source: NEMO/trunk/cfgs/README.rst @ 10460

Last change on this file since 10460 was 10460, checked in by nicolasmartin, 19 months ago

Small modifications regarding README(s) and ReST files

File size: 18.1 KB
Line 
1***************************
2Run built-in configurations
3***************************
4
5.. contents::
6   :local:
7   :depth: 1
8     
9Official configurations
10=======================
11
12| NEMO is distributed with some reference configurations allowing both the user to set up a first application and
13  the developer to validate their developments.
14| :underline:`The NEMO System Team is in charge of these configurations`.
15
16+----------------------+-----+-----+-----+--------+-------+--------------------------+
17|                      | OPA | SI3 | TOP | PISCES | AGRIF | Inputs                   |
18+======================+=====+=====+=====+========+=======+==========================+
19| `AGRIF_DEMO`_        |  X  |  X  |     |        |   X   | - AGRIF_DEMO_v4.0.tar    |
20|                      |     |     |     |        |       | - ORCA2_ICE_v4.0.tar     |
21+----------------------+-----+-----+-----+--------+-------+--------------------------+
22| `AMM12`_             |  X  |     |     |        |       | AMM12_v4.0.tar           |
23+----------------------+-----+-----+-----+--------+-------+--------------------------+
24| `C1D_PAPA`_          |  X  |     |     |        |       | INPUTS_C1D_PAPA_v4.0.tar |
25+----------------------+-----+-----+-----+--------+-------+--------------------------+
26| `GYRE_BFM`_          |  X  |     |  X  |        |       | ``-``                    |
27+----------------------+-----+-----+-----+--------+-------+--------------------------+
28| `GYRE_PISCES`_       |  X  |     |  X  |   X    |       | ``-``                    |
29+----------------------+-----+-----+-----+--------+-------+--------------------------+
30| `ORCA2_ICE_PISCES`_  |  X  |  X  |  X  |   X    |       | - ORCA2_ICE_v4.0.tar     |
31|                      |     |     |     |        |       | - INPUTS_PISCES_v4.0.tar |
32+----------------------+-----+-----+-----+--------+-------+--------------------------+
33| `ORCA2_OFF_PISCES`_  |     |     |  X  |   X    |       | - INPUTS_PISCES_v4.0.tar |
34|                      |     |     |     |        |       | - ORCA2_OFF_v4.0.tar     |
35+----------------------+-----+-----+-----+--------+-------+--------------------------+
36| `ORCA2_OFF_TRC`_     |     |     |  X  |        |       | ORCA2_OFF_v4.0.tar       |
37+----------------------+-----+-----+-----+--------+-------+--------------------------+
38| `ORCA2_SAS_ICE`_     |     |  X  |     |        |       | - ORCA2_ICE_v4.0.tar     |
39|                      |     |     |     |        |       | - INPUTS_SAS_v4.0.tar    |
40+----------------------+-----+-----+-----+--------+-------+--------------------------+
41| `SPITZ12`_           |  X  |  X  |     |        |       | SPITZ12_v4.0.tar         |
42+----------------------+-----+-----+-----+--------+-------+--------------------------+
43
44AGRIF_DEMO
45----------
46
47.. image:: _static/AGRIF_DEMO.jpg
48
49``AGRIF_DEMO`` is based on the ``ORCA2_LIM3_PISCES`` global 2° configuration but
50it includes 3 online nested grids that demonstrate the overall capabilities of AGRIF in a realistic context,
51including nesting sea ice models.
52
53The configuration includes a 1:1 grid in the Pacific and two successively nested grids with odd and
54even refinement ratios over the Arctic ocean.
55The finest grid spanning the whole Svalbard archipelago is of particular interest to check that
56sea ice coupling is done properly.
57The 1:1 grid, used alone, is used as a benchmark to check that the solution is not corrupted by grid exchanges.
58
59Note that since grids interact only at the baroclinic time level,
60numerically exact results can not be achieved in the 1:1 case.
61One has to switch to a fully explicit in place of a split explicit free surface scheme in order to
62retrieve perfect reproducibility.
63
64Corresponding ``AGRIF_FixedGrids.in`` file is given by::
65
66   2
67   42 82 49 91 1 1 1
68   122 153 110 143 4 4 4
69   0
70   1
71   38 80 71 111 3 3 3
72   0
73
74AMM12
75-----
76
77``AMM12`` for *Atlantic Margin Model 12kms* is a `regional model`_ covering the Northwest European Shelf domain on
78a regular lat-lon grid at approximately 12km horizontal resolution.
79The key ``key_amm_12km`` is used to create the correct dimensions of the AMM domain.
80
81| This configuration tests several features of NEMO functionality specific to the shelf seas.
82| In particular, the AMM uses s-coordinates in the vertical rather than z-coordinates and is forced with
83  tidal lateral boundary conditions using a flather boundary condition from the BDY module (``key_bdy``).
84
85The AMM configuration uses the GLS (``key_zdfgls``) turbulence scheme,
86the VVL non-linear free surface (``key_vvl``) and time-splitting (``key_dynspg_ts``).
87
88In addition to the tidal boundary condition, the model may also take open boundary conditions from
89a North Atlantic model.
90Boundaries may be completely ommited by removing the BDY key (key_bdy) in ``./cfgs/AMM12/cpp_AMM12_fcm``.
91
92Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
93The Baltic boundary is included within the river input file and is specified as a river source.
94Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
95
96C1D_PAPA
97--------
98
99``C1D_PAPA`` is a 1D configuration (one water column called NEMO1D, activated with CPP key ``key_c1d``),
100located at the `PAPA station 145W-50N <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_.
101
102| NEMO1D is useful to test vertical physics in NEMO
103  (turbulent closure scheme, solar penetration, interaction ocean/atmosphere.,...)
104| Size of the horizontal domain is 3x3 grid points.
105
106This reference configuration uses a 75 vertical levels grid (1m at the surface),
107the GLS (key_zdfgls) turbulence scheme with K-epsilon closure and the CORE BULK formulae.
108The atmospheric forcing comes from ECMWF operational analysis with a modification of the long and short waves flux.
109This set has been rescaled at a frequency of 1h. 1 year is simulated in outputs,
110see below (June,15 2010 to June,14 2011)
111
112`Reffray 2015`_ describes some tests on vertical physic using this configuration.
113
114The inputs tar file includes:
115
116- forcing files covering the years 2010 and 2011 (``forcing_PAPASTATION_1h_y201*.nc``)
117- initialization file for June,15 2010 deduced from observed data and Levitus 2009 climatology
118  (``init_PAPASTATION_m06d15.nc``)
119- surface chlorophyll file (``chlorophyll_PAPASTATION.nc``) deduced from Seawifs data.
120
121GYRE_BFM
122--------
123
124``GYRE_BFM`` is the same configuration as `GYRE_PISCES`_, except that PISCES is replaced by
125BFM biogeochemichal model in coupled mode.
126
127GYRE_PISCES
128-----------
129
130| Idealized configuration representing double gyres in the North hemisphere, Beta-plane with
131  a regular grid spacing at 1° horizontal resolution (and possible use as a benchmark by
132  easily inscreasing grid size), 101 vertical levels, forced with analytical heat, freshwater and
133  wind-stress fields.
134| This configuration is coupled to `PISCES biogeochemical model`_.
135
136Running GYRE as a benchmark
137^^^^^^^^^^^^^^^^^^^^^^^^^^^
138
139This simple configuration can be used as a benchmark since it is easy to increase resolution
140(and in this case no physical meaning of outputs):
141
1421. Choose the grid size
143
144   In ``./cfgs/GYRE/EXP00``, edit your ``namelist_cfg`` file to change the ``jp_cfg``, ``jpi``, ``jpj``,
145   ``jpk`` variables in &namcfg:
146
147   +------------+---------+---------+---------+------------------+---------------+
148   | ``jp_cfg`` | ``jpi`` | ``jpj`` | ``jpk`` | Number of points | Equivalent to |
149   +============+=========+=========+=========+==================+===============+
150   | 1          | 30      | 20      | 101     | 60600            | GYRE 1°       |
151   +------------+---------+---------+---------+------------------+---------------+
152   | 25         | 750     | 500     | 101     | 37875000         | ORCA 1/2°     |
153   +------------+---------+---------+---------+------------------+---------------+
154   | 50         | 1500    | 1000    | 101     | 151500000        | ORCA 1/4°     |
155   +------------+---------+---------+---------+------------------+---------------+
156   | 150        | 4500    | 3000    | 101     | 1363500000       | ORCA 1/12°    |
157   +------------+---------+---------+---------+------------------+---------------+
158   | 200        | 6000    | 4000    | 101     | 2424000000       | ORCA 1/16°    |
159   +------------+---------+---------+---------+------------------+---------------+
160
1612. In `namelist_cfg` again, avoid problems in the physics (and results will not be meaningful in terms of physics) by setting `nn_bench = 1` in &namctl
162
163.. code-block:: fortran
164   
165   nn_bench    =    1     !  Bench mode (1/0): CAUTION use zero except for bench
166
1673. If you increase domain size, you may need to decrease time-step (for stability) by changing `rn_rdt` value in &namdom (i.e. for `jp_cfg = 150`, ORCA12 equivalent, use `rn_rdt = 1200`)
168
169.. code-block:: fortran
170   
171   rn_rdt      = 1200.     !  time step for the dynamics
172
1734. Optional, in order to increase the number of MPI communication for benchmark purposes:
174   you can change the number of sub-timesteps computed in the time-splitting scheme each iteration.
175   First change the list of active CPP keys for your experiment,
176   in `cfgs/"your configuration name"/cpp_"your configuration name".fcm`:
177   replace ``key_dynspg_flt by key_dynspg_ts`` and recompile/create your executable again
178   
179   .. code-block:: fortran
180   
181   makenemo [...] add_key 'key_dynspg_ts' del_key 'key_dynspg_flt'
182
183In your ``namelist_cfg`` file, edit the &namsplit namelist by adding the following line:
184
185.. code-block:: fortran
186   
187   nn_baro       =    30               !  Number of iterations of barotropic mode/
188
189``nn_baro = 30`` is a kind of minimum (we usually use 30 to 60).
190So than increasing the ``nn_baro`` value will increase the number of MPI communications.
191
192The GYRE CPP keys, namelists and scripts can be explored in the ``GYRE`` configuration directory
193(``./cfgs/GYRE`` and ``./cfgs/GYRE/EXP00``).
194
195Find monthly mean outputs of 1 year run here:
196http://prodn.idris.fr/thredds/catalog/ipsl_public/reee451/NEMO_OUT/GYRE/catalog.html
197
198ORCA2_ICE_PISCES
199----------------
200
201ORCA is the generic name given to global ocean configurations.
202Its specificity lies on the horizontal curvilinear mesh used to overcome the North Pole singularity found for
203geographical meshes.
204SI3 (Sea Ice Integrated Initiative) is a thermodynamic-dynamic sea ice model specifically designed for
205climate studies.
206A brief description of the model is given here.
207
208:underline:`Space-time domain`
209
210The horizontal resolution available through the standard configuration is ORCA2.
211It is based on a 2 degrees Mercator mesh, (i.e. variation of meridian scale factor as cosinus of the latitude).
212In the northern hemisphere the mesh has two poles so that the ratio of anisotropy is nearly one everywhere.
213The mean grid spacing is about 2/3 of the nominal value: for example it is 1.3 degrees for ORCA2.
214Other resolutions (ORCA4, ORCA05 and ORCA025) are running or under development within specific projects.
215In the coarse resolution version (i.e. ORCA2 and ORCA4) the meridional grid spacing is increased near
216the equator to improve the equatorial dynamics.
217Figures in pdf format of mesh and bathymetry can be found and downloaded here.
218The sea-ice model runs on the same grid.
219
220The vertical domain spreads from the surface to a depth of 5000m.
221There are 31 levels, with 10 levels in the top 100m.
222The vertical mesh is deduced from a mathematical function of z ([[AttachmentNum(1)]]).
223The ocean surface corresponds to the w-level k=1, and the ocean bottom to the w-level k=31.
224The last T-level (k=31) is thus always in the ground.The depths of the vertical levels and
225the associated scale factors can be viewed.
226Higher vertical resolution is used in ORCA025 and ORCA12 (see `DRAKKAR project <http://www.drakkar-ocean.eu>`_).
227
228The time step depends on the resolution. It is 1h36' for ORCA2 so that there is 15 time steps in one day.
229
230:underline:`Ocean Physics (for ORCA2)`
231
232- horizontal diffusion on momentum: the eddy viscosity coefficient depends on the geographical position.
233  It is taken as 40000 $m^2/s$, reduced in the equator regions (2000 $m^2/s$) excepted near the western boundaries.
234- isopycnal diffusion on tracers: the diffusion acts along the isopycnal surfaces (neutral surface) with
235  a eddy diffusivity coefficient of 2000 $m^2/s$.
236- Eddy induced velocity parametrization with a coefficient that depends on the growth rate of
237  baroclinic instabilities (it usually varies from 15 $m^2/s$ to 3000 $m^2/s$).
238- lateral boundary conditions : zero fluxes of heat and salt and no-slip conditions are applied through
239  lateral solid boundaries.
240- bottom boundary condition : zero fluxes of heat and salt are applied through the ocean bottom.
241  The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes.
242  A linear friction is applied on momentum.
243- convection: the vertical eddy viscosity and diffusivity coefficients are increased to 1 $m^2/s$ in case of
244  static instability.
245- forcings: the ocean receives heat, freshwater, and momentum fluxes from the atmosphere and/or the sea-ice.
246  The solar radiation penetrates the top meters of the ocean.
247  The downward irradiance I(z) is formulated with two extinction coefficients [Paulson and Simpson, 1977],
248  whose values correspond to a Type I water in Jerlov's classification (i.e the most transparent water)
249
250ORCA2_ICE_PISCES is a reference configuration with the following characteristics:
251
252- global ocean configuration
253- based on a tri-polar ORCA grid, with a 2° horizontal resolution
254- 31 vertical levels
255- forced with climatological surface fields
256- coupled to the sea-ice model SI3.
257- coupled to TOP passive tracer transport module and `PISCES biogeochemical model`_.
258
259:underline:`AGRIF demonstrator`
260
261| From the ``ORCA2_ICE_PISCES`` configuration, a demonstrator using AGRIF nesting can be activated.
262  It includes the global ``ORCA2_ICE_PISCES`` configuration and a nested grid in the Agulhas region.
263| To set up this configuration, after extracting NEMO:
264
265- Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated:
266
267.. code-block:: console
268               
269   $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif'
270
271- Using the ``ORCA2_ICE_PISCES`` input files and namelist, AGRIF test configuration is ready to run
272
273:underline:`On-The-Fly Interpolation`
274
275| NEMO allows to use the interpolation on the fly option allowing to interpolate input data during the run.
276  If you want to use this option you need files giving informations on weights, which have been created.
277| You can find at http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/WEIGHTS/catalog.html
278  2 weights files `bil_weights` for scalar field (bilinear interpolation) and `bic_weights` for
279  vector field (bicubic interpolation).
280| The data files used are `COREII forcing <http://data1.gdfl.noaa.gov/nomads/forms/mom4/COREv2>`_ extrapolated on
281  continents, ready to be used for on the fly option:
282  `COREII`_ forcing files extrapolated on continents
283
284ORCA2_OFF_PISCES
285----------------
286
287``ORCA2_OFF_PISCES`` uses the ORCA2 configuration in which the `PISCES biogeochemical model`_ has been activated in
288standalone using the dynamical fields that are pre calculated.
289
290See `ORCA2_ICE_PISCES`_ for general description of ORCA2.
291
292The input files for PISCES are needed, in addition the dynamical fields are used as input.
293They are coming from a 2000 years of an ORCA2_LIM climatological run using ERA40 atmospheric forcing.
294
295ORCA2_OFF_TRC
296-------------
297
298``ORCA2_OFF_TRC`` uses the ORCA2_LIM configuration in which the tracer passive transport module TOP has been
299activated in standalone using the dynamical fields that are pre calculated.
300
301See `ORCA2_ICE_PISCES`_ for general description of ORCA2.
302
303In ``namelist_top_cfg``, different passive tracers can be activated ( cfc11, cfc12, sf6, c14, age ) or my-trc,
304a user-defined tracer.
305
306The dynamical fields are used as input, they are coming from a 2000 years of an ORCA2_LIM climatological run using
307ERA40 atmospheric forcing.
308
309ORCA2_SAS_ICE
310-------------
311
312``ORCA2_SAS_ICE`` is a demonstrator of the SAS ( Stand-alone Surface module ) based on ORCA2_LIM configuration.
313
314The standalone surface module allows surface elements such as sea-ice, iceberg drift and surface fluxes to
315be run using prescribed model state fields.
316For example, it can be used to inter-compare different bulk formulae or adjust the parameters of
317a given bulk formula
318
319See `ORCA2_ICE_PISCES`_ for general description of ORCA2.
320
321Same input files as `ORCA2_ICE_PISCES`_ are needed plus fields from a previous ORCA2_LIM run.
322
323More informations on input and configuration files in `NEMO manual`_.
324
325SPITZ12
326-------
327
328``SPITZ12``
329
330Unsupported configurations
331==========================
332
333Other configurations are developed and used by some projects with "NEMO inside",
334these projects are welcome to publicize it here: http://www.nemo-ocean.eu/projects/add-project
335
336:underline:`Obviously these "projects configurations" are not under the NEMO System Team's responsibility`.
337
338.. _regional model:               http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128
339.. _AMM12_v4.0.tar:               http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar
340.. _PISCES biogeochemical model:  http://www.geosci-model-dev.net/8/2465/2015
341.. _INPUTS_PISCES_v4.0.tar:       http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_PISCES_v4.0.tar
342.. _ORCA2_OFF_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_OFF_v4.0.tar
343.. _ORCA2_ICE_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar
344.. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar
345.. _INPUTS_C1D_PAPA_v4.0.tar:     http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar
346.. _Reffray 2015:                 http://www.geosci-model-dev.net/8/69/2015
347.. _COREII:                       http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html
348.. _SPITZ12_v4.0.tar:             http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar
349.. _AGRIF_DEMO_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar
Note: See TracBrowser for help on using the repository browser.