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1% ================================================================
2% Chapter Ñ Configurations
3% ================================================================
4\chapter{Configurations}
5\label{CFG}
6\minitoc
7
8\newpage
9$\ $\newline    % force a new ligne
10
11% ================================================================
12% Introduction
13% ================================================================
14\section{Introduction}
15\label{CFG_intro}
16
17
18The purpose of this part of the manual is to introduce the \NEMO predefined configuration.
19These configurations are offered as means to explore various numerical and physical options,
20thus allowing the user to verify that the code is performing in a manner consistent with that
21we are running. This form of verification is critical as one adopts the code for his or her particular
22research purposes. The test cases also provide a sense for some of the options available
23in the code, though by no means are all options exercised in the predefined configurations.
24
25
26%There is several predefined ocean configuration which use is controlled by a specific CPP key.
27
28%The key set the domain sizes (\jp{jpiglo}, \jp{jpjglo}, \jp{jpk}), the mesh and the bathymetry,
29%and, in some cases, add to the model physics some specific treatments.
30
31
32% ================================================================
33% 1D model configuration
34% ================================================================
35\section{Water column model: 1D model (C1D) (\key{c1d})}
36\label{CFG_c1d}
37
38The 1D model option simulates a stand alone water column within the 3D \NEMO system.
39It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers
40or a biogeochemical model. It is set up by defining the \key{c1d} CPP key.
41The 1D model is a very useful tool 
42\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;
43\textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave
44breaking, Langmuir circulation, ...) ;
45\textit{(c)} to compare the behaviour of different vertical mixing schemes  ;
46\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ;
47\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
48
49The methodology is based on the use of the zoom functionality over the smallest possible
50domain : a 3x3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}),
51with some extra routines. There is no need to define a new mesh, bathymetry,
52initial state or forcing, since the 1D model will use those of the configuration it is a zoom of.
53The chosen grid point is set in \mdl{par\_oce} module by setting the \jp{jpizoom} and \jp{jpjzoom} 
54parameters to the indices of the location of the chosen grid point.
55
56The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and
57second, the two components of the velocity are moved on a $T$-point.
58Therefore, defining \key{c1d} changes five main things in the code behaviour:
59\begin{description}
60\item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column
61of the 3x3 domain is imposed over the whole domain ;
62\item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ;
63\item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
64both lateral tendancy terms and lateral physics are not called ;
65\item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity
66has been made) ;
67\item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
68(see \mdl{dyncor\_c1d}).
69\end{description}
70All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
71the \NEMO distribution.
72
73% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
74
75% ================================================================
76% ORCA family configurations
77% ================================================================
78\section{ORCA family: global ocean with tripolar grid (\key{orca\_rX})}
79\label{CFG_orca}
80
81The ORCA family is a series of global ocean configurations that are run together with
82the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model
83(ORCA-LIM-PISCES), using various resolutions.
84
85
86%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
87\begin{figure}[!t]   \begin{center}
88\includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf}
89\caption{  \label{Fig_MISC_ORCA_msh}     
90ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N.
91The two "north pole" are the foci of a series of embedded ellipses (blue curves)
92which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
93Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed
94which provide the j-lines of the mesh (pseudo longitudes).  }
95\end{center}   \end{figure}
96%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
97
98% -------------------------------------------------------------------------------------------------------------
99%       ORCA tripolar grid
100% -------------------------------------------------------------------------------------------------------------
101\subsection{ORCA tripolar grid}
102\label{CFG_orca_grid}
103
104The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
105It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
106the computational domain since two north mesh poles are introduced and placed on lands.
107The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
108computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
109The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north
110poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in
111either the mesh lines or the scale factors, or even the scale factor derivatives over the whole
112ocean domain, as the mesh is not a composite mesh.
113%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
114\begin{figure}[!tbp]  \begin{center}
115\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf}
116\includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf}
117\caption {  \label{Fig_MISC_ORCA_e1e2}
118\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
119\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
120for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$)
121so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole"
122introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island
123(Canadian Arctic Archipelago). }
124\end{center}   \end{figure}
125%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
126
127
128The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward
129of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution
130for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and
131variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy
132($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as
133the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger
134than the smallest one in the southern hemisphere.
135The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} 
136for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along 
137Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island
138in the Canadian Archipelago.
139
140% -------------------------------------------------------------------------------------------------------------
141%       ORCA-LIM(-PISCES) configurations
142% -------------------------------------------------------------------------------------------------------------
143\subsection{ORCA pre-defined resolution}
144\label{CFG_orca_resolution}
145
146
147The NEMO system is provided with five built-in ORCA configurations which differ in the
148horizontal resolution. The value of the resolution is given by the resolution at the Equator
149expressed in degrees. Each of configuration is set through a CPP key, \key{orca\_rX} 
150(with X being an indicator of the resolution), which set the grid size and configuration
151name parameters  (Tab.~\ref{Tab_ORCA}).
152.
153
154%--------------------------------------------------TABLE--------------------------------------------------
155\begin{table}[!t]     \begin{center}
156\begin{tabular}{p{4cm} c c c c}
157CPP key                        & \jp{jp\_cfg} &  \jp{jpiglo} & \jp{jpiglo} &       \\ 
158\hline  \hline
159\key{orca\_r4}        &        4         &         92     &      76      &       \\
160\key{orca\_r2}       &        2         &       182     &    149      &        \\
161\key{orca\_r1}       &        1         &       362     &     292     &        \\
162\key{orca\_r05}     &        05       &       722     &     511     &        \\
163\key{orca\_r025}   &        025     &      1442    &   1021     &        \\
164%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
165%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
166\hline   \hline
167\end{tabular}
168\caption{ \label{Tab_ORCA}   
169Set of predefined parameters for ORCA family configurations.
170In all cases, the name of the configuration is set to "orca" ($i.e.$ \jp{cp\_cfg}~=~orca). }
171\end{center}
172\end{table}
173%--------------------------------------------------------------------------------------------------------------
174
175
176The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,
177local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
178so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied
179with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator.
180
181The ORCA\_R1 configuration has only a local tropical transformation  to refine the meridional
182resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2
183and R1 strongly increases the mesh anisotropy there.
184
185The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
186
187For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,
188otherwise 46 are used. In the other ORCA configurations, 31 levels are used
189(see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
190
191Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
192It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC
193assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution
194to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.
195
196This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m)
197in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
198The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
199The default forcing employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
200which was developed for the purpose of running global coupled ocean-ice simulations
201without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available
202through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
203The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution
204since release v3.3.
205
206ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas
207current area ( \key{agrif}  defined) and,  by setting the key \key{arctic} or \key{antarctic},
208a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations
209using sponge layers at open boundaries.
210
211% -------------------------------------------------------------------------------------------------------------
212%       GYRE family: double gyre basin
213% -------------------------------------------------------------------------------------------------------------
214\section{GYRE family: double gyre basin (\key{gyre})}
215\label{CFG_gyre}
216
217The GYRE configuration \citep{Levy_al_OM10} have been built to simulated
218the seasonal cycle of a double-gyre box model. It consist in an idealized domain
219similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,
220Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
221over which an analytical seasonal forcing is applied. This allows to investigate the
222spontaneous generation of a large number of interacting, transient mesoscale eddies
223and their contribution to the large scale circulation.
224
225The domain geometry is a closed rectangular basin on the $\beta$-plane centred
226at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide
227and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).
228The domain is bounded by vertical walls and by a flat bottom. The configuration is
229meant to represent an idealized North Atlantic or North Pacific basin.
230The circulation is forced by analytical profiles of wind and buoyancy fluxes.
231The applied forcings vary seasonally in a sinusoidal manner between winter
232and summer extrema \citep{Levy_al_OM10}.
233The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N.
234It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain
235and a small recirculation gyre in the southern corner.
236The net heat flux takes the form of a restoring toward a zonal apparent air
237temperature profile. A portion of the net heat flux which comes from the solar radiation
238is allowed to penetrate within the water column.
239The fresh water flux is also prescribed and varies zonally.
240It is determined such as, at each time step, the basin-integrated flux is zero.
241The basin is initialised at rest with vertical profiles of temperature and salinity
242uniformly applied to the whole domain.
243
244The GYRE configuration is set through the \key{gyre} CPP key. Its horizontal resolution
245(and thus the size of the domain) is determined by setting \jp{jp\_cfg} in \hf{par\_GYRE} file: \\
246\jp{jpiglo} $= 30 \times$ \jp{jp\_cfg} + 2   \\
247\jp{jpjglo} $= 20 \times$ \jp{jp\_cfg} + 2   \\
248Obviously, the namelist parameters have to be adjusted to the chosen resolution.
249In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}).
250
251The GYRE configuration is also used in benchmark test as it is very simple to increase
252its resolution and as it does not requires any input file. For example, keeping a same model size
253on each processor while increasing the number of processor used is very easy, even though the
254physical integrity of the solution can be compromised.
255
256%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
257\begin{figure}[!t]   \begin{center}
258\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf}
259\caption{  \label{Fig_GYRE}   
260Snapshot of relative vorticity at the surface of the model domain
261in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
262\end{center}   \end{figure}
263%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
264
265% -------------------------------------------------------------------------------------------------------------
266%       EEL family configuration
267% -------------------------------------------------------------------------------------------------------------
268\section{EEL family: periodic channel}
269\label{MISC_config_EEL}
270
271\begin{description}
272\item[\key{eel\_r2}]  to be described....
273\item[\key{eel\_r5}] 
274\item[\key{eel\_r6}] 
275\end{description}
276
277% -------------------------------------------------------------------------------------------------------------
278%       AMM configuration
279% -------------------------------------------------------------------------------------------------------------
280\section{AMM: atlantic margin configuration (\key{amm\_12km})}
281\label{MISC_config_AMM}
282
283The AMM, Atlantic Margins Model, is a regional model covering the
284Northwest European Shelf domain on a regular lat-lon grid at
285approximately 12km horizontal resolution. The key \key{amm\_12km}
286is used to create the correct dimensions of the AMM domain.
287
288This configuration tests several features of NEMO functionality specific
289to the shelf seas.
290In particular, the AMM uses $S$-coordinates in the vertical rather than
291$z$-coordinates and is forced with tidal lateral boundary conditions
292using a flather boundary condition from the BDY module (key\_bdy).
293The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the
294VVL non-linear free surface(key\_vvl) and time-splitting
295(key\_dynspg\_ts).
296
297In addition to the tidal boundary condition the model may also take
298open boundary conditions from a North Atlantic model. Boundaries may be
299completely ommited by removing the BDY key (key\_bdy).
300Sample surface fluxes, river forcing and a sample initial restart file
301are included to test a realistic model run. The Baltic boundary is
302included within the river input file and is specified as a river source.
303Unlike ordinary river points the Baltic inputs also include salinity and
304temperature data.
305
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