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Chap_CFG.tex in trunk/DOC/TexFiles/Chapters – NEMO

source: trunk/DOC/TexFiles/Chapters/Chap_CFG.tex @ 7646

Last change on this file since 7646 was 7646, checked in by timgraham, 7 years ago

Merge of dev_merge_2016 into trunk. UPDATE TO ARCHFILES NEEDED for XIOS2.
LIM_SRC_s/limrhg.F90 to follow in next commit due to change of kind (I'm unable to do it in this commit).
Merged using the following steps:

1) svn merge --reintegrate svn+ssh:// .
2) Resolve minor conflicts in and namelist_cfg for ORCA2LIM3 (due to a change in trunk after branch was created)
3) svn commit
4) svn switch svn+ssh://
5) svn merge svn+ssh:// .
6) At this stage I checked out a clean copy of the branch to compare against what is about to be committed to the trunk.
6) svn commit #Commit code to the trunk

In this commit I have also reverted a change to which was causing problems on the Paris machine.

File size: 17.8 KB
3% ================================================================
4% Chapter � Configurations
5% ================================================================
11$\ $\newline    % force a new ligne
13% ================================================================
14% Introduction
15% ================================================================
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
23we are running. This form of verification is critical as one adopts the code for his or her particular
24research purposes. The test cases also provide a sense for some of the options available
25in the code, though by no means are all options exercised in the reference configurations.
27Configuration is defined mainly through the \ngn{namcfg} namelist variables:
32% ================================================================
33% 1D model configuration
34% ================================================================
35\section{Water column model: 1D model (C1D) (\key{c1d}) }
38The 1D model option simulates a stand alone water column within the 3D \NEMO system.
39It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers
40or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid
41(see \textit{CONFIG/SHARED/namelist\_ref} ).
42The 1D model is a very useful tool 
43\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;
44\textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave
45breaking, Langmuir circulation, ...) ;
46\textit{(c)} to compare the behaviour of different vertical mixing schemes  ;
47\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ;
48\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
50The methodology is based on the use of the zoom functionality over the smallest possible
51domain : a 3x3 domain centered on the grid point of interest,
52with some extra routines. There is no need to define a new mesh, bathymetry,
53initial state or forcing, since the 1D model will use those of the configuration it is a zoom of.
54The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom} 
55parameters to the indices of the location of the chosen grid point.
57The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and
58second, the two components of the velocity are moved on a $T$-point.
59Therefore, defining \key{c1d} changes five main things in the code behaviour:
61\item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column
62of the 3x3 domain is imposed over the whole domain ;
63\item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ;
64\item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
65both lateral tendancy terms and lateral physics are not called ;
66\item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity
67has been made) ;
68\item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
69(see \mdl{dyncor\_c1d}).
71All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
72the \NEMO distribution.
74% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
76% ================================================================
77% ORCA family configurations
78% ================================================================
79\section{ORCA family: global ocean with tripolar grid }
82The ORCA family is a series of global ocean configurations that are run together with
83the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model
84(ORCA-LIM-PISCES), using various resolutions.
85The appropriate \textit{\&namcfg} namelist is available in \textit{CONFIG/ORCA2\_LIM/EXP00/namelist\_cfg} 
86for ORCA2 and in \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} 
87for other resolutions
91\begin{figure}[!t]   \begin{center}
93\caption{  \label{Fig_MISC_ORCA_msh}     
94ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN.
95The two "north pole" are the foci of a series of embedded ellipses (blue curves)
96which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
97Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed
98which provide the j-lines of the mesh (pseudo longitudes).  }
99\end{center}   \end{figure}
102% -------------------------------------------------------------------------------------------------------------
103%       ORCA tripolar grid
104% -------------------------------------------------------------------------------------------------------------
105\subsection{ORCA tripolar grid}
108The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
109It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
110the computational domain since two north mesh poles are introduced and placed on lands.
111The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
112computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
113The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north
114poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in
115either the mesh lines or the scale factors, or even the scale factor derivatives over the whole
116ocean domain, as the mesh is not a composite mesh.
118\begin{figure}[!tbp]  \begin{center}
121\caption {  \label{Fig_MISC_ORCA_e1e2}
122\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
123\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
124for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$)
125so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole"
126introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island
127(Canadian Arctic Archipelago). }
128\end{center}   \end{figure}
132The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward
133of 20\degN, so that the Equator is a mesh line, which provides a better numerical solution
134for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and
135variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy
136($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as
137the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger
138than the smallest one in the southern hemisphere.
139The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} 
140for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along 
141Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island
142in the Canadian Archipelago.
144% -------------------------------------------------------------------------------------------------------------
145%       ORCA-LIM(-PISCES) configurations
146% -------------------------------------------------------------------------------------------------------------
147\subsection{ORCA pre-defined resolution}
151The NEMO system is provided with five built-in ORCA configurations which differ in the
152horizontal resolution. The value of the resolution is given by the resolution at the Equator
153expressed in degrees. Each of configuration is set through the \textit{\ngn{namcfg}} namelist,
154which sets the grid size and configuration
155name parameters  (Tab. \ref{Tab_ORCA}).
159\begin{table}[!t]     \begin{center}
160\begin{tabular}{p{4cm} c c c c}
161Horizontal Grid                         & \np{jp\_cfg} &  \np{jpiglo} & \np{jpjglo} &       \\ 
162\hline  \hline
163\~4\deg     &        4         &         92     &      76      &       \\
164\~2\deg        &        2         &       182     &    149      &        \\
165\~1\deg        &        1         &       362     &     292     &        \\
166\~0.5\deg     &        05       &       722     &     511     &        \\
167\~0.25\deg   &        025     &      1442    &   1021     &        \\
168%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
169%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
170\hline   \hline
172\caption{ \label{Tab_ORCA}   
173Set of predefined parameters for ORCA family configurations.
174In all cases, the name of the configuration is set to "orca" ($i.e.$ \np{cp\_cfg}~=~orca). }
180The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,
181local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
182so that the resolution is 1\deg \time 1\deg there. A local transformation were also applied
183with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator.
185The ORCA\_R1 configuration has only a local tropical transformation  to refine the meridional
186resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2
187and R1 strongly increases the mesh anisotropy there.
189The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. 
191For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,
192otherwise 46 are used. In the other ORCA configurations, 31 levels are used
193(see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
195Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
196It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC
197assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution
198to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.
200This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m)
201in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
202The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
203The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
204which was developed for the purpose of running global coupled ocean-ice simulations
205without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available
206through the \href{}{GFDL web site}.
207The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution
208since release v3.3.
210ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas
211current area ( \key{agrif}  defined) and,  by setting the appropriate variables in
212\textit{\&namcfg}, see \textit{CONFIG/SHARED/namelist\_ref}
213a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations
214using sponge layers at open boundaries.
216% -------------------------------------------------------------------------------------------------------------
217%       GYRE family: double gyre basin
218% -------------------------------------------------------------------------------------------------------------
219\section{GYRE family: double gyre basin }
222The GYRE configuration \citep{Levy_al_OM10} has been built to simulate
223the seasonal cycle of a double-gyre box model. It consists in an idealized domain
224similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,
225Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
226over which an analytical seasonal forcing is applied. This allows to investigate the
227spontaneous generation of a large number of interacting, transient mesoscale eddies
228and their contribution to the large scale circulation.
230The domain geometry is a closed rectangular basin on the $\beta$-plane centred
231at $\sim$ 30\degN and rotated by 45\deg, 3180~km long, 2120~km wide
232and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).
233The domain is bounded by vertical walls and by a flat bottom. The configuration is
234meant to represent an idealized North Atlantic or North Pacific basin.
235The circulation is forced by analytical profiles of wind and buoyancy fluxes.
236The applied forcings vary seasonally in a sinusoidal manner between winter
237and summer extrema \citep{Levy_al_OM10}.
238The wind stress is zonal and its curl changes sign at 22\degN and 36\degN.
239It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain
240and a small recirculation gyre in the southern corner.
241The net heat flux takes the form of a restoring toward a zonal apparent air
242temperature profile. A portion of the net heat flux which comes from the solar radiation
243is allowed to penetrate within the water column.
244The fresh water flux is also prescribed and varies zonally.
245It is determined such as, at each time step, the basin-integrated flux is zero.
246The basin is initialised at rest with vertical profiles of temperature and salinity
247uniformly applied to the whole domain.
249The GYRE configuration is set through the \textit{\&namcfg} namelist defined in the reference
250configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution
251(and thus the size of the domain) is determined by setting \np{jp\_cfg} : \\
252\np{jpiglo} $= 30 \times$ \np{jp\_cfg} + 2   \\
253\np{jpjglo} $= 20 \times$ \np{jp\_cfg} + 2   \\
254Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations
255pages on the NEMO web site (Using NEMO\/Configurations) .
256In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}).
258The GYRE configuration is also used in benchmark test as it is very simple to increase
259its resolution and as it does not requires any input file. For example, keeping a same model size
260on each processor while increasing the number of processor used is very easy, even though the
261physical integrity of the solution can be compromised.
264\begin{figure}[!t]   \begin{center}
266\caption{  \label{Fig_GYRE}   
267Snapshot of relative vorticity at the surface of the model domain
268in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
269\end{center}   \end{figure}
272% -------------------------------------------------------------------------------------------------------------
273%       EEL family configuration
274% -------------------------------------------------------------------------------------------------------------
275\section{EEL family: periodic channel}
279\item[eel\_r2]  to be described....
283The appropriate \textit{\&namcfg} namelists are available in 
285% -------------------------------------------------------------------------------------------------------------
286%       AMM configuration
287% -------------------------------------------------------------------------------------------------------------
288\section{AMM: atlantic margin configuration }
291The AMM, Atlantic Margins Model, is a regional model covering the
292Northwest European Shelf domain on a regular lat-lon grid at
293approximately 12km horizontal resolution. The appropriate
294\textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
295It is used to build the correct dimensions of the AMM domain.
297This configuration tests several features of NEMO functionality specific
298to the shelf seas.
299In particular, the AMM uses $S$-coordinates in the vertical rather than
300$z$-coordinates and is forced with tidal lateral boundary conditions
301using a flather boundary condition from the BDY module.
302The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the
303VVL non-linear free surface(key\_vvl) and time-splitting
306In addition to the tidal boundary condition the model may also take
307open boundary conditions from a North Atlantic model. Boundaries may be
308completely omitted by setting \np{ln\_bdy} to false.
309Sample surface fluxes, river forcing and a sample initial restart file
310are included to test a realistic model run. The Baltic boundary is
311included within the river input file and is specified as a river source.
312Unlike ordinary river points the Baltic inputs also include salinity and
313temperature data.
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