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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 (\protect\key{c1d}) }
37\label{sec:CFG_c1d}
38
39The 1D model option simulates a stand alone water column within the 3D NEMO system.
40It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
41It is set up by defining the position of the 1D water column in the grid
42(see \textit{cfgs/SHARED/namelist\_ref}).
43The 1D model is a very useful tool
44\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
45\textit{(b)} to investigate suitable parameterisations of unresolved turbulence
46(surface wave breaking, Langmuir circulation, ...);
47\textit{(c)} to compare the behaviour of different vertical mixing schemes;
48\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain;
49\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
50
51The methodology is based on the configuration of the smallest possible domain:
52a 3x3 domain with 75 vertical levels.
53
54The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
55and second, the two components of the velocity are moved on a $T$-point.
56Therefore, defining \key{c1d} changes some things in the code behaviour:
57\begin{description}
58\item[(1)]
59  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
60  both lateral tendancy terms and lateral physics are not called;
61\item[(2)]
62  the vertical velocity is zero
63  (so far, no attempt at introducing a Ekman pumping velocity has been made);
64\item[(3)]
65  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
66  (see \mdl{dyncor\_c1d}).
67\end{description}
68All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of
69the NEMO distribution.
70
71% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
72
73% ================================================================
74% ORCA family configurations
75% ================================================================
76\section{ORCA family: global ocean with tripolar grid}
77\label{sec:CFG_orca}
78
79The ORCA family is a series of global ocean configurations that are run together with
80the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
81An appropriate namelist is available in \path{cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
82The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
83this file is available in tar file on the NEMO community zenodo platform: \\
84https://doi.org/10.5281/zenodo.2640723
85
86In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.
87
88%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
89\begin{figure}[!t]
90  \begin{center}
91    \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh}
92    \caption{
93      \protect\label{fig:MISC_ORCA_msh}
94      ORCA mesh conception.
95      The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
96      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
97      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
98      Then, following \citet{madec.imbard_CD96}, the normal to the series of ellipses (red curves) is computed which
99      provides the j-lines of the mesh (pseudo longitudes).
100    }
101  \end{center}
102\end{figure}
103%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
104
105% -------------------------------------------------------------------------------------------------------------
106%       ORCA tripolar grid
107% -------------------------------------------------------------------------------------------------------------
108\subsection{ORCA tripolar grid}
109\label{subsec:CFG_orca_grid}
110
111The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{madec.imbard_CD96}.
112It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
113the computational domain since two north mesh poles are introduced and placed on lands.
114The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
115computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
116The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles
117(\autoref{fig:MISC_ORCA_msh}).
118The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
119or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
120%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
121\begin{figure}[!tbp]
122  \begin{center}
123    \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
124    \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso}
125    \caption {
126      \protect\label{fig:MISC_ORCA_e1e2}
127      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
128      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
129      for ORCA 0.5\deg ~mesh.
130      South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
131      Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
132      vicinity of Victoria Island (Canadian Arctic Archipelago).
133    }
134  \end{center}
135\end{figure}
136%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
137
138The method is applied to Mercator grid (\ie same zonal and meridional grid spacing) poleward of 20\deg{N},
139so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
140The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
141is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
142(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
143the northern hemisphere larger than the smallest one in the southern hemisphere.
144The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for
145a half a degree grid (ORCA\_R05).
146The smallest ocean scale factor is found in along Antarctica,
147while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
148
149% -------------------------------------------------------------------------------------------------------------
150%       ORCA-ICE(-PISCES) configurations
151% -------------------------------------------------------------------------------------------------------------
152\subsection{ORCA pre-defined resolution}
153\label{subsec:CFG_orca_resolution}
154
155The NEMO system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
156The value of the resolution is given by the resolution at the Equator expressed in degrees.
157Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
158which sets the grid size and configuration name parameters.
159The NEMO System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
160(Tab. \autoref{tab:ORCA}).
161
162%--------------------------------------------------TABLE--------------------------------------------------
163\begin{table}[!t]
164  \begin{center}
165    \begin{tabular}{p{4cm} c c c c}
166      Horizontal Grid                         & \np{ORCA\_index} &  \np{jpiglo} & \np{jpjglo} &       \\
167      \hline
168      \hline
169      \~4\deg     &        4         &         92     &      76      &       \\
170      \~2\deg        &        2         &       182     &    149      &        \\
171      \~1\deg        &        1         &       362     &     292     &        \\
172      \~0.5\deg     &        05       &       722     &     511     &        \\
173      \~0.25\deg   &        025     &      1442    &   1021     &        \\
174      % \key{orca\_r8}       &        8         &      2882    &   2042     &        \\
175      % \key{orca\_r12}     &      12         &      4322    &   3062      &       \\
176      \hline
177      \hline
178    \end{tabular}
179    \caption{
180      \protect\label{tab:ORCA}
181      Domain size of ORCA family configurations.
182      The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.
183    }
184  \end{center}
185\end{table}
186%--------------------------------------------------------------------------------------------------------------
187
188
189The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh,
190local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
191so that the resolution is 1\deg~ there.
192A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
1930.5\deg~ at the Equator.
194
195The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
1961/3\deg~at the Equator.
197Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
198
199The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
200
201For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
202In the other ORCA configurations, 31 levels are used
203(see \autoref{tab:orca_zgr}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
204
205Only the ORCA\_R2 is provided with all its input files in the NEMO distribution.
206%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
207%climate change (Marti et al., 2009).
208%It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
209%documented in \citet{griffies.biastoch.ea_OM09}.
210
211This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
212(see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).
213The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
214The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_core}),
215which was developed for the purpose of running global coupled ocean-ice simulations without
216an interactive atmosphere.
217This \citet{large.yeager_rpt04} dataset is available through
218the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
219The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the NEMO distribution since release v3.3.
220
221ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area
222(\key{agrif} defined) and, by setting the appropriate variables, see \path{cfgs/SHARED/namelist_ref}.
223A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
224sponge layers at open boundaries.
225
226% -------------------------------------------------------------------------------------------------------------
227%       GYRE family: double gyre basin
228% -------------------------------------------------------------------------------------------------------------
229\section{GYRE family: double gyre basin }
230\label{sec:CFG_gyre}
231
232The GYRE configuration \citep{levy.klein.ea_OM10} has been built to
233simulate the seasonal cycle of a double-gyre box model.
234It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and
235\citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00},
236over which an analytical seasonal forcing is applied.
237This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
238and their contribution to the large scale circulation.
239
240The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
241The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
242rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
243The domain is bounded by vertical walls and by a flat bottom.
244The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
245The circulation is forced by analytical profiles of wind and buoyancy fluxes.
246The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}.
247The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
248It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
249a small recirculation gyre in the southern corner.
250The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
251A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
252The fresh water flux is also prescribed and varies zonally.
253It is determined such as, at each time step, the basin-integrated flux is zero.
254The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
255the whole domain.
256
257The GYRE configuration is set like an analytical configuration.
258Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in
259the reference configuration \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
260analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
261Its horizontal resolution (and thus the size of the domain) is determined by
262setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\
263
264\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
265
266\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
267
268Obviously, the namelist parameters have to be adjusted to the chosen resolution,
269see the Configurations pages on the NEMO web site (NEMO Configurations).
270In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
271
272The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
273as it does not requires any input file.
274For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
275even though the physical integrity of the solution can be compromised.
276Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in
277namelist \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
278
279%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
280\begin{figure}[!t]
281  \begin{center}
282    \includegraphics[width=1.0\textwidth]{Fig_GYRE}
283    \caption{
284      \protect\label{fig:GYRE}
285      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
286      From \citet{levy.klein.ea_OM10}.
287    }
288  \end{center}
289\end{figure}
290%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
291
292% -------------------------------------------------------------------------------------------------------------
293%       AMM configuration
294% -------------------------------------------------------------------------------------------------------------
295\section{AMM: atlantic margin configuration}
296\label{sec:MISC_config_AMM}
297
298The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
299a regular lat-lon grid at approximately 12km horizontal resolution.
300The appropriate \textit{\&namcfg} namelist  is available in \textit{cfgs/AMM12/EXPREF/namelist\_cfg}.
301It is used to build the correct dimensions of the AMM domain.
302
303This configuration tests several features of NEMO functionality specific to the shelf seas.
304In particular, the AMM uses $S$-coordinates in the vertical rather than $z$-coordinates and
305is forced with tidal lateral boundary conditions using a flather boundary condition from the BDY module.
306The AMM configuration uses the GLS (\key{zdfgls}) turbulence scheme,
307the VVL non-linear free surface(\key{vvl}) and time-splitting (\key{dynspg\_ts}).
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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