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1\documentclass[../main/NEMO_manual]{subfiles}
2
3\begin{document}
4% ================================================================
5% Chapter Configurations
6% ================================================================
7\chapter{Configurations}
8\label{chap:CFG}
9
10\minitoc
11
12\newpage
13
14% ================================================================
15% Introduction
16% ================================================================
17\section{Introduction}
18\label{sec:CFG_intro}
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 we are running.
23This form of verification is critical as one adopts the code for his or her particular research purposes.
24The reference configurations also provide a sense for some of the options available in the code,
25though by no means are all options exercised in the reference configurations.
26Configuration is defined manually through the \textit{namcfg} namelist variables.
27
28%------------------------------------------namcfg----------------------------------------------------
29
30\nlst{namcfg}
31%-------------------------------------------------------------------------------------------------------------
32
33% ================================================================
34% 1D model configuration
35% ================================================================
36\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]
37{C1D: 1D Water column model (\protect\key{c1d})}
38\label{sec: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 or a biogeochemical model.
42It is set up by defining the position of the 1D water column in the grid
43(see \textit{cfgs/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
47(surface wave breaking, 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 configuration of the smallest possible domain:
53a 3x3 domain with 75 vertical levels.
54
55The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
56and second, the two components of the velocity are moved on a $T$-point.
57Therefore, defining \key{c1d} changes some things in the code behaviour:
58\begin{description}
59\item[(1)]
60  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
61  both lateral tendancy terms and lateral physics are not called;
62\item[(2)]
63  the vertical velocity is zero
64  (so far, no attempt at introducing a Ekman pumping velocity has been made);
65\item[(3)]
66  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 src/OCE/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{sec:CFG_orca}
79
80The ORCA family is a series of global ocean configurations that are run together with
81the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
82An appropriate namelist is available in \path{cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
83The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
84this file is available in tar file on the NEMO community zenodo platform: \\
85https://doi.org/10.5281/zenodo.2640723
86
87In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.
88
89%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
90\begin{figure}[!t]
91  \begin{center}
92    \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh}
93    \caption{
94      \protect\label{fig:MISC_ORCA_msh}
95      ORCA mesh conception.
96      The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
97      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
98      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
99      Then, following \citet{madec.imbard_CD96}, the normal to the series of ellipses (red curves) is computed which
100      provides the j-lines of the mesh (pseudo longitudes).
101    }
102  \end{center}
103\end{figure}
104%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
105
106% -------------------------------------------------------------------------------------------------------------
107%       ORCA tripolar grid
108% -------------------------------------------------------------------------------------------------------------
109\subsection{ORCA tripolar grid}
110\label{subsec:CFG_orca_grid}
111
112The ORCA grid is a tripolar grid 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 poles
118(\autoref{fig:MISC_ORCA_msh}).
119The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
120or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
121%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
122\begin{figure}[!tbp]
123  \begin{center}
124    \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
125    \includegraphics[width=\textwidth]{Fig_ORCA_aniso}
126    \caption {
127      \protect\label{fig:MISC_ORCA_e1e2}
128      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
129      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
130      for ORCA 0.5\deg ~mesh.
131      South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
132      Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
133      vicinity of Victoria Island (Canadian Arctic Archipelago).
134    }
135  \end{center}
136\end{figure}
137%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
138
139The method is applied to Mercator grid (\ie same zonal and meridional grid spacing) poleward of 20\deg{N},
140so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
141The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
142is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
143(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
144the northern hemisphere larger than the smallest one in the southern hemisphere.
145The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for
146a half a degree grid (ORCA\_R05).
147The smallest ocean scale factor is found in along Antarctica,
148while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
149
150% -------------------------------------------------------------------------------------------------------------
151%       ORCA-ICE(-PISCES) configurations
152% -------------------------------------------------------------------------------------------------------------
153\subsection{ORCA pre-defined resolution}
154\label{subsec:CFG_orca_resolution}
155
156The NEMO system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
157The value of the resolution is given by the resolution at the Equator expressed in degrees.
158Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
159which sets the grid size and configuration name parameters.
160The NEMO System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
161(Tab. \autoref{tab:ORCA}).
162
163%--------------------------------------------------TABLE--------------------------------------------------
164\begin{table}[!t]
165  \begin{center}
166    \begin{tabular}{p{4cm} c c c c}
167      Horizontal Grid                         & \np{ORCA\_index} &  \np{jpiglo} & \np{jpjglo} &       \\
168      \hline
169      \hline
170      \~4\deg     &        4         &         92     &      76      &       \\
171      \~2\deg        &        2         &       182     &    149      &        \\
172      \~1\deg        &        1         &       362     &     292     &        \\
173      \~0.5\deg     &        05       &       722     &     511     &        \\
174      \~0.25\deg   &        025     &      1442    &   1021     &        \\
175      % \key{orca\_r8}       &        8         &      2882    &   2042     &        \\
176      % \key{orca\_r12}     &      12         &      4322    &   3062      &       \\
177      \hline
178      \hline
179    \end{tabular}
180    \caption{
181      \protect\label{tab:ORCA}
182      Domain size of ORCA family configurations.
183      The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.
184    }
185  \end{center}
186\end{table}
187%--------------------------------------------------------------------------------------------------------------
188
189
190The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh,
191local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
192so that the resolution is 1\deg~ there.
193A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
1940.5\deg~ at the Equator.
195
196The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
1971/3\deg~at the Equator.
198Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
199
200The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
201
202For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
203In the other ORCA configurations, 31 levels are used
204(see \autoref{tab:orca_zgr}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
205
206Only the ORCA\_R2 is provided with all its input files in the NEMO distribution.
207%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
208%climate change (Marti et al., 2009).
209%It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
210%documented in \citet{griffies.biastoch.ea_OM09}.
211
212This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
213(see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).
214The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
215The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_core}),
216which was developed for the purpose of running global coupled ocean-ice simulations without
217an interactive atmosphere.
218This \citet{large.yeager_rpt04} dataset is available through
219the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
220The "normal year" of \citet{large.yeager_rpt04} has been chosen of the NEMO distribution since release v3.3.
221
222ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie with AGRIF, \key{agrif} defined). This is available as the AGRIF\_DEMO configuration that can be found in the \path{cfgs/AGRIF_DEMO/} directory.
223
224A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
225sponge layers at open boundaries.
226
227% -------------------------------------------------------------------------------------------------------------
228%       GYRE family: double gyre basin
229% -------------------------------------------------------------------------------------------------------------
230\section{GYRE family: double gyre basin}
231\label{sec:CFG_gyre}
232
233The GYRE configuration \citep{levy.klein.ea_OM10} has been built to
234simulate the seasonal cycle of a double-gyre box model.
235It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and
236\citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00},
237over which an analytical seasonal forcing is applied.
238This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
239and their contribution to the large scale circulation.
240
241The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
242The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
243rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
244The domain is bounded by vertical walls and by a flat bottom.
245The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
246The circulation is forced by analytical profiles of wind and buoyancy fluxes.
247The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}.
248The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
249It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
250a small recirculation gyre in the southern corner.
251The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
252A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
253The fresh water flux is also prescribed and varies zonally.
254It is determined such as, at each time step, the basin-integrated flux is zero.
255The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
256the whole domain.
257
258The GYRE configuration is set like an analytical configuration.
259Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in
260the reference configuration \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
261analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
262Its horizontal resolution (and thus the size of the domain) is determined by
263setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\
264
265\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
266
267\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
268
269Obviously, the namelist parameters have to be adjusted to the chosen resolution,
270see the Configurations pages on the NEMO web site (NEMO Configurations).
271In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
272
273The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
274as it does not requires any input file.
275For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
276even though the physical integrity of the solution can be compromised.
277Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in
278namelist \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
279
280%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
281\begin{figure}[!t]
282  \begin{center}
283    \includegraphics[width=\textwidth]{Fig_GYRE}
284    \caption{
285      \protect\label{fig:GYRE}
286      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
287      From \citet{levy.klein.ea_OM10}.
288    }
289  \end{center}
290\end{figure}
291%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
292
293% -------------------------------------------------------------------------------------------------------------
294%       AMM configuration
295% -------------------------------------------------------------------------------------------------------------
296\section{AMM: atlantic margin configuration}
297\label{sec:MISC_config_AMM}
298
299The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
300a regular lat-lon grid at approximately 12km horizontal resolution.
301The appropriate \textit{\&namcfg} namelist  is available in \textit{cfgs/AMM12/EXPREF/namelist\_cfg}.
302It is used to build the correct dimensions of the AMM domain.
303
304This configuration tests several features of NEMO functionality specific to the shelf seas.
305In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and
306is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module.
307Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln\_zdfgls} \forcode{= .true.}).
308
309In addition to the tidal boundary condition the model may also take open boundary conditions from
310a North Atlantic model.
311Boundaries may be completely omitted by setting \np{ln\_bdy} to false.
312Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
313The Baltic boundary is included within the river input file and is specified as a river source.
314Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
315
316\biblio
317
318\pindex
319
320\end{document}
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