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[2376]4% ================================================================
[10414]5% Chapter Configurations
[2376]6% ================================================================
14% ================================================================
15% Introduction
16% ================================================================
[10354]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.
32% ================================================================
[3764]33% 1D model configuration
[2376]34% ================================================================
[9393]35\section{C1D: 1D Water column model (\protect\key{c1d}) }
[9019]38BE careful: to be re-written according to suppression of jpizoom and jpjzoom !!!!
[10354]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
[4147]43(see \textit{CONFIG/SHARED/namelist\_ref} ).
[10354]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;
[2376]50\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
[10354]52The methodology is based on the use of the zoom functionality over the smallest possible domain:
53a 3x3 domain centered on the grid point of interest, with some extra routines.
54There is no need to define a new mesh, bathymetry, initial state or forcing,
55since the 1D model will use those of the configuration it is a zoom of.
56The chosen grid point is set in \textit{\ngn{namcfg}} namelist by
57setting the \np{jpizoom} and \np{jpjzoom} parameters to the indices of the location of the chosen grid point.
[10354]59The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
60and second, the two components of the velocity are moved on a $T$-point.
[3764]61Therefore, defining \key{c1d} changes five main things in the code behaviour:
64  the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column of
65  the 3x3 domain is imposed over the whole domain;
[10442]67  a call to \rou{lbc\_lnk} is systematically done when reading input data (\ie in \mdl{iom});
69  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
70  both lateral tendancy terms and lateral physics are not called;
72  the vertical velocity is zero
73  (so far, no attempt at introducing a Ekman pumping velocity has been made);
75  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
76  (see \mdl{dyncor\_c1d}).
[10354]78All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
[2381]79the \NEMO distribution.
[2381]81% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
[2376]83% ================================================================
84% ORCA family configurations
85% ================================================================
[9393]86\section{ORCA family: global ocean with tripolar grid}
[10354]89The ORCA family is a series of global ocean configurations that are run together with
90the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model (ORCA-LIM-PISCES),
91using various resolutions.
92An appropriate namelist is available in \path{CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg} for ORCA2.
93The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
94this file is available in tar file in the wiki of NEMO: \\
[9019]95\_LIM3\_PISCES \\
96In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.
100  \begin{center}
101    \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh}
[10414]102    \caption{
103      \protect\label{fig:MISC_ORCA_msh}
[10354]104      ORCA mesh conception.
[10442]105      The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
[10354]106      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
107      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
108      Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed which
[10414]109      provides the j-lines of the mesh (pseudo longitudes).
110    }
[10354]111  \end{center}
[2376]115% -------------------------------------------------------------------------------------------------------------
116%       ORCA tripolar grid
117% -------------------------------------------------------------------------------------------------------------
118\subsection{ORCA tripolar grid}
[10354]121The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
122It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
[2376]123the computational domain since two north mesh poles are introduced and placed on lands.
[10354]124The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
125computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
126The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles
128The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
129or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
132  \begin{center}
133    \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
134    \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso}
[10414]135    \caption {
136      \protect\label{fig:MISC_ORCA_e1e2}
[10354]137      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
138      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
139      for ORCA 0.5\deg ~mesh.
[10442]140      South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
141      Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
[10414]142      vicinity of Victoria Island (Canadian Arctic Archipelago).
143    }
144  \end{center}
[10442]148The method is applied to Mercator grid (\ie same zonal and meridional grid spacing) poleward of 20\deg{N},
[10354]149so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
150The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
151is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
152(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
153the northern hemisphere larger than the smallest one in the southern hemisphere.
154The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for
155a half a degree grid (ORCA\_R05).
156The smallest ocean scale factor is found in along Antarctica,
157while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
159% -------------------------------------------------------------------------------------------------------------
160%       ORCA-LIM(-PISCES) configurations
161% -------------------------------------------------------------------------------------------------------------
[2381]162\subsection{ORCA pre-defined resolution}
[10354]165The NEMO system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
166The value of the resolution is given by the resolution at the Equator expressed in degrees.
167Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
168which sets the grid size and configuration name parameters.
169The NEMO System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
170(Tab. \autoref{tab:ORCA}).
174  \begin{center}
175    \begin{tabular}{p{4cm} c c c c}
176      Horizontal Grid                         & \np{ORCA\_index} &  \np{jpiglo} & \np{jpjglo} &       \\
177      \hline
178      \hline
179      \~4\deg     &        4         &         92     &      76      &       \\
180      \~2\deg        &        2         &       182     &    149      &        \\
181      \~1\deg        &        1         &       362     &     292     &        \\
182      \~0.5\deg     &        05       &       722     &     511     &        \\
183      \~0.25\deg   &        025     &      1442    &   1021     &        \\
184      % \key{orca\_r8}       &        8         &      2882    &   2042     &        \\
185      % \key{orca\_r12}     &      12         &      4322    &   3062      &       \\
186      \hline
187      \hline
188    \end{tabular}
189    \caption{
190      \protect\label{tab:ORCA}
191      Domain size of ORCA family configurations.
192      The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.
193    }
194  \end{center}
[10354]199The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh,
200local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
201so that the resolution is 1\deg \time 1\deg there.
202A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
2030.5\deg at the Equator.
[10354]205The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
2061/3\deg~at the Equator.
207Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
[2381]209The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
[10354]211For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
212In the other ORCA configurations, 31 levels are used
[10442]213(see \autoref{tab:orca_zgr} %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
[10354]215Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
216It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
217climate change (Marti et al., 2009).
218It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
219documented in \citet{Griffies_al_OM09}.
[10354]221This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
222(see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).
[2381]223The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
[9407]224The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \autoref{subsec:SBC_blk_core}),
[10354]225which was developed for the purpose of running global coupled ocean-ice simulations without
226an interactive atmosphere.
227This \citet{Large_Yeager_Rep04} dataset is available through
228the \href{}{GFDL web site}.
229The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution since release v3.3.
[10354]231ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area
232(\key{agrif} defined) and, by setting the appropriate variables, see \path{CONFIG/SHARED/namelist_ref}.
233A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
234sponge layers at open boundaries.
236% -------------------------------------------------------------------------------------------------------------
237%       GYRE family: double gyre basin
238% -------------------------------------------------------------------------------------------------------------
[4147]239\section{GYRE family: double gyre basin }
[10354]242The GYRE configuration \citep{Levy_al_OM10} has been built to
243simulate the seasonal cycle of a double-gyre box model.
244It consists in an idealized domain similar to that used in the studies of \citet{Drijfhout_JPO94} and
245\citet{Hazeleger_Drijfhout_JPO98, Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
246over which an analytical seasonal forcing is applied.
247This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
[2376]248and their contribution to the large scale circulation.
[10442]250The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
[10354]251rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
252The domain is bounded by vertical walls and by a flat bottom.
253The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
254The circulation is forced by analytical profiles of wind and buoyancy fluxes.
255The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{Levy_al_OM10}.
[10442]256The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
[10354]257It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
258a small recirculation gyre in the southern corner.
259The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
260A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
261The fresh water flux is also prescribed and varies zonally.
262It is determined such as, at each time step, the basin-integrated flux is zero.
263The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
264the whole domain.
[10354]266The GYRE configuration is set like an analytical configuration.
267Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in
268the reference configuration \path{CONFIG/GYRE/EXP00/namelist_cfg}
269analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
270Its horizontal resolution (and thus the size of the domain) is determined by
271setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\
[9393]272\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
273\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
[10354]274Obviously, the namelist parameters have to be adjusted to the chosen resolution,
275see the Configurations pages on the NEMO web site (Using NEMO\/Configurations).
[9407]276In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
[10354]278The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
279as it does not requires any input file.
280For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
281even though the physical integrity of the solution can be compromised.
282Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in
283namelist \path{CONFIG/GYRE/EXP00/namelist_cfg}.
287  \begin{center}
288    \includegraphics[width=1.0\textwidth]{Fig_GYRE}
[10414]289    \caption{
290      \protect\label{fig:GYRE}
[10354]291      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
[10414]292      From \citet{Levy_al_OM10}.
293    }
[10354]294  \end{center}
298% -------------------------------------------------------------------------------------------------------------
[3294]299%       AMM configuration
[2376]300% -------------------------------------------------------------------------------------------------------------
[9393]301\section{AMM: atlantic margin configuration}
[10354]304The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
305a regular lat-lon grid at approximately 12km horizontal resolution.
306The appropriate \textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
[4147]307It is used to build the correct dimensions of the AMM domain.
[10354]309This configuration tests several features of NEMO functionality specific to the shelf seas.
310In particular, the AMM uses $S$-coordinates in the vertical rather than $z$-coordinates and
311is forced with tidal lateral boundary conditions using a flather boundary condition from the BDY module.
312The AMM configuration uses the GLS (\key{zdfgls}) turbulence scheme,
313the VVL non-linear free surface(\key{vvl}) and time-splitting (\key{dynspg\_ts}).
[10354]315In addition to the tidal boundary condition the model may also take open boundary conditions from
316a North Atlantic model.
317Boundaries may be completely omitted by setting \np{ln\_bdy} to false.
318Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
319The Baltic boundary is included within the river input file and is specified as a river source.
320Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
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