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