG}
8\minitoc
9
10\newpage
11$\ $\newline    % force a new ligne
12
13% ================================================================
14% Introduction
15% ================================================================
16\section{Introduction}
17\label{sec:CFG_intro}
18
19
20The purpose of this part of the manual is to introduce the \NEMO reference configurations.
21These configurations are offered as means to explore various numerical and physical options,
22thus allowing the user to verify that the code is performing in a manner consistent with that we are running.
23This form of verification is critical as one adopts the code for his or her particular research purposes.
24The reference configurations also provide a sense for some of the options available in the code,
25though by no means are all options exercised in the reference configurations.
26
27%------------------------------------------namcfg----------------------------------------------------
28
29\nlst{namcfg}
30%-------------------------------------------------------------------------------------------------------------
31
32% ================================================================
33% 1D model configuration
34% ================================================================
35\section{C1D: 1D Water column model (\protect\key{c1d}) }
36\label{sec:CFG_c1d}
37
38$\ $\newline
39BE careful: to be re-written according to suppression of jpizoom and jpjzoom !!!!
40$\ $\newline
41
42The 1D model option simulates a stand alone water column within the 3D \NEMO system.
43It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
44It is set up by defining the position of the 1D water column in the grid
45(see \textit{CONFIG/SHARED/namelist\_ref} ).
46The 1D model is a very useful tool
47\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
48\textit{(b)} to investigate suitable parameterisations of unresolved turbulence
49(surface wave breaking, Langmuir circulation, ...);
50\textit{(c)} to compare the behaviour of different vertical mixing schemes;
51\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain;
52\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
53
54The methodology is based on the use of the zoom functionality over the smallest possible domain:
55a 3x3 domain centered on the grid point of interest, with some extra routines.
56There is no need to define a new mesh, bathymetry, initial state or forcing,
57since the 1D model will use those of the configuration it is a zoom of.
58The chosen grid point is set in \textit{\ngn{namcfg}} namelist by
59setting the \np{jpizoom} and \np{jpjzoom} parameters to the indices of the location of the chosen grid point.
60
61The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
62and second, the two components of the velocity are moved on a $T$-point.
63Therefore, defining \key{c1d} changes five main things in the code behaviour:
64\begin{description}
65\item[(1)]
66  the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column of
67  the 3x3 domain is imposed over the whole domain;
68\item[(3)]
69  a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom});
70\item[(3)]
71  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
72  both lateral tendancy terms and lateral physics are not called;
73\item[(4)]
74  the vertical velocity is zero
75  (so far, no attempt at introducing a Ekman pumping velocity has been made);
76\item[(5)]
77  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
78  (see \mdl{dyncor\_c1d}).
79\end{description}
80All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
81the \NEMO distribution.
82
83% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
84
85% ================================================================
86% ORCA family configurations
87% ================================================================
88\section{ORCA family: global ocean with tripolar grid}
89\label{sec:CFG_orca}
90
91The ORCA family is a series of global ocean configurations that are run together with
92the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model (ORCA-LIM-PISCES),
93using various resolutions.
94An appropriate namelist is available in \path{CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg} for ORCA2.
95The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
96this file is available in tar file in the wiki of NEMO: \\
97https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ReferenceConfigurations/ORCA2\_LIM3\_PISCES \\
98In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.
99
100%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
101\begin{figure}[!t]
102  \begin{center}
103    \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh}
104    \caption{  \protect\label{fig:MISC_ORCA_msh}
105      ORCA mesh conception.
106      The departure from an isotropic Mercator grid start poleward of 20\degN.
107      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
108      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
109      Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed which
110      provides the j-lines of the mesh (pseudo longitudes).  }
111  \end{center}
112\end{figure}
113%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
114
115% -------------------------------------------------------------------------------------------------------------
116%       ORCA tripolar grid
117% -------------------------------------------------------------------------------------------------------------
118\subsection{ORCA tripolar grid}
119\label{subsec:CFG_orca_grid}
120
121The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
122It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
123the computational domain since two north mesh poles are introduced and placed on lands.
124The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
125computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
126The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles
127(\autoref{fig:MISC_ORCA_msh}).
128The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
129or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
130%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
131\begin{figure}[!tbp]
132  \begin{center}
133    \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
134    \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso}
135    \caption {  \protect\label{fig:MISC_ORCA_e1e2}
136      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
137      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
138      for ORCA 0.5\deg ~mesh.
139      South of 20\degN a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
140      Poleward of 20\degN, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
141      vicinity of Victoria Island (Canadian Arctic Archipelago). }
142\end{center}   \end{figure}
143%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
144
145
146The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward of 20\degN,
147so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
148The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
149is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
150(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
151the northern hemisphere larger than the smallest one in the southern hemisphere.
152The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for
153a half a degree grid (ORCA\_R05).
154The smallest ocean scale factor is found in along Antarctica,
155while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
156
157% -------------------------------------------------------------------------------------------------------------
158%       ORCA-LIM(-PISCES) configurations
159% -------------------------------------------------------------------------------------------------------------
160\subsection{ORCA pre-defined resolution}
161\label{subsec:CFG_orca_resolution}
162
163
164The NEMO system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
165The value of the resolution is given by the resolution at the Equator expressed in degrees.
166Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
167which sets the grid size and configuration name parameters.
168The NEMO System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
169(Tab. \autoref{tab:ORCA}).
170
171
172
173
174%--------------------------------------------------TABLE--------------------------------------------------
175\begin{table}[!t]     \begin{center}
176\begin{tabular}{p{4cm} c c c c}
177Horizontal Grid                         & \np{ORCA\_index} &  \np{jpiglo} & \np{jpjglo} &       \\ 
178\hline  \hline
179\~4\deg     &        4         &         92     &      76      &       \\
180\~2\deg        &        2         &       182     &    149      &        \\
181\~1\deg        &        1         &       362     &     292     &        \\
182\~0.5\deg     &        05       &       722     &     511     &        \\
183\~0.25\deg   &        025     &      1442    &   1021     &        \\
184%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
185%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
186\hline   \hline
187\end{tabular}
188\caption{ \protect\label{tab:ORCA}
189  Domain size of ORCA family configurations.
190  The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. }
191\end{center}
192\end{table}
193%--------------------------------------------------------------------------------------------------------------
194
195
196The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh,
197local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
198so that the resolution is 1\deg \time 1\deg there.
199A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
2000.5\deg at the Equator.
201
202The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
2031/3\deg~at the Equator.
204Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
205
206The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
207
208For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
209In the other ORCA configurations, 31 levels are used
210(see \autoref{tab:orca_zgr} \sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
211
212Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
213It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
214climate change (Marti et al., 2009).
215It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
216documented in \citet{Griffies_al_OM09}.
217
218This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
219(see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).
220The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
221The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \autoref{subsec:SBC_blk_core}),
222which was developed for the purpose of running global coupled ocean-ice simulations without
223an interactive atmosphere.
224This \citet{Large_Yeager_Rep04} dataset is available through
225the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
226The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution since release v3.3.
227
228ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area
229(\key{agrif} defined) and, by setting the appropriate variables, see \path{CONFIG/SHARED/namelist_ref}.
230A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
231sponge layers at open boundaries.
232
233% -------------------------------------------------------------------------------------------------------------
234%       GYRE family: double gyre basin
235% -------------------------------------------------------------------------------------------------------------
236\section{GYRE family: double gyre basin }
237\label{sec:CFG_gyre}
238
239The GYRE configuration \citep{Levy_al_OM10} has been built to
240simulate the seasonal cycle of a double-gyre box model.
241It consists in an idealized domain similar to that used in the studies of \citet{Drijfhout_JPO94} and
242\citet{Hazeleger_Drijfhout_JPO98, Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
243over which an analytical seasonal forcing is applied.
244This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
245and their contribution to the large scale circulation.
246
247The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\degN and
248rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
249The domain is bounded by vertical walls and by a flat bottom.
250The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
251The circulation is forced by analytical profiles of wind and buoyancy fluxes.
252The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{Levy_al_OM10}.
253The wind stress is zonal and its curl changes sign at 22\degN and 36\degN.
254It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
255a small recirculation gyre in the southern corner.
256The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
257A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
258The fresh water flux is also prescribed and varies zonally.
259It is determined such as, at each time step, the basin-integrated flux is zero.
260The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
261the whole domain.
262
263The GYRE configuration is set like an analytical configuration.
264Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in
265the reference configuration \path{CONFIG/GYRE/EXP00/namelist_cfg}
266analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
267Its horizontal resolution (and thus the size of the domain) is determined by
268setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\
269\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
270\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
271Obviously, the namelist parameters have to be adjusted to the chosen resolution,
272see the Configurations pages on the NEMO web site (Using NEMO\/Configurations).
273In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
274
275The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
276as it does not requires any input file.
277For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
278even though the physical integrity of the solution can be compromised.
279Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in
280namelist \path{CONFIG/GYRE/EXP00/namelist_cfg}.
281
282%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
283\begin{figure}[!t]
284  \begin{center}
285    \includegraphics[width=1.0\textwidth]{Fig_GYRE}
286    \caption{  \protect\label{fig:GYRE}
287      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
288      From \citet{Levy_al_OM10}.}
289  \end{center}
290\end{figure}
291%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
292
293% -------------------------------------------------------------------------------------------------------------
294%       AMM configuration
295% -------------------------------------------------------------------------------------------------------------
296\section{AMM: atlantic margin configuration}
297\label{sec:MISC_config_AMM}
298
299The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
300a regular lat-lon grid at approximately 12km horizontal resolution.
301The appropriate \textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
302It is used to build the correct dimensions of the AMM domain.
303
304This configuration tests several features of NEMO functionality specific to the shelf seas.
305In particular, the AMM uses $S$-coordinates in the vertical rather than $z$-coordinates and
306is forced with tidal lateral boundary conditions using a flather boundary condition from the BDY module.
307The AMM configuration uses the GLS (\key{zdfgls}) turbulence scheme,
308the VVL non-linear free surface(\key{vvl}) and time-splitting (\key{dynspg\_ts}).
309
310In addition to the tidal boundary condition the model may also take open boundary conditions from
311a North Atlantic model.
312Boundaries may be completely omitted by setting \np{ln\_bdy} to false.
313Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
314The Baltic boundary is included within the river input file and is specified as a river source.
315Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
316
317\end{document}
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