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#2534: Minor update to GYRE documentation

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12\paragraph{Changes record} ~\\
15  \begin{tabularx}{\textwidth}{l||X|X}
16    Release & Author(s) & Modifications \\
17    \hline
18    {\em   4.0} & {\em ...} & {\em ...} \\
19    {\em   3.6} & {\em ...} & {\em ...} \\
20    {\em   3.4} & {\em ...} & {\em ...} \\
21    {\em <=3.4} & {\em ...} & {\em ...}
22  \end{tabularx}
27%% =================================================================================================
31The purpose of this part of the manual is to introduce the \NEMO\ reference configurations.
32These configurations are offered as means to explore various numerical and physical options,
33thus allowing the user to verify that the code is performing in a manner consistent with that we are running.
34This form of verification is critical as one adopts the code for his or her particular research purposes.
35The reference configurations also provide a sense for some of the options available in the code,
36though by no means are all options exercised in the reference configurations.
37Configuration is defined manually through the \nam{cfg}{cfg} namelist variables.
40  \nlst{namcfg}
41  \caption{\forcode{&namcfg}}
42  \label{lst:namcfg}
45%% =================================================================================================
46\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]{C1D: 1D Water column model (\protect\key{c1d})}
49The 1D model option simulates a stand alone water column within the 3D \NEMO\ system.
50It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
51It is set up by defining the position of the 1D water column in the grid
52(see \path{./cfgs/SHARED/namelist\_ref}).
53The 1D model is a very useful tool
54\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
55\textit{(b)} to investigate suitable parameterisations of unresolved turbulence
56(surface wave breaking, Langmuir circulation, ...);
57\textit{(c)} to compare the behaviour of different vertical mixing schemes;
58\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain;
59\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
61The methodology is based on the configuration of the smallest possible domain:
62a 3x3 domain with 75 vertical levels.
64The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
65and second, the two components of the velocity are moved on a $T$-point.
66Therefore, defining \key{c1d} changes some things in the code behaviour:
68\item a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
69  both lateral tendancy terms and lateral physics are not called;
70\item the vertical velocity is zero
71  (so far, no attempt at introducing a Ekman pumping velocity has been made);
72\item a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
73  (see \mdl{dyncor\_c1d}).
75All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of
76the \NEMO\ distribution.
78% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
80%% =================================================================================================
81\section{ORCA family: global ocean with tripolar grid}
84The ORCA family is a series of global ocean configurations that are run together with
85the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
86An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
87The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
88this file is available in tar file on the \NEMO\ community zenodo platform: \\
91In this namelist\_cfg the name of domain input file is set in \nam{cfg}{cfg} block of namelist.
94  \centering
95  \includegraphics[width=0.66\textwidth]{CFGS_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}
107%% =================================================================================================
108\subsection{ORCA tripolar grid}
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
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.
121  \centering
122  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_msh05_e1_e2}
123  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_aniso}
124  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{
125    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
126    \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
127    for ORCA 0.5\deg\ mesh.
128    South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
129    Poleward of 20\deg{N},
130    the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
131    vicinity of Victoria Island (Canadian Arctic Archipelago).}
132  \label{fig:CFGS_ORCA_e1e2}
135The method is applied to Mercator grid (\ie\ same zonal and meridional grid spacing) poleward of 20\deg{N},
136so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
137The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
138is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
139(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
140the northern hemisphere larger than the smallest one in the southern hemisphere.
141The resulting mesh is shown in \autoref{fig:CFGS_ORCA_msh} and \autoref{fig:CFGS_ORCA_e1e2} for
142a half a degree grid (ORCA\_R05).
143The smallest ocean scale factor is found in along Antarctica,
144while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
146%% =================================================================================================
147\subsection{ORCA pre-defined resolution}
150The \NEMO\ system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
151The value of the resolution is given by the resolution at the Equator expressed in degrees.
152Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
153which sets the grid size and configuration name parameters.
154The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
158  \centering
159  \begin{tabular}{p{4cm} c c c c}
160    Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\
161    \hline \hline
162    % 4   \deg\ &              4   &          92 &          76 \\
163    2   \deg\ &              2   &         182 &         149 \\
164    1   \deg\ &              1   &         362 &         292 \\
165    0.5 \deg\ &              05  &         722 &         511 \\
166    0.25\deg\ &              025 &        1442 &        1021 \\
167    \hline \hline
168  \end{tabular}
169  \caption[Domain size of ORCA family configurations]{
170    Domain size of ORCA family configurations.
171    The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.}
172  \label{tab:CFGS_ORCA}
175The ORCA\_R2 configuration has the following specificity: starting from a 2\deg\ ORCA mesh,
176local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
177so that the resolution is 1\deg\ there.
178A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
1790.5\deg\ at the Equator.
181The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
1821/3\deg\ at the Equator.
183Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
185The ORCA\_R05 and higher global configurations do not incorporate any regional refinements.
187For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
188In the other ORCA configurations, 31 levels are used
189(see \autoref{tab:CFGS_ORCA}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:DOM_zgr_e3}).
191Only the ORCA\_R2 is provided with all its input files in the \NEMO\ distribution.
192%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
193%climate change (Marti et al., 2009).
194%It is also the basis for the \NEMO\ contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
195%documented in \citet{griffies.biastoch.ea_OM09}.
197This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
198(see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}).
199The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
200The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}),
201which was developed for the purpose of running global coupled ocean-ice simulations without
202an interactive atmosphere.
203This \citet{large.yeager_trpt04} dataset is available through
204the \href{}{GFDL web site}.
205The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3.
207ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined).
208This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory.
210A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
211sponge layers at open boundaries.
213%% =================================================================================================
214\section{GYRE family: double gyre basin}
217The GYRE configuration \citep{levy.klein.ea_OM10} has been built to
218simulate the seasonal cycle of a double-gyre box model.
219It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and
220\citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00},
221over which an analytical seasonal forcing is applied.
222This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
223and their contribution to the large scale circulation.
225The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
226The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
227rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
228The domain is bounded by vertical walls and by a flat bottom.
229The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
230The circulation is forced by analytical profiles of wind and buoyancy fluxes.
231The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}.
232The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
233It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
234a small recirculation gyre in the southern corner.
235The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
236A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
237The fresh water flux is also prescribed and varies zonally.
238It is determined such as, at each time step, the basin-integrated flux is zero.
239The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
240the whole domain.
242The GYRE configuration is set like an analytical configuration.
243Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in
244the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
245analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines.
246Its horizontal resolution (and thus the size of the domain) is determined by
247setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}:
249  \jp{jpiglo} = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\
250  \jp{jpjglo} = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}}
253Obviously, the namelist parameters have to be adjusted to the chosen resolution,
254see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
255In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}).
258  \begin{forlines}
260&namusr_def    !   GYRE user defined namelist 
262   nn_GYRE     =     1     !  GYRE resolution [1/degrees]
263   ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
264   jpkglo      =    31     !  number of model levels
266  \end{forlines}
267  \caption{\forcode{&namusr_def}}
268  \label{lst:namusr_def}
271The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
272as it does not requires any input file.
273For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
274even though the physical integrity of the solution can be compromised.
275Benchmark is activate via \np[=.true.]{ln_bench}{ln\_bench} in \nam{usr_def}{usr\_def} in
276namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
279  \centering
280  \includegraphics[width=0.66\textwidth]{CFGS_GYRE}
281  \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{
282    Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
283    From \citet{levy.klein.ea_OM10}.}
284  \label{fig:CFGS_GYRE}
287%% =================================================================================================
288\section{AMM: atlantic margin configuration}
291The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
292a regular lat-lon grid at approximately 12km horizontal resolution.
293The appropriate \textit{\&namcfg} namelist  is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}.
294It is used to build the correct dimensions of the AMM domain.
296This configuration tests several features of \NEMO\ functionality specific to the shelf seas.
297In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and
298is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module.
299Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np[=.true.]{ln_zdfgls}{ln\_zdfgls}).
301In addition to the tidal boundary condition the model may also take open boundary conditions from
302a North Atlantic model.
303Boundaries may be completely omitted by setting \np{ln_bdy}{ln\_bdy} to false.
304Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
305The Baltic boundary is included within the river input file and is specified as a river source.
306Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
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