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chap_CONFIG.tex in NEMO/trunk/doc/latex/NEMO/subfiles – NEMO

source: NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex @ 11435

Last change on this file since 11435 was 11435, checked in by nicolasmartin, 5 years ago

Various corrections on chapters

Cleaning the indexes by fixing/removing wrong entries (or appending a ? to unknown items) and
improve the classification with new index definitions for CPP keys and namelist blocks:

  • from \key{...} cmd, key_ prefix no longer precedes the index entry
  • namelist block declaration moves from \ngn{nam...} to \nam{...} (i.e. \ngn{namtra\_ldf} -> \nam{tra\_ldf}) The expected prefix nam is added to the printed word but not the index entry.

Now we have indexes with a better sorting instead of all CPP keys under 'K' and namelists blocks under 'N'.

Fix missing space issues with alias commands by adding a trailing backslash (\NEMO\, \ie\, \eg\, ...).
There is no perfect solution for this, and I prefer not using a particular package to solve it.

Review the initial LaTeX code snippet for the historic changes in chapters

Finally, for readability and future diff visualisations, please avoid writing paragraphs with continuous lines.
Break the lines around 80 to 100 characters long

File size: 17.2 KB
4% ================================================================
5% Chapter Configurations
6% ================================================================
14% ================================================================
15% Introduction
16% ================================================================
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.
33% ================================================================
34% 1D model configuration
35% ================================================================
36\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]
37{C1D: 1D Water column model (\protect\key{c1d})}
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
43(see \path{./cfgs/SHARED/namelist\_ref}).
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;
50\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
52The methodology is based on the configuration of the smallest possible domain:
53a 3x3 domain with 75 vertical levels.
55The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
56and second, the two components of the velocity are moved on a $T$-point.
57Therefore, defining \key{c1d} changes some things in the code behaviour:
60  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
61  both lateral tendancy terms and lateral physics are not called;
63  the vertical velocity is zero
64  (so far, no attempt at introducing a Ekman pumping velocity has been made);
66  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
67  (see \mdl{dyncor\_c1d}).
69All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of
70the \NEMO\ distribution.
72% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
74% ================================================================
75% ORCA family configurations
76% ================================================================
77\section{ORCA family: global ocean with tripolar grid}
80The ORCA family is a series of global ocean configurations that are run together with
81the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
82An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
83The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
84this file is available in tar file on the \NEMO\ community zenodo platform: \\
87In this namelist\_cfg the name of domain input file is set in \nam{cfg} block of namelist.
91  \begin{center}
92    \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh}
93    \caption{
94      \protect\label{fig:MISC_ORCA_msh}
95      ORCA mesh conception.
96      The departure from an isotropic Mercator grid start poleward of 20\deg{N}.
97      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which
98      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
99      Then, following \citet{madec.imbard_CD96}, the normal to the series of ellipses (red curves) is computed which
100      provides the j-lines of the mesh (pseudo longitudes).
101    }
102  \end{center}
106% -------------------------------------------------------------------------------------------------------------
107%       ORCA tripolar grid
108% -------------------------------------------------------------------------------------------------------------
109\subsection{ORCA tripolar grid}
112The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{madec.imbard_CD96}.
113It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
114the computational domain since two north mesh poles are introduced and placed on lands.
115The method involves defining an analytical set of mesh parallels in the stereographic polar plan,
116computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.
117The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles
119The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors,
120or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.
123  \begin{center}
124    \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2}
125    \includegraphics[width=\textwidth]{Fig_ORCA_aniso}
126    \caption {
127      \protect\label{fig:MISC_ORCA_e1e2}
128      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
129      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
130      for ORCA 0.5\deg ~mesh.
131      South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1.
132      Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in
133      vicinity of Victoria Island (Canadian Arctic Archipelago).
134    }
135  \end{center}
139The method is applied to Mercator grid (\ie\ same zonal and meridional grid spacing) poleward of 20\deg{N},
140so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics.
141The choice of the series of embedded ellipses (position of the foci and variation of the ellipses)
142is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean
143(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in
144the northern hemisphere larger than the smallest one in the southern hemisphere.
145The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for
146a half a degree grid (ORCA\_R05).
147The smallest ocean scale factor is found in along Antarctica,
148while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.
150% -------------------------------------------------------------------------------------------------------------
151%       ORCA-ICE(-PISCES) configurations
152% -------------------------------------------------------------------------------------------------------------
153\subsection{ORCA pre-defined resolution}
156The \NEMO\ system is provided with five built-in ORCA configurations which differ in the horizontal resolution.
157The value of the resolution is given by the resolution at the Equator expressed in degrees.
158Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
159which sets the grid size and configuration name parameters.
160The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
165  \begin{center}
166    \begin{tabular}{p{4cm} c c c c}
167      Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\
168      \hline \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      \hline \hline
175    \end{tabular}
176    \caption{
177      \protect\label{tab:ORCA}
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    }
181  \end{center}
186The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh,
187local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
188so that the resolution is 1\deg~ there.
189A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
1900.5\deg~ at the Equator.
192The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
1931/3\deg~at the Equator.
194Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there.
196The ORCA\_R05 and higher global configurations do not incorporate any regional refinements.
198For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
199In the other ORCA configurations, 31 levels are used
200(see \autoref{tab:orca_zgr}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
202Only the ORCA\_R2 is provided with all its input files in the \NEMO\ distribution.
203%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
204%climate change (Marti et al., 2009).
205%It is also the basis for the \NEMO\ contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
206%documented in \citet{griffies.biastoch.ea_OM09}.
208This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
209(see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).
210The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
211The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_core}),
212which was developed for the purpose of running global coupled ocean-ice simulations without
213an interactive atmosphere.
214This \citet{large.yeager_rpt04} dataset is available through
215the \href{}{GFDL web site}.
216The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3.
218ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined).
219This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory.
221A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
222sponge layers at open boundaries.
224% -------------------------------------------------------------------------------------------------------------
225%       GYRE family: double gyre basin
226% -------------------------------------------------------------------------------------------------------------
227\section{GYRE family: double gyre basin}
230The GYRE configuration \citep{levy.klein.ea_OM10} has been built to
231simulate the seasonal cycle of a double-gyre box model.
232It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and
233\citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00},
234over which an analytical seasonal forcing is applied.
235This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies
236and their contribution to the large scale circulation.
238The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
239The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
240rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
241The domain is bounded by vertical walls and by a flat bottom.
242The configuration is meant to represent an idealized North Atlantic or North Pacific basin.
243The circulation is forced by analytical profiles of wind and buoyancy fluxes.
244The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}.
245The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}.
246It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and
247a small recirculation gyre in the southern corner.
248The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile.
249A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column.
250The fresh water flux is also prescribed and varies zonally.
251It is determined such as, at each time step, the basin-integrated flux is zero.
252The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to
253the whole domain.
255The GYRE configuration is set like an analytical configuration.
256Through \np{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in
257the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
258analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
259Its horizontal resolution (and thus the size of the domain) is determined by
260setting \np{nn\_GYRE} in \nam{usr\_def}: \\
262\jp{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
264\jp{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
266Obviously, the namelist parameters have to be adjusted to the chosen resolution,
267see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
268In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
270The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
271as it does not requires any input file.
272For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
273even though the physical integrity of the solution can be compromised.
274Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \nam{usr\_def} in
275namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
279  \begin{center}
280    \includegraphics[width=\textwidth]{Fig_GYRE}
281    \caption{
282      \protect\label{fig:GYRE}
283      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54.
284      From \citet{levy.klein.ea_OM10}.
285    }
286  \end{center}
290% -------------------------------------------------------------------------------------------------------------
291%       AMM configuration
292% -------------------------------------------------------------------------------------------------------------
293\section{AMM: atlantic margin configuration}
296The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
297a regular lat-lon grid at approximately 12km horizontal resolution.
298The appropriate \textit{\&namcfg} namelist  is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}.
299It is used to build the correct dimensions of the AMM domain.
301This configuration tests several features of \NEMO\ functionality specific to the shelf seas.
302In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and
303is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module.
304Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln\_zdfgls} \forcode{= .true.}).
306In addition to the tidal boundary condition the model may also take open boundary conditions from
307a North Atlantic model.
308Boundaries may be completely omitted by setting \np{ln\_bdy} to false.
309Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
310The Baltic boundary is included within the river input file and is specified as a river source.
311Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
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