source: NEMO/branches/2019/dev_r11643_ENHANCE-11_CEthe_Shaconemo_diags/cfgs/README.rst @ 11998

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1************************
2Reference configurations
3************************
4
5NEMO is distributed with a set of reference configurations allowing both
6the user to set up his own first applications and
7the developer to test/validate his NEMO developments (using SETTE package).
8
9.. attention::
10
11   Concerning the configurations,
12   the NEMO System Team is only in charge of the so-called reference configurations described below.
13
14.. hint::
15
16   Configurations developed by external research projects or initiatives that
17   make use of NEMO are welcome to be publicized through the website by
18   filling up the form :website:`to add an associated project<projects/add>`.
19
20How to compile an experiment from a reference configuration
21===========================================================
22
23A user who wants to compile the ORCA2_ICE_PISCES_ reference configuration using ``makenemo``
24should use the following, by selecting among available architecture file or providing a user defined one:
25
26.. code-block:: console
27               
28   $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4'
29
30A new ``EXP00`` folder will be created within the selected reference configurations,
31namely ``./cfgs/ORCA2_ICE_PISCES/EXP00``,
32where it will be necessary to uncompress the Input & Forcing Files listed in the above table.
33
34Then it will be possible to launch the execution of the model through a runscript
35(opportunely adapted to the user system).
36   
37List of Configurations
38======================
39
40All forcing files listed below in the table are available from |NEMO archives URL|_
41
42.. |NEMO archives URL| image:: https://www.zenodo.org/badge/DOI/10.5281/zenodo.1472245.svg
43.. _NEMO archives URL: https://doi.org/10.5281/zenodo.1472245
44
45====================== ===== ===== ===== ======== ======= ================================================
46 Configuration                     Component(s)                            Input & Forcing File(s)
47---------------------- ---------------------------------- ------------------------------------------------
48 Name                   OPA   SI3   TOP   PISCES   AGRIF
49====================== ===== ===== ===== ======== ======= ================================================
50 AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar, ORCA2_ICE_v4.0.tar
51 AMM12_                  X                                 AMM12_v4.0.tar
52 C1D_PAPA_               X                                 INPUTS_C1D_PAPA_v4.0.tar
53 GYRE_BFM_               X           X                     *none*
54 GYRE_PISCES_            X           X      X              *none*
55 ORCA2_ICE_PISCES_       X     X     X      X              ORCA2_ICE_v4.0.tar, INPUTS_PISCES_v4.0.tar
56 ORCA2_OFF_PISCES_                   X      X              ORCA2_OFF_v4.0.tar, INPUTS_PISCES_v4.0.tar
57 ORCA2_OFF_TRC_                      X                     ORCA2_OFF_v4.0.tar
58 ORCA2_SAS_ICE_                X                           ORCA2_ICE_v4.0.tar, INPUTS_SAS_v4.0.tar
59 SPITZ12_                X     X                           SPITZ12_v4.0.tar
60====================== ===== ===== ===== ======== ======= ================================================
61
62AGRIF_DEMO
63----------
64
65``AGRIF_DEMO`` is based on the ``ORCA2_ICE_PISCES`` global configuration at 2° of resolution with
66the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF in
67a realistic context (including the nesting of sea ice models).
68
69The configuration includes a 1:1 grid in the Pacific and two successively nested grids with
70odd and even refinement ratios over the Arctic ocean,
71with the finest grid spanning the whole Svalbard archipelago that is of
72particular interest to test sea ice coupling.
73
74The 1:1 grid can be used alone as a benchmark to check that
75the model solution is not corrupted by grid exchanges.
76Note that since grids interact only at the baroclinic time level,
77numerically exact results can not be achieved in the 1:1 case.
78Perfect reproducibility is obtained only by switching to a fully explicit setup instead of a split explicit free surface scheme.
79
80AMM12
81-----
82
83``AMM12`` stands for *Atlantic Margin Model at 12 km* that is
84a regional configuration covering the Northwest European Shelf domain on
85a regular horizontal grid of ~12 km of resolution (see :cite:`ODEA2012`).
86
87This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.
88In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme,
89tidal lateral boundary conditions using a flather scheme (see more in ``BDY``).
90Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.
91
92Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run
93(``AMM12_v4.0.tar``).
94
95Note that, the Baltic boundary is included within the river input file and is specified as a river source,
96but unlike ordinary river points the Baltic inputs also include salinity and temperature data.
97
98C1D_PAPA
99--------
100
101``C1D_PAPA`` is a 1D configuration for the `PAPA station <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_ located in the northern-eastern Pacific Ocean at 50.1°N, 144.9°W.
102See `Reffray et al. (2015) <http://www.geosci-model-dev.net/8/69/2015>`_ for the description of its physical and numerical turbulent-mixing behaviour.
103
104The water column setup, called NEMO1D, is activated with the inclusion of the CPP key ``key_c1d`` and
105has a horizontal domain of 3x3 grid points.
106
107This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae.
108Data provided with ``INPUTS_C1D_PAPA_v4.0.tar`` file account for:
109
110- ``forcing_PAPASTATION_1h_y201[0-1].nc`` : ECMWF operational analysis atmospheric forcing rescaled to 1h (with long and short waves flux correction) for years 2010 and 2011
111- ``init_PAPASTATION_m06d15.nc`` : Initial Conditions from observed data and Levitus 2009 climatology
112- ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data
113
114GYRE_BFM
115--------
116
117``GYRE_BFM`` shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in ``./cfgs/GYRE_BFM/README``.
118
119GYRE_PISCES
120-----------
121
122``GYRE_PISCES`` is an idealized configuration representing a Northern hemisphere double gyres system,
123in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels,
124with PISCES BGC model :cite:`gmd-8-2465-2015`.
125Analytical forcing for heat, freshwater and wind-stress fields are applied. 
126
127This configuration acts also as demonstrator of the **user defined setup** (``ln_read_cfg = .false.``) and
128grid setting are handled through the ``&namusr_def`` controls in ``namelist_cfg``:
129
130.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg
131   :language: fortran
132   :lines: 34-42
133
134Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and
135vertical levels are set by ``jpkglo``.
136The specific code changes can be inspected in ``./src/OCE/USR``.
137
138**Running GYRE as a benchmark** :
139this simple configuration can be used as a benchmark since it is easy to increase resolution,
140with the drawback of getting results that have a very limited physical meaning.
141
142GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE`` (integer multiplier scaling factor), as described in the following table:
143
144=========== ========= ========== ============ ===================
145``nn_GYRE``  *jpiglo*  *jpjglo*   ``jpkglo``   **Equivalent to**
146=========== ========= ========== ============ ===================
147 1           30        20         31           GYRE 1°
148 25          750       500        101          ORCA 1/2°
149 50          1500      1000       101          ORCA 1/4°
150 150         4500      3000       101          ORCA 1/12°
151 200         6000      4000       101          ORCA 1/16°
152=========== ========= ========== ============ ===================
153
154Note that, it is necessary to set ``ln_bench = .true.`` in ``namusr_def`` to
155avoid problems in the physics computation and that
156the model timestep should be adequately rescaled.
157
158For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid,
159the timestep ``rn_rdt = 1200`` should be set to 1200 seconds
160
161Differently from previous versions of NEMO,
162the code uses by default the time-splitting scheme and
163internally computes the number of sub-steps.
164
165ORCA2_ICE_PISCES
166----------------
167
168``ORCA2_ICE_PISCES`` is a reference configuration for the global ocean with
169a 2°x2° curvilinear horizontal mesh and 31 vertical levels,
170distributed using z-coordinate system and with 10 levels in the top 100m.
171ORCA is the generic name given to global ocean Mercator mesh,
172(i.e. variation of meridian scale factor as cosinus of the latitude),
173with two poles in the northern hemisphere so that
174the ratio of anisotropy is nearly one everywhere
175
176this configuration uses the three components
177
178- |OPA|, the ocean dynamical core
179- |SI3|, the thermodynamic-dynamic sea ice model.
180- |TOP|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015`
181
182All components share the same grid.
183
184The model is forced with CORE-II normal year atmospheric forcing and
185it uses the NCAR bulk formulae.
186
187In this ``ORCA2_ICE_PISCES`` configuration,
188AGRIF nesting can be activated that includes a nested grid in the Agulhas region.
189
190To set up this configuration, after extracting NEMO:
191
192Build your AGRIF configuration directory from ``ORCA2_ICE_PISCES``,
193with the ``key_agrif`` CPP key activated:
194
195.. code-block:: console
196               
197        $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif'
198
199By using the input files and namelists for ``ORCA2_ICE_PISCES``,
200the AGRIF test configuration is ready to run.
201
202**Ocean Physics**
203
204- *horizontal diffusion on momentum*: the eddy viscosity coefficient depends on the geographical position. It is taken as 40000 m^2/s, reduced in the equator regions (2000 m^2/s) excepted near the western boundaries.
205- *isopycnal diffusion on tracers*: the diffusion acts along the isopycnal surfaces (neutral surface) with an eddy diffusivity coefficient of 2000 m^2/s.
206- *Eddy induced velocity parametrization* with a coefficient that depends on the growth rate of baroclinic instabilities (it usually varies from 15 m^2/s to 3000 m^2/s).
207- *lateral boundary conditions* : zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries.
208- *bottom boundary condition* : zero fluxes of heat and salt are applied through the ocean bottom.
209  The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes.
210  A linear friction is applied on momentum.
211- *convection*: the vertical eddy viscosity and diffusivity coefficients are increased to 1 m^2/s in case of static instability.
212- *time step* is 5760sec (1h36') so that there is 15 time steps in one day.
213
214ORCA2_OFF_PISCES
215----------------
216
217``ORCA2_OFF_PISCES`` shares the same general offline configuration of ``ORCA2_ICE_TRC``,
218but only PISCES model is an active component of TOP.
219
220
221ORCA2_OFF_TRC
222-------------
223
224``ORCA2_OFF_TRC`` is based on the ORCA2 global ocean configuration
225(see ORCA2_ICE_PISCES_ for general description) along with the tracer passive transport module (TOP), but dynamical fields are pre-calculated and read with specific time frequency.
226
227This enables for an offline coupling of TOP components,
228here specifically inorganic carbon compounds (cfc11, cfc12, sf6, c14) and water age module (age).
229See ``namelist_top_cfg`` to inspect the selection of each component with the dedicated logical keys.
230
231Pre-calculated dynamical fields are provided to NEMO using
232the namelist ``&namdta_dyn``  in ``namelist_cfg``,
233in this case with a 5 days frequency (120 hours):
234
235.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_ref
236   :language: fortran
237   :lines: 935-960
238
239Input dynamical fields for this configuration (``ORCA2_OFF_v4.0.tar``) comes from
240a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing.
241
242Note that, this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that
243model mesh is not varying in time and
244it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that
245requires the provision of bbl coefficients through ``sn_ubl`` and ``sn_vbl`` fields.
246
247It is also possible to activate PISCES model (see ``ORCA2_OFF_PISCES``) or
248a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.``
249(and adaptation of ``./src/TOP/MY_TRC`` routines).
250
251In addition, the offline module (OFF) allows for the provision of further fields:
252
2531. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and
254   by including an input datastream similarly to the following:
255
256.. code-block:: fortran
257
258   sn_rnf  = 'dyna_grid_T', 120, 'sorunoff' , .true., .true., 'yearly', '', '', ''
259
2602. **VVL dynamical fields**,
261   in the case input data were produced by a dyamical core using variable volume (``ln_linssh = .false.``)
262   it necessary to provide also diverce and E-P at before timestep by
263   including input datastreams similarly to the following
264
265.. code-block:: fortran
266
267   sn_div  = 'dyna_grid_T', 120, 'e3t'      , .true., .true., 'yearly', '', '', ''
268   sn_empb = 'dyna_grid_T', 120, 'sowaflupb', .true., .true., 'yearly', '', '', ''
269
270
271More details can be found by inspecting the offline data manager in
272the routine ``./src/OFF/dtadyn.F90``.
273
274ORCA2_SAS_ICE
275-------------
276
277ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and
278it relies on ORCA2 global ocean configuration (see ORCA2_ICE_PISCES_ for general description).
279
280The standalone surface module allows surface elements such as sea-ice, iceberg drift, and
281surface fluxes to be run using prescribed model state fields.
282It can profitably be used to compare different bulk formulae or
283adjust the parameters of a given bulk formula.
284
285More informations about SAS can be found in NEMO manual.
286
287SPITZ12
288-------
289
290``SPITZ12`` is a regional configuration around the Svalbard archipelago
291at 1/12° of horizontal resolution and 75 vertical levels.
292See `Rousset et al. (2015) <https://www.geosci-model-dev.net/8/2991/2015/>`_ for more details.
293
294This configuration references to year 2002,
295with atmospheric forcing provided every 2 hours using NCAR bulk formulae,
296while lateral boundary conditions for dynamical fields have 3 days time frequency.
297
298References
299==========
300
301.. bibliography:: configurations.bib
302   :all:
303   :style: unsrt
304   :labelprefix: C
305
306.. Links and substitutions
307
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