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1\documentclass[../main/NEMO_manual]{subfiles}
2
3\begin{document}
4
5\chapter{Configurations}
6\label{chap:CFGS}
7
8\chaptertoc
9
10\paragraph{Changes record} ~\\
11
12{\footnotesize
13  \begin{tabularx}{\textwidth}{l||X|X}
14    Release & Author(s) & Modifications \\
15    \hline
16    {\em   4.0} & {\em ...} & {\em ...} \\
17    {\em   3.6} & {\em ...} & {\em ...} \\
18    {\em   3.4} & {\em ...} & {\em ...} \\
19    {\em <=3.4} & {\em ...} & {\em ...}
20  \end{tabularx}
21}
22
23\clearpage
24
25%% =================================================================================================
26\section{Introduction}
27\label{sec:CFGS_intro}
28
29The purpose of this part of the manual is to introduce the \NEMO\ reference configurations.
30These configurations are offered as means to explore various numerical and physical options,
31thus allowing the user to verify that the code is performing in a manner consistent with that we are running.
32This form of verification is critical as one adopts the code for his or her particular research purposes.
33The reference configurations also provide a sense for some of the options available in the code,
34though by no means are all options exercised in the reference configurations.
35Configuration is defined manually through the \nam{cfg}{cfg} namelist variables.
36
37\begin{listing}
38  \nlst{namcfg}
39  \caption{\forcode{&namcfg}}
40  \label{lst:namcfg}
41\end{listing}
42
43%% =================================================================================================
44\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]{C1D: 1D Water column model (\protect\key{c1d})}
45\label{sec:CFGS_c1d}
46
47The 1D model option simulates a stand alone water column within the 3D \NEMO\ system.
48It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
49It is set up by defining the position of the 1D water column in the grid
50(see \path{./cfgs/SHARED/namelist\_ref}).
51The 1D model is a very useful tool
52\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
53\textit{(b)} to investigate suitable parameterisations of unresolved turbulence
54(surface wave breaking, Langmuir circulation, ...);
55\textit{(c)} to compare the behaviour of different vertical mixing schemes;
56\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain;
57\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
58
59The methodology is based on the configuration of the smallest possible domain:
60a 3x3 domain with 75 vertical levels.
61
62The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
63and second, the two components of the velocity are moved on a $T$-point.
64Therefore, defining \key{c1d} changes some things in the code behaviour:
65\begin{enumerate}
66\item a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
67  both lateral tendancy terms and lateral physics are not called;
68\item the vertical velocity is zero
69  (so far, no attempt at introducing a Ekman pumping velocity has been made);
70\item a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
71  (see \mdl{dyncor\_c1d}).
72\end{enumerate}
73All the relevant \textit{\_c1d} modules can be found in the src/OCE/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\section{ORCA family: global ocean with tripolar grid}
80\label{sec:CFGS_orca}
81
82The ORCA family is a series of global ocean configurations that are run together with
83the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
84An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
85The domain of ORCA2 configuration is defined in \textit{ORCA\_R2\_zps\_domcfg.nc} file,
86this file is available in tar file on the \NEMO\ community zenodo platform: \\
87https://doi.org/10.5281/zenodo.2640723
88
89In this namelist\_cfg the name of domain input file is set in \nam{cfg}{cfg} block of namelist.
90
91\begin{figure}[!t]
92  \centering
93  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_mesh}
94  \caption[ORCA mesh conception]{
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},
100    the normal to the series of ellipses (red curves) is computed which
101    provides the j-lines of the mesh (pseudo longitudes).}
102  \label{fig:CFGS_ORCA_msh}
103\end{figure}
104
105%% =================================================================================================
106\subsection{ORCA tripolar grid}
107\label{subsec:CFGS_orca_grid}
108
109The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{madec.imbard_CD96}.
110It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
111the computational domain since two north mesh poles are introduced and placed on lands.
112The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
113computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
114The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles
115(\autoref{fig:CFGS_ORCA_msh}).
116The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
117or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
118\begin{figure}[!tbp]
119  \centering
120  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_msh05_e1_e2}
121  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_aniso}
122  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{
123    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
124    \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
125    for ORCA 0.5\deg\ mesh.
126    South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
127    Poleward of 20\deg{N},
128    the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
129    vicinity of Victoria Island (Canadian Arctic Archipelago).}
130  \label{fig:CFGS_ORCA_e1e2}
131\end{figure}
132
133The method is applied to Mercator grid (\ie\ same zonal and meridional grid spacing) poleward of 20\deg{N},
134so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
135The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
136is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
137(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
138the northern hemisphere larger than the smallest one in the southern hemisphere.
139The resulting mesh is shown in \autoref{fig:CFGS_ORCA_msh} and \autoref{fig:CFGS_ORCA_e1e2} for
140a half a degree grid (ORCA\_R05).
141The smallest ocean scale factor is found in along Antarctica,
142while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
143
144%% =================================================================================================
145\subsection{ORCA pre-defined resolution}
146\label{subsec:CFGS_orca_resolution}
147
148The \NEMO\ system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
149The value of the resolution is given by the resolution at the Equator expressed in degrees.
150Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
151which sets the grid size and configuration name parameters.
152The \NEMO\ System Team provides only ORCA2 domain input file "\textit{ORCA\_R2\_zps\_domcfg.nc}" file
153(\autoref{tab:CFGS_ORCA}).
154
155\begin{table}[!t]
156  \centering
157  \begin{tabular}{p{4cm} c c c c}
158    Horizontal Grid & \texttt{ORCA\_index} & \texttt{jpiglo} & \texttt{jpjglo} \\
159    \hline \hline
160    % 4   \deg\ &              4   &          92 &          76 \\
161    2   \deg\ &              2   &         182 &         149 \\
162    1   \deg\ &              1   &         362 &         292 \\
163    0.5 \deg\ &              05  &         722 &         511 \\
164    0.25\deg\ &              025 &        1442 &        1021 \\
165    \hline \hline
166  \end{tabular}
167  \caption[Domain size of ORCA family configurations]{
168    Domain size of ORCA family configurations.
169    The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.}
170  \label{tab:CFGS_ORCA}
171\end{table}
172
173The ORCA\_R2 configuration has the following specificity: starting from a 2\deg\ ORCA mesh,
174local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
175so that the resolution is 1\deg\ there.
176A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
1770.5\deg\ at the Equator.
178
179The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
1801/3\deg\ at the Equator.
181Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
182
183The ORCA\_R05 and higher global configurations do not incorporate any regional refinements.
184
185For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
186In the other ORCA configurations, 31 levels are used
187(see \autoref{tab:CFGS_ORCA}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:DOM_zgr_e3}).
188
189Only the ORCA\_R2 is provided with all its input files in the \NEMO\ distribution.
190%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
191%climate change (Marti et al., 2009).
192%It is also the basis for the \NEMO\ contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
193%documented in \citet{griffies.biastoch.ea_OM09}.
194
195This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
196(see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}).
197The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
198The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}),
199which was developed for the purpose of running global coupled ocean-ice simulations without
200an interactive atmosphere.
201This \citet{large.yeager_trpt04} dataset is available through
202the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
203The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3.
204
205ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined).
206This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory.
207
208A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
209sponge layers at open boundaries.
210
211%% =================================================================================================
212\section{GYRE family: double gyre basin}
213\label{sec:CFGS_gyre}
214
215The GYRE configuration \citep{levy.klein.ea_OM10} has been built to
216simulate the seasonal cycle of a double-gyre box model.
217It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and
218\citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00},
219over which an analytical seasonal forcing is applied.
220This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
221and their contribution to the large scale circulation.
222
223The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
224The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
225rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
226The domain is bounded by vertical walls and by a flat bottom.
227The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
228The circulation is forced by analytical profiles of wind and buoyancy fluxes.
229The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}.
230The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
231It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
232a small recirculation gyre in the southern corner.
233The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
234A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
235The fresh water flux is also prescribed and varies zonally.
236It is determined such as, at each time step, the basin-integrated flux is zero.
237The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
238the whole domain.
239
240The GYRE configuration is set like an analytical configuration.
241Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in
242the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
243analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines.
244Its horizontal resolution (and thus the size of the domain) is determined by
245setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}:
246
247\begin{align*}
248   jpiglo = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\
249   jpjglo = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}}
250\end{align*}
251
252Obviously, the namelist parameters have to be adjusted to the chosen resolution,
253see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
254In the vertical, GYRE uses the default 30 ocean levels (\forcode{jpk = 31}, \autoref{fig:DOM_zgr_e3}).
255
256\begin{listing}
257  \begin{forlines}
258!-----------------------------------------------------------------------
259&namusr_def    !   GYRE user defined namelist 
260!-----------------------------------------------------------------------
261   nn_GYRE     =     1     !  GYRE resolution [1/degrees]
262   ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
263   jpkglo      =    31     !  number of model levels
264/
265  \end{forlines}
266  \caption{\forcode{&namusr_def}}
267  \label{lst:namusr_def}
268\end{listing}
269
270The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
271as it does not requires any input file.
272For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
273even though the physical integrity of the solution can be compromised.
274Benchmark is activate via \np[=.true.]{ln_bench}{ln\_bench} in \nam{usr_def}{usr\_def} in
275namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
276
277\begin{figure}[!t]
278  \centering
279  \includegraphics[width=0.66\textwidth]{CFGS_GYRE}
280  \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{
281    Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
282    From \citet{levy.klein.ea_OM10}.}
283  \label{fig:CFGS_GYRE}
284\end{figure}
285
286%% =================================================================================================
287\section{AMM: atlantic margin configuration}
288\label{sec:CFGS_config_AMM}
289
290The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
291a regular lat-lon grid at approximately 12km horizontal resolution.
292The appropriate \textit{\&namcfg} namelist  is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}.
293It is used to build the correct dimensions of the AMM domain.
294
295This configuration tests several features of \NEMO\ functionality specific to the shelf seas.
296In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and
297is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module.
298Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np[=.true.]{ln_zdfgls}{ln\_zdfgls}).
299
300In addition to the tidal boundary condition the model may also take open boundary conditions from
301a North Atlantic model.
302Boundaries may be completely omitted by setting \np{ln_bdy}{ln\_bdy} to false.
303Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
304The Baltic boundary is included within the river input file and is specified as a river source.
305Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
306
307\subinc{\input{../../global/epilogue}}
308
309\end{document}
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