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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 functionality
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 3 x 3 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 par\_oce.F90 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.
57Therefore a simplified \rou{step} routine is used (\rou{step\_c1d}) in which both lateral tendancy
58terms and lateral physics are not called, and the vertical velocity is zero (so far, no attempt at
59introducing a Ekman pumping velocity has been made).
60Second, the two components of the velocity are moved on a $T$-point.
61This requires a specific treatment of the Coriolis term (see \rou{dyncor\_c1d}) and of the
62dynamic time stepping (\rou{dynnxt\_c1d}).
63All the relevant modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
64the \NEMO distribution.
65
66% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
67
68% ================================================================
69% ORCA family configurations
70% ================================================================
71\section{ORCA family: global ocean with tripolar grid (\key{orca\_rX})}
72\label{CFG_orca}
73
74The ORCA family is a series of global ocean configurations that are run together with
75the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model
76(ORCA-LIM-PISCES), using various resolutions.
77
78
79%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
80\begin{figure}[!t]   \begin{center}
81\includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf}
82\caption{  \label{Fig_MISC_ORCA_msh}     
83ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N.
84The two "north pole" are the foci of a series of embedded ellipses (blue curves)
85which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
86Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed
87which provide the j-lines of the mesh (pseudo longitudes).  }
88\end{center}   \end{figure}
89%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
90
91% -------------------------------------------------------------------------------------------------------------
92%       ORCA tripolar grid
93% -------------------------------------------------------------------------------------------------------------
94\subsection{ORCA tripolar grid}
95\label{CFG_orca_grid}
96
97The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
98It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
99the computational domain since two north mesh poles are introduced and placed on lands.
100The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
101computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
102The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north
103poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in
104either the mesh lines or the scale factors, or even the scale factor derivatives over the whole
105ocean domain, as the mesh is not a composite mesh.
106%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
107\begin{figure}[!tbp]  \begin{center}
108\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf}
109\includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf}
110\caption {  \label{Fig_MISC_ORCA_e1e2}
111\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
112\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
113for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$)
114so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole"
115introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island
116(Canadian Arctic Archipelago). }
117\end{center}   \end{figure}
118%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
119
120
121The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward
122of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution
123for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and
124variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy
125($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as
126the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger
127than the smallest one in the southern hemisphere.
128The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} 
129for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along 
130Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island
131in the Canadian Archipelago.
132
133% -------------------------------------------------------------------------------------------------------------
134%       ORCA-LIM(-PISCES) configurations
135% -------------------------------------------------------------------------------------------------------------
136\subsection{ORCA pre-defined resolution}
137\label{CFG_orca_resolution}
138
139
140The NEMO system is provided with five built-in ORCA configurations which differ in the
141horizontal resolution. The value of the resolution is given by the resolution at the Equator
142expressed in degrees. Each of configuration is set through a CPP key, \key{orca\_rX} 
143(with X being an indicator of the resolution), which set the grid size and configuration
144name parameters  (Tab.~\ref{Tab_ORCA}).
145.
146
147%--------------------------------------------------TABLE--------------------------------------------------
148\begin{table}[!t]     \begin{center}
149\begin{tabular}{p{4cm} c c c c}
150CPP key                        & \jp{jp\_cfg} &  \jp{jpiglo} & \jp{jpiglo} &       \\ 
151\hline  \hline
152\key{orca\_r4}        &        4         &         92     &      76      &       \\
153\key{orca\_r2}       &        2         &       182     &    149      &        \\
154\key{orca\_r1}       &        1         &       362     &     292     &        \\
155\key{orca\_r05}     &        05       &       722     &     511     &        \\
156\key{orca\_r025}   &        025     &      1442    &   1021     &        \\
157%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
158%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
159\hline   \hline
160\end{tabular}
161\caption{ \label{Tab_ORCA}   
162Set of predefined parameters for ORCA family configurations.
163In all cases, the name of the configuration is set to "orca" ($i.e.$ \jp{cp\_cfg}~=~orca). }
164\end{center}
165\end{table}
166%--------------------------------------------------------------------------------------------------------------
167
168
169The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,
170local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
171so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied
172with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator.
173
174The ORCA\_R1 configuration has only a local tropical transformation  to refine the meridional
175resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2
176and R1 strongly increases the mesh anisotropy there.
177
178The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
179
180For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,
181otherwise 46 are used. In the other ORCA configurations, 31 levels are used
182(see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
183
184Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
185It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC
186assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution
187to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.
188
189This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m)
190in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
191The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
192The default forcing employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
193which was developed for the purpose of running global coupled ocean-ice simulations
194without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available
195through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
196The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution
197since release v3.3.
198
199ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas
200current area ( \key{agrif}  defined) and,  by setting the key \key{arctic} or \key{antarctic},
201a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations
202using sponge layers at open boundaries.
203
204% -------------------------------------------------------------------------------------------------------------
205%       GYRE family: double gyre basin
206% -------------------------------------------------------------------------------------------------------------
207\section{GYRE family: double gyre basin (\key{gyre})}
208\label{MISC_config_gyre}
209
210The GYRE configuration \citep{Levy_al_OM10} have been built to simulated
211the seasonal cycle of a double-gyre box model. It consist in an idealized domain
212similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,
213Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
214over which an analytical seasonal forcing is applied. This allows to investigate the
215spontaneous generation of a large number of interacting, transient mesoscale eddies
216and their contribution to the large scale circulation.
217
218The domain geometry is a closed rectangular basin on the $\beta$-plane centred
219at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide
220and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).
221The domain is bounded by vertical walls and by a ßat bottom. The configuration is
222meant to represent an idealized North Atlantic or North Pacific basin.
223The circulation is forced by analytical profiles of wind and buoyancy ßuxes.
224The applied forcings vary seasonally in a sinusoidal manner between winter
225and summer extrema \citep{Levy_al_OM10}.
226The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N.
227It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain
228and a small recirculation gyre in the southern corner.
229The net heat ßux takes the form of a restoring toward a zonal apparent air
230temperature profile. A portion of the net heat ßux which comes from the solar radiation
231is allowed to penetrate within the water column.
232The fresh water ßux is also prescribed and varies zonally.
233It is determined such as, at each time step, the basin-integrated ßux is zero.
234The basin is initialised at rest with vertical profiles of temperature and salinity
235uniformly applied to the whole domain.
236
237The GYRE configuration is set through the \key{gyre} CPP key. Its horizontal resolution
238(and thus the size of the domain) is determined by setting \jp{jp\_cfg} in \hf{par\_GYRE} file: \\
239\jp{jpiglo} $= 30 \times$ \jp{jp\_cfg} + 2   \\
240\jp{jpjglo} $= 20 \times$ \jp{jp\_cfg} + 2   \\
241Obviously, the namelist parameters have to be adjusted to the chosen resolution.
242In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}).
243
244The GYRE configuration is also used in benchmark test as it is very simple to increase
245its resolution and as it does not requires any input file. For example, keeping a same model size
246on each processor while increasing the number of processor used is very easy, even though the
247physical integrity of the solution can be compromised.
248
249%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
250\begin{figure}[!t]   \begin{center}
251\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf}
252\caption{  \label{Fig_GYRE}   
253Snapshot of relative vorticity at the surface of the model domain
254in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
255\end{center}   \end{figure}
256%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
257
258% -------------------------------------------------------------------------------------------------------------
259%       EEL family configuration
260% -------------------------------------------------------------------------------------------------------------
261\section{EEL family: periodic channel}
262\label{MISC_config_EEL}
263
264\begin{description}
265\item[\key{eel\_r2}]  to be described....
266\item[\key{eel\_r5}] 
267\item[\key{eel\_r6}] 
268\end{description}
269
270% -------------------------------------------------------------------------------------------------------------
271%       POMME configuration
272% -------------------------------------------------------------------------------------------------------------
273\section{POMME: mid-latitude sub-domain}
274\label{MISC_config_POMME}
275
276
277\key{pomme\_r025} : to be described....
278
279
280
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