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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:CFGS}
9
10\chaptertoc
11
12\newpage
13
14% ================================================================
15% Introduction
16% ================================================================
17\section{Introduction}
18\label{sec:CFGS_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 \nam{cfg} namelist variables.
27
28%------------------------------------------namcfg----------------------------------------------------
29
30\begin{listing}
31  \nlst{namcfg}
32  \caption{\forcode{&namcfg}}
33  \label{lst:namcfg}
34\end{listing}
35%-------------------------------------------------------------------------------------------------------------
36
37% ================================================================
38% 1D model configuration
39% ================================================================
40\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]{C1D: 1D Water column model (\protect\key{c1d})}
41\label{sec:CFGS_c1d}
42
43The 1D model option simulates a stand alone water column within the 3D \NEMO\ system.
44It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
45It is set up by defining the position of the 1D water column in the grid
46(see \path{./cfgs/SHARED/namelist\_ref}).
47The 1D model is a very useful tool
48\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
49\textit{(b)} to investigate suitable parameterisations of unresolved turbulence
50(surface wave breaking, Langmuir circulation, ...);
51\textit{(c)} to compare the behaviour of different vertical mixing schemes;
52\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain;
53\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
54
55The methodology is based on the configuration of the smallest possible domain:
56a 3x3 domain with 75 vertical levels.
57
58The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
59and second, the two components of the velocity are moved on a $T$-point.
60Therefore, defining \key{c1d} changes some things in the code behaviour:
61\begin{description}
62\item[(1)]
63  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
64  both lateral tendancy terms and lateral physics are not called;
65\item[(2)]
66  the vertical velocity is zero
67  (so far, no attempt at introducing a Ekman pumping velocity has been made);
68\item[(3)]
69  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
70  (see \mdl{dyncor\_c1d}).
71\end{description}
72All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of
73the \NEMO\ distribution.
74
75% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
76
77% ================================================================
78% ORCA family configurations
79% ================================================================
80\section{ORCA family: global ocean with tripolar grid}
81\label{sec:CFGS_orca}
82
83The ORCA family is a series of global ocean configurations that are run together with
84the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
85An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
86The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
87this file is available in tar file on the \NEMO\ community zenodo platform: \\
88https://doi.org/10.5281/zenodo.2640723
89
90In this namelist\_cfg the name of domain input file is set in \nam{cfg} block of namelist.
91
92%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
93\begin{figure}[!t]
94  \centering
95  \includegraphics[width=0.66\textwidth]{Fig_ORCA_NH_mesh}
96  \caption[ORCA mesh conception]{
97    ORCA mesh conception.
98    The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
99    The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
100    are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
101    Then, following \citet{madec.imbard_CD96},
102    the normal to the series of ellipses (red curves) is computed which
103    provides the j-lines of the mesh (pseudo longitudes).}
104  \label{fig:CFGS_ORCA_msh}
105\end{figure}
106%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
107
108% -------------------------------------------------------------------------------------------------------------
109%       ORCA tripolar grid
110% -------------------------------------------------------------------------------------------------------------
111\subsection{ORCA tripolar grid}
112\label{subsec:CFGS_orca_grid}
113
114The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{madec.imbard_CD96}.
115It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
116the computational domain since two north mesh poles are introduced and placed on lands.
117The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
118computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
119The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles
120(\autoref{fig:CFGS_ORCA_msh}).
121The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
122or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
123%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
124\begin{figure}[!tbp]
125  \centering
126  \includegraphics[width=0.66\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
127  \includegraphics[width=0.66\textwidth]{Fig_ORCA_aniso}
128  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{
129    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
130    \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
131    for ORCA 0.5\deg\ mesh.
132    South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
133    Poleward of 20\deg{N},
134    the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
135    vicinity of Victoria Island (Canadian Arctic Archipelago).}
136  \label{fig:CFGS_ORCA_e1e2}
137\end{figure}
138%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
139
140The method is applied to Mercator grid (\ie\ same zonal and meridional grid spacing) poleward of 20\deg{N},
141so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
142The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
143is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
144(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
145the northern hemisphere larger than the smallest one in the southern hemisphere.
146The resulting mesh is shown in \autoref{fig:CFGS_ORCA_msh} and \autoref{fig:CFGS_ORCA_e1e2} for
147a half a degree grid (ORCA\_R05).
148The smallest ocean scale factor is found in along Antarctica,
149while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
150
151% -------------------------------------------------------------------------------------------------------------
152%       ORCA-ICE(-PISCES) configurations
153% -------------------------------------------------------------------------------------------------------------
154\subsection{ORCA pre-defined resolution}
155\label{subsec:CFGS_orca_resolution}
156
157The \NEMO\ system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
158The value of the resolution is given by the resolution at the Equator expressed in degrees.
159Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
160which sets the grid size and configuration name parameters.
161The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
162(\autoref{tab:CFGS_ORCA}).
163
164%--------------------------------------------------TABLE--------------------------------------------------
165\begin{table}[!t]
166  \centering
167  \begin{tabular}{p{4cm} c c c c}
168    Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\
169    \hline \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    \hline \hline
176  \end{tabular}
177  \caption[Domain size of ORCA family configurations]{
178    Domain size of ORCA family configurations.
179    The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.}
180  \label{tab:CFGS_ORCA}
181\end{table}
182%--------------------------------------------------------------------------------------------------------------
183
184
185The ORCA\_R2 configuration has the following specificity: starting from a 2\deg\ ORCA mesh,
186local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
187so that the resolution is 1\deg\ there.
188A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
1890.5\deg\ at the Equator.
190
191The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
1921/3\deg\ at the Equator.
193Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
194
195The ORCA\_R05 and higher global configurations do not incorporate any regional refinements.
196
197For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
198In the other ORCA configurations, 31 levels are used
199(see \autoref{tab:CFGS_ORCA}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:DOM_zgr_e3}).
200
201Only the ORCA\_R2 is provided with all its input files in the \NEMO\ distribution.
202%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
203%climate change (Marti et al., 2009).
204%It is also the basis for the \NEMO\ contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
205%documented in \citet{griffies.biastoch.ea_OM09}.
206
207This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
208(see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}).
209The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
210The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_ocean}),
211which was developed for the purpose of running global coupled ocean-ice simulations without
212an interactive atmosphere.
213This \citet{large.yeager_rpt04} dataset is available through
214the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
215The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3.
216
217ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined).
218This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory.
219
220A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
221sponge layers at open boundaries.
222
223% -------------------------------------------------------------------------------------------------------------
224%       GYRE family: double gyre basin
225% -------------------------------------------------------------------------------------------------------------
226\section{GYRE family: double gyre basin}
227\label{sec:CFGS_gyre}
228
229The GYRE configuration \citep{levy.klein.ea_OM10} has been built to
230simulate the seasonal cycle of a double-gyre box model.
231It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and
232\citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00},
233over which an analytical seasonal forcing is applied.
234This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
235and their contribution to the large scale circulation.
236
237The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
238The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
239rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
240The domain is bounded by vertical walls and by a flat bottom.
241The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
242The circulation is forced by analytical profiles of wind and buoyancy fluxes.
243The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}.
244The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
245It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
246a small recirculation gyre in the southern corner.
247The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
248A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
249The fresh water flux is also prescribed and varies zonally.
250It is determined such as, at each time step, the basin-integrated flux is zero.
251The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
252the whole domain.
253
254The GYRE configuration is set like an analytical configuration.
255Through \np{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in
256the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
257analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
258Its horizontal resolution (and thus the size of the domain) is determined by
259setting \np{nn\_GYRE} in \nam{usr\_def}: \\
260
261\jp{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
262
263\jp{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
264
265Obviously, the namelist parameters have to be adjusted to the chosen resolution,
266see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
267In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}).
268
269The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
270as it does not requires any input file.
271For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
272even though the physical integrity of the solution can be compromised.
273Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \nam{usr\_def} in
274namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
275
276%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
277\begin{figure}[!t]
278  \centering
279  \includegraphics[width=0.66\textwidth]{Fig_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% -------------------------------------------------------------------------------------------------------------
288%       AMM configuration
289% -------------------------------------------------------------------------------------------------------------
290\section{AMM: atlantic margin configuration}
291\label{sec:CFGS_config_AMM}
292
293The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
294a regular lat-lon grid at approximately 12km horizontal resolution.
295The appropriate \textit{\&namcfg} namelist  is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}.
296It is used to build the correct dimensions of the AMM domain.
297
298This configuration tests several features of \NEMO\ functionality specific to the shelf seas.
299In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and
300is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module.
301Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln\_zdfgls} \forcode{= .true.}).
302
303In addition to the tidal boundary condition the model may also take open boundary conditions from
304a North Atlantic model.
305Boundaries may be completely omitted by setting \np{ln\_bdy} to false.
306Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
307The Baltic boundary is included within the river input file and is specified as a river source.
308Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
309
310\biblio
311
312\pindex
313
314\end{document}
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