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1\documentclass[NEMO_book]{subfiles}
2\begin{document}
3% ================================================================
4% Chapter � Configurations
5% ================================================================
6\chapter{Configurations}
7\label{CFG}
8\minitoc
9
10\newpage
11$\ $\newline    % force a new ligne
12
13% ================================================================
14% Introduction
15% ================================================================
16\section{Introduction}
17\label{CFG_intro}
18
19
20The purpose of this part of the manual is to introduce the \NEMO reference configurations.
21These configurations are offered as means to explore various numerical and physical options,
22thus allowing the user to verify that the code is performing in a manner consistent with that
23we are running. This form of verification is critical as one adopts the code for his or her particular
24research purposes. The reference configurations also provide a sense for some of the options available
25in the code, though by no means are all options exercised in the reference configurations.
26
27%------------------------------------------namcfg----------------------------------------------------
28\namdisplay{namcfg}
29%-------------------------------------------------------------------------------------------------------------
30
31% ================================================================
32% 1D model configuration
33% ================================================================
34\section{Water column model: 1D model (C1D) (\protect\key{c1d}) }
35\label{CFG_c1d}
36
37$\ $\newline
38BE careful: to be re-written according to suppression of jpizoom and jpjzoom !!!!
39$\ $\newline
40
41The 1D model option simulates a stand alone water column within the 3D \NEMO system.
42It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers
43or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid
44(see \textit{CONFIG/SHARED/namelist\_ref} ).
45The 1D model is a very useful tool 
46\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;
47\textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave
48breaking, Langmuir circulation, ...) ;
49\textit{(c)} to compare the behaviour of different vertical mixing schemes  ;
50\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ;
51\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
52
53The methodology is based on the use of the zoom functionality over the smallest possible
54domain : a 3x3 domain centered on the grid point of interest,
55with some extra routines. There is no need to define a new mesh, bathymetry,
56initial state or forcing, since the 1D model will use those of the configuration it is a zoom of.
57The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom} 
58parameters to the indices of the location of the chosen grid point.
59
60The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and
61second, the two components of the velocity are moved on a $T$-point.
62Therefore, defining \key{c1d} changes five main things in the code behaviour:
63\begin{description}
64\item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column
65of the 3x3 domain is imposed over the whole domain ;
66\item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ;
67\item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
68both lateral tendancy terms and lateral physics are not called ;
69\item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity
70has been made) ;
71\item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
72(see \mdl{dyncor\_c1d}).
73\end{description}
74All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
75the \NEMO distribution.
76
77% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
78
79% ================================================================
80% ORCA family configurations
81% ================================================================
82\section{ORCA family: global ocean with tripolar grid }
83\label{CFG_orca}
84
85The ORCA family is a series of global ocean configurations that are run together with
86the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model
87(ORCA-LIM-PISCES), using various resolutions.
88An appropriate namelist is available in \textit{CONFIG/ORCA2\_LIM3\_PISCES/EXP00/namelist\_cfg} 
89for ORCA2.
90The domain of ORCA2 configuration is defined in ORCA\_R2\_zps\_domcfg.nc file, this file is available in tar file in the wiki of NEMO : \\
91https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ReferenceConfigurations/ORCA2\_LIM3\_PISCES \\
92In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.
93
94%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
95\begin{figure}[!t]   \begin{center}
96\includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh}
97\caption{  \protect\label{Fig_MISC_ORCA_msh}     
98ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN.
99The two "north pole" are the foci of a series of embedded ellipses (blue curves)
100which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
101Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed
102which provide the j-lines of the mesh (pseudo longitudes).  }
103\end{center}   \end{figure}
104%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
105
106% -------------------------------------------------------------------------------------------------------------
107%       ORCA tripolar grid
108% -------------------------------------------------------------------------------------------------------------
109\subsection{ORCA tripolar grid}
110\label{CFG_orca_grid}
111
112The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
113It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
114the computational domain since two north mesh poles are introduced and placed on lands.
115The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
116computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
117The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north
118poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in
119either the mesh lines or the scale factors, or even the scale factor derivatives over the whole
120ocean domain, as the mesh is not a composite mesh.
121%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
122\begin{figure}[!tbp]  \begin{center}
123\includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
124\includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso}
125\caption {  \protect\label{Fig_MISC_ORCA_e1e2}
126\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
127\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
128for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$)
129so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole"
130introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island
131(Canadian Arctic Archipelago). }
132\end{center}   \end{figure}
133%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
134
135
136The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward
137of 20\degN, so that the Equator is a mesh line, which provides a better numerical solution
138for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and
139variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy
140($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as
141the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger
142than the smallest one in the southern hemisphere.
143The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} 
144for a half a degree grid (ORCA\_R05).
145The smallest ocean scale factor is found in along  Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island
146in the Canadian Archipelago.
147
148% -------------------------------------------------------------------------------------------------------------
149%       ORCA-LIM(-PISCES) configurations
150% -------------------------------------------------------------------------------------------------------------
151\subsection{ORCA pre-defined resolution}
152\label{CFG_orca_resolution}
153
154
155The NEMO system is provided with five built-in ORCA configurations which differ in the
156horizontal resolution. The value of the resolution is given by the resolution at the Equator
157expressed in degrees. Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
158which sets the grid size and configuration name parameters. The NEMO System Team provides only ORCA2 domain input file "ORCA\_R2\_zps\_domcfg.nc" file  (Tab. \ref{Tab_ORCA}).
159
160
161
162
163%--------------------------------------------------TABLE--------------------------------------------------
164\begin{table}[!t]     \begin{center}
165\begin{tabular}{p{4cm} c c c c}
166Horizontal Grid                         & \np{ORCA\_index} &  \np{jpiglo} & \np{jpjglo} &       \\ 
167\hline  \hline
168\~4\deg     &        4         &         92     &      76      &       \\
169\~2\deg        &        2         &       182     &    149      &        \\
170\~1\deg        &        1         &       362     &     292     &        \\
171\~0.5\deg     &        05       &       722     &     511     &        \\
172\~0.25\deg   &        025     &      1442    &   1021     &        \\
173%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
174%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
175\hline   \hline
176\end{tabular}
177\caption{ \protect\label{Tab_ORCA}   
178Domain size of ORCA family configurations.
179The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. }
180\end{center}
181\end{table}
182%--------------------------------------------------------------------------------------------------------------
183
184
185The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,
186local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
187so that the resolution is 1\deg \time 1\deg there. A local transformation were also applied
188with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator.
189
190The ORCA\_R1 configuration has only a local tropical transformation  to refine the meridional
191resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2
192and R1 strongly increases the mesh anisotropy there.
193
194The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
195
196For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,
197otherwise 46 are used. In the other ORCA configurations, 31 levels are used
198(see Tab.~\ref{Tab_orca_zgr} \sfcomment{HERE I need to put new table for ORCA2 values} and Fig.~\ref{Fig_zgr}).
199
200Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
201It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC
202assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution
203to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.
204
205This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m)
206in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
207The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
208The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
209which was developed for the purpose of running global coupled ocean-ice simulations
210without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available
211through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
212The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution
213since release v3.3.
214
215ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas
216current area ( \key{agrif}  defined) and, by setting the appropriate variables, see \textit{CONFIG/SHARED/namelist\_ref}
217a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations
218using sponge layers at open boundaries.
219
220% -------------------------------------------------------------------------------------------------------------
221%       GYRE family: double gyre basin
222% -------------------------------------------------------------------------------------------------------------
223\section{GYRE family: double gyre basin }
224\label{CFG_gyre}
225
226The GYRE configuration \citep{Levy_al_OM10} has been built to simulate
227the seasonal cycle of a double-gyre box model. It consists in an idealized domain
228similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,
229Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
230over which an analytical seasonal forcing is applied. This allows to investigate the
231spontaneous generation of a large number of interacting, transient mesoscale eddies
232and their contribution to the large scale circulation.
233
234The domain geometry is a closed rectangular basin on the $\beta$-plane centred
235at $\sim$ 30\degN and rotated by 45\deg, 3180~km long, 2120~km wide
236and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).
237The domain is bounded by vertical walls and by a flat bottom. The configuration is
238meant to represent an idealized North Atlantic or North Pacific basin.
239The circulation is forced by analytical profiles of wind and buoyancy fluxes.
240The applied forcings vary seasonally in a sinusoidal manner between winter
241and summer extrema \citep{Levy_al_OM10}.
242The wind stress is zonal and its curl changes sign at 22\degN and 36\degN.
243It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain
244and a small recirculation gyre in the southern corner.
245The net heat flux takes the form of a restoring toward a zonal apparent air
246temperature profile. A portion of the net heat flux which comes from the solar radiation
247is allowed to penetrate within the water column.
248The fresh water flux is also prescribed and varies zonally.
249It is determined such as, at each time step, the basin-integrated flux is zero.
250The basin is initialised at rest with vertical profiles of temperature and salinity
251uniformly applied to the whole domain.
252
253The GYRE configuration is set like an analytical configuration. Through \np{ln\_read\_cfg\textit{=false}} in \textit{namcfg} namelist defined in the reference configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg} anaylitical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. Its horizontal resolution
254(and thus the size of the domain) is determined by setting \np{nn\_GYRE} in  \ngn{namusr\_def}: \\
255\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
256\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
257Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations
258pages on the NEMO web site (Using NEMO\/Configurations) .
259In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}).
260
261The GYRE configuration is also used in benchmark test as it is very simple to increase
262its resolution and as it does not requires any input file. For example, keeping a same model size
263on each processor while increasing the number of processor used is very easy, even though the
264physical integrity of the solution can be compromised. Benchmark is activate via \np{ln\_bench\textit{=true}} in \ngn{namusr\_def} in namelist  \textit{CONFIG/GYRE/EXP00/namelist\_cfg}.
265
266%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
267\begin{figure}[!t]   \begin{center}
268\includegraphics[width=1.0\textwidth]{Fig_GYRE}
269\caption{  \protect\label{Fig_GYRE}   
270Snapshot of relative vorticity at the surface of the model domain
271in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
272\end{center}   \end{figure}
273%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
274
275% -------------------------------------------------------------------------------------------------------------
276%       AMM configuration
277% -------------------------------------------------------------------------------------------------------------
278\section{AMM: atlantic margin configuration }
279\label{MISC_config_AMM}
280
281The AMM, Atlantic Margins Model, is a regional model covering the
282Northwest European Shelf domain on a regular lat-lon grid at
283approximately 12km horizontal resolution. The appropriate
284\textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
285It is used to build the correct dimensions of the AMM domain.
286
287This configuration tests several features of NEMO functionality specific
288to the shelf seas.
289In particular, the AMM uses $S$-coordinates in the vertical rather than
290$z$-coordinates and is forced with tidal lateral boundary conditions
291using a flather boundary condition from the BDY module.
292The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the
293VVL non-linear free surface(key\_vvl) and time-splitting
294(key\_dynspg\_ts).
295
296In addition to the tidal boundary condition the model may also take
297open boundary conditions from a North Atlantic model. Boundaries may be
298completely omitted by setting \np{ln\_bdy} to false.
299Sample surface fluxes, river forcing and a sample initial restart file
300are included to test a realistic model run. The Baltic boundary is
301included within the river input file and is specified as a river source.
302Unlike ordinary river points the Baltic inputs also include salinity and
303temperature data.
304
305\end{document}
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