source: NEMO/trunk/cfgs/README.rst @ 12377

Last change on this file since 12377 was 11743, checked in by nicolasmartin, 14 months ago

Review README for configuration setup

File size: 14.0 KB
Line 
1********************************
2Run the Reference configurations
3********************************
4
5.. todo::
6
7   Lack of illustrations for ref. cfgs, and more generally in the guide.
8
9NEMO is distributed with a set of reference configurations allowing both
10the user to set up his own first applications and
11the developer to test/validate his NEMO developments (using SETTE package).
12
13.. contents::
14   :local:
15   :depth: 1
16
17.. attention::
18
19   Concerning the configurations,
20   the NEMO System Team is only in charge of the so-called reference configurations described below.
21
22.. hint::
23
24   Configurations developed by external research projects or initiatives that
25   make use of NEMO are welcome to be publicized through the website by
26   filling up the form :website:`to add an associated project<projects/add>`.
27
28How to compile an experiment from a reference configuration
29===========================================================
30
31To compile the ORCA2_ICE_PISCES_ reference configuration using :file:`makenemo`,
32one should use the following, by selecting among available architecture file or
33providing a user defined one:
34
35.. code-block:: console
36
37   $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my_arch' -j '4'
38
39A new ``EXP00`` folder will be created within the selected reference configurations,
40namely ``./cfgs/ORCA2_ICE_PISCES/EXP00``.
41It will be necessary to uncompress the archives listed in the above table for
42the given reference configuration that includes input & forcing files.
43
44Then it will be possible to launch the execution of the model through a runscript
45(opportunely adapted to the user system).
46
47List of Configurations
48======================
49
50All forcing files listed below in the table are available from |DOI data|_
51
52=================== === === === === === ==================================
53 Configuration       Component(s)        Archives (input & forcing files)
54------------------- ------------------- ----------------------------------
55 Name                O   S   T   P   A
56=================== === === === === === ==================================
57 AGRIF_DEMO_         X   X           X   AGRIF_DEMO_v4.0.tar,
58                                         ORCA2_ICE_v4.0.tar
59 AMM12_              X                   AMM12_v4.0.tar
60 C1D_PAPA_           X                   INPUTS_C1D_PAPA_v4.0.tar
61 GYRE_BFM_           X       X           *none*
62 GYRE_PISCES_        X       X   X       *none*
63 ORCA2_ICE_PISCES_   X   X   X   X       ORCA2_ICE_v4.0.tar,
64                                         INPUTS_PISCES_v4.0.tar
65 ORCA2_OFF_PISCES_           X   X       ORCA2_OFF_v4.0.tar,
66                                         INPUTS_PISCES_v4.0.tar
67 ORCA2_OFF_TRC_              X           ORCA2_OFF_v4.0.tar
68 ORCA2_SAS_ICE_          X               ORCA2_ICE_v4.0.tar,
69                                         INPUTS_SAS_v4.0.tar
70 SPITZ12_            X   X               SPITZ12_v4.0.tar
71=================== === === === === === ==================================
72
73.. admonition:: Legend for component combination
74
75   O for OCE, S for SI\ :sup:`3`, T for TOP, P for PISCES and A for AGRIF
76
77AGRIF_DEMO
78----------
79
80``AGRIF_DEMO`` is based on the ``ORCA2_ICE_PISCES`` global configuration at 2° of resolution with
81the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF in
82a realistic context (including the nesting of sea ice models).
83
84The configuration includes a 1:1 grid in the Pacific and two successively nested grids with
85odd and even refinement ratios over the Arctic ocean,
86with the finest grid spanning the whole Svalbard archipelago that is of
87particular interest to test sea ice coupling.
88
89.. image:: _static/AGRIF_DEMO_no_cap.jpg
90   :scale: 66%
91   :align: center
92
93The 1:1 grid can be used alone as a benchmark to check that
94the model solution is not corrupted by grid exchanges.
95Note that since grids interact only at the baroclinic time level,
96numerically exact results can not be achieved in the 1:1 case.
97Perfect reproducibility is obtained only by switching to a fully explicit setup instead of
98a split explicit free surface scheme.
99
100AMM12
101-----
102
103``AMM12`` stands for *Atlantic Margin Model at 12 km* that is
104a regional configuration covering the Northwest European Shelf domain on
105a regular horizontal grid of ~12 km of resolution (see :cite:`ODEA2012`).
106
107.. image:: _static/AMM_domain.png
108   :align: center
109
110This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.
111In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme,
112tidal lateral boundary conditions using a flather scheme (see more in ``BDY``).
113Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.
114
115Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run
116(``AMM12_v4.0.tar``).
117
118Note that, the Baltic boundary is included within the river input file and is specified as a river source,
119but unlike ordinary river points the Baltic inputs also include salinity and temperature data.
120
121C1D_PAPA
122--------
123
124.. figure:: _static/Papa2015.jpg
125   :height: 225px
126   :align:  left
127
128``C1D_PAPA`` is a 1D configuration for the `PAPA station`_ located in
129the northern-eastern Pacific Ocean at 50.1°N, 144.9°W.
130See :gmd:`Reffray et al. (2015) <8/69/2015>` for the description of
131its physical and numerical turbulent-mixing behaviour.
132
133| The water column setup, called NEMO1D, is activated with
134  the inclusion of the CPP key ``key_c1d`` and
135  has a horizontal domain of 3x3 grid points.
136| This reference configuration uses 75 vertical levels grid (1m at the surface),
137  GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae.
138
139Data provided with ``INPUTS_C1D_PAPA_v4.0.tar`` file account for:
140
141- :file:`forcing_PAPASTATION_1h_y201[0-1].nc`:
142  ECMWF operational analysis atmospheric forcing rescaled to 1h
143  (with long and short waves flux correction) for years 2010 and 2011
144- :file:`init_PAPASTATION_m06d15.nc`: Initial Conditions from
145  observed data and Levitus 2009 climatology
146- :file:`chlorophyll_PAPASTATION.nc`: surface chlorophyll file from Seawifs data
147
148GYRE_BFM
149--------
150
151``GYRE_BFM`` shares the same physical setup of GYRE_PISCES_,
152but NEMO is coupled with the `BFM`_ biogeochemical model as described in ``./cfgs/GYRE_BFM/README``.
153
154GYRE_PISCES
155-----------
156
157``GYRE_PISCES`` is an idealized configuration representing a Northern hemisphere double gyres system,
158in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels,
159with PISCES BGC model :cite:`gmd-8-2465-2015`.
160Analytical forcing for heat, freshwater and wind-stress fields are applied.
161
162This configuration acts also as demonstrator of the **user defined setup**
163(``ln_read_cfg = .false.``) and grid setting are handled through
164the ``&namusr_def`` controls in :file:`namelist_cfg`:
165
166.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg
167   :language: fortran
168   :lines:    35-41
169
170Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and
171vertical levels are set by ``jpkglo``.
172The specific code changes can be inspected in :file:`./src/OCE/USR`.
173
174.. rubric:: Running GYRE as a benchmark
175
176| This simple configuration can be used as a benchmark since it is easy to increase resolution,
177  with the drawback of getting results that have a very limited physical meaning.
178| GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE``
179  (integer multiplier scaling factor), as described in the following table:
180
181=========== ============ ============ ============ ===============
182``nn_GYRE``  ``jpiglo``   ``jpjglo``   ``jpkglo``   Equivalent to
183=========== ============ ============ ============ ===============
184 1           30           20           31           GYRE 1°
185 25          750          500          101          ORCA 1/2°
186 50          1500         1000         101          ORCA 1/4°
187 150         4500         3000         101          ORCA 1/12°
188 200         6000         4000         101          ORCA 1/16°
189=========== ============ ============ ============ ===============
190
191| Note that, it is necessary to set ``ln_bench = .true.`` in ``&namusr_def`` to
192  avoid problems in the physics computation and that
193  the model timestep should be adequately rescaled.
194| For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid,
195  the timestep ``rn_rdt`` should be set to 1200 seconds
196  Differently from previous versions of NEMO, the code uses by default the time-splitting scheme and
197  internally computes the number of sub-steps.
198
199ORCA2_ICE_PISCES
200----------------
201
202``ORCA2_ICE_PISCES`` is a reference configuration for the global ocean with
203a 2°x2° curvilinear horizontal mesh and 31 vertical levels,
204distributed using z-coordinate system and with 10 levels in the top 100m.
205ORCA is the generic name given to global ocean Mercator mesh,
206(i.e. variation of meridian scale factor as cosinus of the latitude),
207with two poles in the northern hemisphere so that
208the ratio of anisotropy is nearly one everywhere
209
210This configuration uses the three components
211
212- |OCE|, the ocean dynamical core
213- |ICE|, the thermodynamic-dynamic sea ice model.
214- |MBG|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015`
215
216All components share the same grid.
217The model is forced with CORE-II normal year atmospheric forcing and
218it uses the NCAR bulk formulae.
219
220.. rubric:: Ocean Physics
221
222:horizontal diffusion on momentum:
223   the eddy viscosity coefficient depends on the geographical position.
224   It is taken as 40000 m\ :sup:`2`/s, reduced in the equator regions (2000 m\ :sup:`2`/s)
225   excepted near the western boundaries.
226:isopycnal diffusion on tracers:
227   the diffusion acts along the isopycnal surfaces (neutral surface) with
228   an eddy diffusivity coefficient of 2000 m\ :sup:`2`/s.
229:Eddy induced velocity parametrization:
230   With a coefficient that depends on the growth rate of baroclinic instabilities
231   (it usually varies from 15 m\ :sup:`2`/s to 3000 m\ :sup:`2`/s).
232:lateral boundary conditions:
233   Zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries.
234:bottom boundary condition:
235   Zero fluxes of heat and salt are applied through the ocean bottom.
236   The Beckmann [19XX] simple bottom boundary layer parameterization is applied along
237   continental slopes.
238   A linear friction is applied on momentum.
239:convection:
240   The vertical eddy viscosity and diffusivity coefficients are increased to 1 m\ :sup:`2`/s in
241   case of static instability.
242:time step: is 5760sec (1h36') so that there is 15 time steps in one day.
243
244ORCA2_OFF_PISCES
245----------------
246
247``ORCA2_OFF_PISCES`` shares the same general offline configuration of ``ORCA2_ICE_TRC``,
248but only PISCES model is an active component of TOP.
249
250ORCA2_OFF_TRC
251-------------
252
253| ``ORCA2_OFF_TRC`` is based on the ORCA2 global ocean configuration
254  (see ORCA2_ICE_PISCES_ for general description) along with
255  the tracer passive transport module (TOP),
256  but dynamical fields are pre-calculated and read with specific time frequency.
257| This enables for an offline coupling of TOP components,
258  here specifically inorganic carbon compounds (CFC11, CFC12, SF6, C14) and water age module (age).
259  See :file:`namelist_top_cfg` to inspect the selection of
260  each component with the dedicated logical keys.
261
262Pre-calculated dynamical fields are provided to NEMO using
263the namelist ``&namdta_dyn``  in :file:`namelist_cfg`,
264in this case with a 5 days frequency (120 hours):
265
266.. literalinclude:: ../../namelists/namdta_dyn
267   :language: fortran
268
269Input dynamical fields for this configuration (:file:`ORCA2_OFF_v4.0.tar`) comes from
270a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing.
271
272| Note that,
273  this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that
274  model mesh is not varying in time and
275  it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that
276  requires the provision of BBL coefficients through ``sn_ubl`` and ``sn_vbl`` fields.
277| It is also possible to activate PISCES model (see ``ORCA2_OFF_PISCES``) or
278  a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.``
279  (and adaptation of ``./src/TOP/MY_TRC`` routines).
280
281In addition, the offline module (OFF) allows for the provision of further fields:
282
2831. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and
284   by including an input datastream similarly to the following:
285
286   .. code-block:: fortran
287
288      sn_rnf  = 'dyna_grid_T', 120, 'sorunoff' , .true., .true., 'yearly', '', '', ''
289
2902. **VVL dynamical fields**, in the case input data were produced by a dyamical core using
291   variable volume (``ln_linssh = .false.``)
292   it is necessary to provide also diverce and E-P at before timestep by
293   including input datastreams similarly to the following
294
295   .. code-block:: fortran
296
297      sn_div  = 'dyna_grid_T', 120, 'e3t'      , .true., .true., 'yearly', '', '', ''
298      sn_empb = 'dyna_grid_T', 120, 'sowaflupb', .true., .true., 'yearly', '', '', ''
299
300More details can be found by inspecting the offline data manager in
301the routine :file:`./src/OFF/dtadyn.F90`.
302
303ORCA2_SAS_ICE
304-------------
305
306| ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and
307  it relies on ORCA2 global ocean configuration (see ORCA2_ICE_PISCES_ for general description).
308| The standalone surface module allows surface elements such as sea-ice, iceberg drift, and
309  surface fluxes to be run using prescribed model state fields.
310  It can profitably be used to compare different bulk formulae or
311  adjust the parameters of a given bulk formula.
312
313More informations about SAS can be found in :doc:`NEMO manual <cite>`.
314
315SPITZ12
316-------
317
318``SPITZ12`` is a regional configuration around the Svalbard archipelago
319at 1/12° of horizontal resolution and 75 vertical levels.
320See :gmd:`Rousset et al. (2015) <8/2991/2015>` for more details.
321
322This configuration references to year 2002,
323with atmospheric forcing provided every 2 hours using NCAR bulk formulae,
324while lateral boundary conditions for dynamical fields have 3 days time frequency.
325
326.. rubric:: References
327
328.. bibliography:: cfgs.bib
329   :all:
330   :style: unsrt
331   :labelprefix: C
Note: See TracBrowser for help on using the repository browser.