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1% ================================================================
2% Chapter � 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 reference configurations.
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 reference configurations.
24
25Configuration is defined mainly through the \ngn{namcfg} namelist variables:
26%------------------------------------------namcfg----------------------------------------------------
27\namdisplay{namcfg}
28%-------------------------------------------------------------------------------------------------------------
29
30% ================================================================
31% 1D model configuration
32% ================================================================
33\section{Water column model: 1D model (C1D) (\key{c1d}) }
34\label{CFG_c1d}
35
36The 1D model option simulates a stand alone water column within the 3D \NEMO system.
37It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers
38or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid
39(see \textit{CONFIG/SHARED/namelist\_ref} ).
40The 1D model is a very useful tool 
41\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;
42\textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave
43breaking, Langmuir circulation, ...) ;
44\textit{(c)} to compare the behaviour of different vertical mixing schemes  ;
45\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ;
46\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
47
48The methodology is based on the use of the zoom functionality over the smallest possible
49domain : a 3x3 domain centered on the grid point of interest,
50with some extra routines. There is no need to define a new mesh, bathymetry,
51initial state or forcing, since the 1D model will use those of the configuration it is a zoom of.
52The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom} 
53parameters to the indices of the location of the chosen grid point.
54
55The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and
56second, the two components of the velocity are moved on a $T$-point.
57Therefore, defining \key{c1d} changes five main things in the code behaviour:
58\begin{description}
59\item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column
60of the 3x3 domain is imposed over the whole domain ;
61\item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ;
62\item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
63both lateral tendancy terms and lateral physics are not called ;
64\item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity
65has been made) ;
66\item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
67(see \mdl{dyncor\_c1d}).
68\end{description}
69All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
70the \NEMO distribution.
71
72% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
73
74% ================================================================
75% ORCA family configurations
76% ================================================================
77\section{ORCA family: global ocean with tripolar grid }
78\label{CFG_orca}
79
80The ORCA family is a series of global ocean configurations that are run together with
81the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model
82(ORCA-LIM-PISCES), using various resolutions.
83The appropriate \textit{\&namcfg} namelist is available in \textit{CONFIG/ORCA2\_LIM/EXP00/namelist\_cfg} 
84for ORCA2 and in \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} 
85for other resolutions
86
87
88%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
89\begin{figure}[!t]   \begin{center}
90\includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf}
91\caption{  \label{Fig_MISC_ORCA_msh}     
92ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N.
93The two "north pole" are the foci of a series of embedded ellipses (blue curves)
94which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
95Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed
96which provide the j-lines of the mesh (pseudo longitudes).  }
97\end{center}   \end{figure}
98%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
99
100% -------------------------------------------------------------------------------------------------------------
101%       ORCA tripolar grid
102% -------------------------------------------------------------------------------------------------------------
103\subsection{ORCA tripolar grid}
104\label{CFG_orca_grid}
105
106The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
107It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
108the computational domain since two north mesh poles are introduced and placed on lands.
109The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
110computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
111The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north
112poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in
113either the mesh lines or the scale factors, or even the scale factor derivatives over the whole
114ocean domain, as the mesh is not a composite mesh.
115%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
116\begin{figure}[!tbp]  \begin{center}
117\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf}
118\includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf}
119\caption {  \label{Fig_MISC_ORCA_e1e2}
120\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
121\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
122for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$)
123so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole"
124introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island
125(Canadian Arctic Archipelago). }
126\end{center}   \end{figure}
127%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
128
129
130The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward
131of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution
132for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and
133variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy
134($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as
135the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger
136than the smallest one in the southern hemisphere.
137The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} 
138for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along 
139Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island
140in the Canadian Archipelago.
141
142% -------------------------------------------------------------------------------------------------------------
143%       ORCA-LIM(-PISCES) configurations
144% -------------------------------------------------------------------------------------------------------------
145\subsection{ORCA pre-defined resolution}
146\label{CFG_orca_resolution}
147
148
149The NEMO system is provided with five built-in ORCA configurations which differ in the
150horizontal resolution. The value of the resolution is given by the resolution at the Equator
151expressed in degrees. Each of configuration is set through the \textit{\ngn{namcfg}} namelist,
152which sets the grid size and configuration
153name parameters  (Tab. \ref{Tab_ORCA}).
154.
155
156%--------------------------------------------------TABLE--------------------------------------------------
157\begin{table}[!t]     \begin{center}
158\begin{tabular}{p{4cm} c c c c}
159Horizontal Grid                         & \np{jp\_cfg} &  \np{jpiglo} & \np{jpjglo} &       \\ 
160\hline  \hline
161\~4\deg     &        4         &         92     &      76      &       \\
162\~2\deg        &        2         &       182     &    149      &        \\
163\~1\deg        &        1         &       362     &     292     &        \\
164\~0.5\deg     &        05       &       722     &     511     &        \\
165\~0.25\deg   &        025     &      1442    &   1021     &        \\
166%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
167%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
168\hline   \hline
169\end{tabular}
170\caption{ \label{Tab_ORCA}   
171Set of predefined parameters for ORCA family configurations.
172In all cases, the name of the configuration is set to "orca" ($i.e.$ \np{cp\_cfg}~=~orca). }
173\end{center}
174\end{table}
175%--------------------------------------------------------------------------------------------------------------
176
177
178The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,
179local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
180so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied
181with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator.
182
183The ORCA\_R1 configuration has only a local tropical transformation  to refine the meridional
184resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2
185and R1 strongly increases the mesh anisotropy there.
186
187The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
188
189For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,
190otherwise 46 are used. In the other ORCA configurations, 31 levels are used
191(see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
192
193Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
194It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC
195assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution
196to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.
197
198This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m)
199in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
200The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
201The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
202which was developed for the purpose of running global coupled ocean-ice simulations
203without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available
204through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
205The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution
206since release v3.3.
207
208ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas
209current area ( \key{agrif}  defined) and,  by setting the appropriate variables in
210\textit{\&namcfg}, see \textit{CONFIG/SHARED/namelist\_ref}
211a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations
212using sponge layers at open boundaries.
213
214% -------------------------------------------------------------------------------------------------------------
215%       GYRE family: double gyre basin
216% -------------------------------------------------------------------------------------------------------------
217\section{GYRE family: double gyre basin }
218\label{CFG_gyre}
219
220The GYRE configuration \citep{Levy_al_OM10} has been built to simulate
221the seasonal cycle of a double-gyre box model. It consists in an idealized domain
222similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,
223Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
224over which an analytical seasonal forcing is applied. This allows to investigate the
225spontaneous generation of a large number of interacting, transient mesoscale eddies
226and their contribution to the large scale circulation.
227
228The domain geometry is a closed rectangular basin on the $\beta$-plane centred
229at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide
230and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).
231The domain is bounded by vertical walls and by a flat bottom. The configuration is
232meant to represent an idealized North Atlantic or North Pacific basin.
233The circulation is forced by analytical profiles of wind and buoyancy fluxes.
234The applied forcings vary seasonally in a sinusoidal manner between winter
235and summer extrema \citep{Levy_al_OM10}.
236The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N.
237It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain
238and a small recirculation gyre in the southern corner.
239The net heat flux takes the form of a restoring toward a zonal apparent air
240temperature profile. A portion of the net heat flux which comes from the solar radiation
241is allowed to penetrate within the water column.
242The fresh water flux is also prescribed and varies zonally.
243It is determined such as, at each time step, the basin-integrated flux is zero.
244The basin is initialised at rest with vertical profiles of temperature and salinity
245uniformly applied to the whole domain.
246
247The GYRE configuration is set through the \textit{\&namcfg} namelist defined in the reference
248configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution
249(and thus the size of the domain) is determined by setting \np{jp\_cfg} : \\
250\np{jpiglo} $= 30 \times$ \np{jp\_cfg} + 2   \\
251\np{jpjglo} $= 20 \times$ \np{jp\_cfg} + 2   \\
252Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations
253pages on the NEMO web site (Using NEMO\/Configurations) .
254In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}).
255
256The GYRE configuration is also used in benchmark test as it is very simple to increase
257its resolution and as it does not requires any input file. For example, keeping a same model size
258on each processor while increasing the number of processor used is very easy, even though the
259physical integrity of the solution can be compromised.
260
261%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
262\begin{figure}[!t]   \begin{center}
263\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf}
264\caption{  \label{Fig_GYRE}   
265Snapshot of relative vorticity at the surface of the model domain
266in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
267\end{center}   \end{figure}
268%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
269
270% -------------------------------------------------------------------------------------------------------------
271%       EEL family configuration
272% -------------------------------------------------------------------------------------------------------------
273\section{EEL family: periodic channel}
274\label{MISC_config_EEL}
275
276\begin{description}
277\item[eel\_r2]  to be described....
278\item[eel\_r5] 
279\item[eel\_r6] 
280\end{description}
281The appropriate \textit{\&namcfg} namelists are available in 
282\textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg}
283% -------------------------------------------------------------------------------------------------------------
284%       AMM configuration
285% -------------------------------------------------------------------------------------------------------------
286\section{AMM: atlantic margin configuration }
287\label{MISC_config_AMM}
288
289The AMM, Atlantic Margins Model, is a regional model covering the
290Northwest European Shelf domain on a regular lat-lon grid at
291approximately 12km horizontal resolution. The appropriate
292\textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
293It is used to build the correct dimensions of the AMM domain.
294
295This configuration tests several features of NEMO functionality specific
296to the shelf seas.
297In particular, the AMM uses $S$-coordinates in the vertical rather than
298$z$-coordinates and is forced with tidal lateral boundary conditions
299using a flather boundary condition from the BDY module (key\_bdy).
300The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the
301VVL non-linear free surface(key\_vvl) and time-splitting
302(key\_dynspg\_ts).
303
304In addition to the tidal boundary condition the model may also take
305open boundary conditions from a North Atlantic model. Boundaries may be
306completely ommited by removing the BDY key (key\_bdy).
307Sample surface fluxes, river forcing and a sample initial restart file
308are included to test a realistic model run. The Baltic boundary is
309included within the river input file and is specified as a river source.
310Unlike ordinary river points the Baltic inputs also include salinity and
311temperature data.
312
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