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1************************
2Reference configurations
3************************
4
5NEMO is distributed with a set of reference configurations allowing both the user to set up his own first applications and the developer to test/validate his NEMO developments (using SETTE package).
6*The NEMO System Team is in charge only for these configurations.*
7
8Configurations developed by external research projects or initiatives that make use of NEMO are welcome to be publicized also through the NEMO website by filling up the form `Add project <http://www.nemo-ocean.eu/projects/add>`_
9
10Available Configurations
11------------------------
12====================== ===== ===== ===== ======== ======= ================================================
13 Configuration                     Component(s)                            Input & Forcing File(s)
14---------------------- ---------------------------------- ------------------------------------------------
15 Name                   OPA   SI3   TOP   PISCES   AGRIF
16====================== ===== ===== ===== ======== ======= ================================================
17 AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar_, ORCA2_ICE_v4.0.tar_
18 AMM12_                  X                                 AMM12_v4.0.tar_
19 C1D_PAPA_               X                                 INPUTS_C1D_PAPA_v4.0.tar_
20 GYRE_BFM_               X           X                     *none*
21 GYRE_PISCES_            X           X      X              *none*
22 ORCA2_ICE_PISCES_       X     X     X      X              ORCA2_ICE_v4.0.tar_, INPUTS_PISCES_v4.0.tar_
23 ORCA2_OFF_PISCES_                   X      X              ORCA2_OFF_v4.0.tar_, INPUTS_PISCES_v4.0.tar_
24 ORCA2_OFF_TRC_                      X                     ORCA2_OFF_v4.0.tar_
25 ORCA2_SAS_ICE_                X                           ORCA2_ICE_v4.0.tar_, INPUTS_SAS_v4.0.tar_
26 SPITZ12_                X     X                           SPITZ12_v4.0.tar_
27====================== ===== ===== ===== ======== ======= ================================================
28
29**How to compile an experiment from a reference configuration**
30
31A user who wants to compile the ORCA2_ICE_PISCES_ reference configuration using makenemo should use the following, by selecting among available architecture file or providing a user defined one:
32
33
34.. code-block:: console
35               
36        $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4'
37
38A new EXP00 folder will be created within the selected reference configurations, namely ``trunk/cfgs/ORCA2_ICE_PISCES/EXP00``, where it will be necessary to uncompress the Input & Forcing Files listed in the above table.
39
40Then it will be possible to launch the execution of the model through a runscript (opportunely adapted to the user system).
41
42AGRIF_DEMO
43----------
44
45AGRIF_DEMO is based on the ORCA2_ICE_PISCES_ global configuration at 2° of resolution with the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF (Adaptive Grid Refinement In Fortran) in a realistic context (including the nesting of sea ice models).
46
47The configuration includes a 1:1 grid in the Pacific and two successively nested grids with odd and even refinement ratios over the Arctic ocean, with the finest grid spanning the whole Svalbard archipelago that is of particular interest to test sea ice coupling.
48
49The 1:1 grid can be used alone as a benchmark to check that the model solution is not corrupted by grid exchanges.
50Note that since grids interact only at the baroclinic time level, numerically exact results can not be achieved in the 1:1 case. Perfect reproducibility is obtained only by switching to a fully explicit setip instead of a split explicit free surface scheme.
51
52AMM12
53-----
54
55AMM12 stands for *Atlantic Margin Model at 12 km* that is a regional configuration covering the Northwest European Shelf domain on a regular horizontal grid of ~12 km of resolution (see `O'Dea et al., 2012 <http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128>`_).
56
57This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.
58In particular, AMM12  accounts for vertical s-coordinates system, GLS turbulence scheme, tidal lateral boundary conditions using a flather scheme (see more in BDY).
59Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.
60
61Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run (AMM12_v4.0.tar_).
62
63Note that, the Baltic boundary is included within the river input file and is specified as a river source, but unlike ordinary river points the Baltic inputs also include salinity and temperature data.
64
65C1D_PAPA
66--------
67
68C1D_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. See `Reffray et al. (2015) <http://www.geosci-model-dev.net/8/69/2015>`_ for the description of its physical and numerical turbulent-mixing behaviour.
69
70The water column setup, called NEMO1D, is activated with the inclusion of the CPP key ``key_c1d`` and has a horizontal domain of 3x3 grid points.
71
72This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae.
73Data provided with INPUTS_C1D_PAPA_v4.0.tar_ file account for :
74
75- ``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
76- ``init_PAPASTATION_m06d15.nc`` : Initial Conditions from observed data and Levitus 2009 climatology
77- ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data
78
79
80GYRE_BFM
81--------
82
83GYRE_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 :forge:`browser/NEMO/trunk/cfgs/GYRE_BFM/README`.
84
85
86GYRE_PISCES
87-----------
88
89GYRE_PISCES is an idealized configuration representing a Northern hemisphere double gyres system,  in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels, which is coupled with `PISCES biogeochemical model`_. Analytical forcing for heat, freshwater and wind-stress fields are applied. 
90
91This configuration act also as demonstrator of the **USER DEFINED setup** (``ln_read_cfg = .false.``) and grid setting are handled through the ``&namusr_def`` controls in namelist_cfg:
92
93.. code-block:: fortran
94
95  !-----------------------------------------------------------------------
96  &namusr_def    !   GYRE user defined namelist
97  !-----------------------------------------------------------------------
98     nn_GYRE     =     1     !  GYRE resolution [1/degrees]
99     ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
100     jpkglo      =    31     !  number of model levels
101  /
102
103Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and vertical levels are set by ``jpkglo``. The specific code changes can be inspected at :forge:`browser/NEMO/trunk/src/OCE/USR` 
104
105**Running GYRE as a benchmark** :  this simple configuration can be used as a benchmark since it is easy to increase resolution, with the drawback of getting results that have a very limited physical meaning.
106
107GYRE 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:
108
109=========== ========= ========== ============ ===================
110``nn_GYRE``  *jpiglo*  *jpjglo*   ``jpkglo``   **Equivalent to**
111=========== ========= ========== ============ ===================
112 1           30        20         31           GYRE 1°
113 25          750       500        101          ORCA 1/2°
114 50          1500      1000       101          ORCA 1/4°
115 150         4500      3000       101          ORCA 1/12°
116 200         6000      4000       101          ORCA 1/16°
117=========== ========= ========== ============ ===================
118
119Note that,  it is necessary to set ``ln_bench = .true.`` in ``namusr_def`` to avoid problems in the physics computation and that the model timestep should be adequately rescaled.
120
121For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, the timestep should be set to 1200 seconds
122
123.. code-block:: fortran
124   
125   rn_rdt      = 1200.     !  time step for the dynamics
126
127Differently from previous versions of NEMO, the code uses by default  the time-splitting scheme and internally computes the number of sub-steps.
128
129
130ORCA2_ICE_PISCES
131----------------
132
133ORCA2_ICE_PISCES is a reference configuration for the global ocean with a 2°x2° curvilinear horizontal mesh and 31 vertical levels, distributed using z-coordinate system and with 10 levels in the top 100m.
134ORCA is the generic name given to global ocean Mercator mesh, (i.e. variation of meridian scale factor as cosinus of the latitude), with two poles in the northern hemisphere so that the ratio of anisotropy is nearly one everywhere
135
136In this configuration, the ocean dynamical core  is coupled to 
137
138- **ICE**, namely SI3 (Sea Ice Integrated Initiative) a thermodynamic-dynamic sea ice model specifically designed for climate studies.
139- **TOP**, passive tracer transport module and `PISCES biogeochemical model`_
140
141All components share the same grid.
142
143The model is forced with CORE-II normal year atmospheric forcing and it uses the NCAR bulk formulae.
144
145**Ocean Physics configuration**
146
147- *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.
148- *isopycnal diffusion on tracers*: the diffusion acts along the isopycnal surfaces (neutral surface) with an eddy diffusivity coefficient of 2000 m^2/s.
149- *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).
150- *lateral boundary conditions* : zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries.
151- *bottom boundary condition* : zero fluxes of heat and salt are applied through the ocean bottom.
152  The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes.
153  A linear friction is applied on momentum.
154- *convection*: the vertical eddy viscosity and diffusivity coefficients are increased to 1 m^2/s in case of static instability.
155- *time step* is 5760sec (1h36') so that there is 15 time steps in one day.
156
157
158
159**AGRIF demonstrator**
160
161From the ORCA2_ICE_PISCES configuration, a demonstrator using AGRIF nesting can be activated that includes a nested grid in the Agulhas region.
162
163To set up this configuration, after extracting NEMO:
164
165Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated:
166
167.. code-block:: console
168               
169        $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif'
170
171By using the input files and namelists for ORCA2_ICE_PISCES, the AGRIF test configuration is ready to run.
172
173
174ORCA2_OFF_PISCES
175----------------
176
177ORCA2_OFF_PISCES  shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP.
178
179
180ORCA2_OFF_TRC
181-------------
182
183ORCA2_OFF_TRC is based on the ORCA2 global ocean configuration (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.
184
185This enables for an offline coupling of TOP components, here specifically inorganic carbon compounds (cfc11, cfc12, sf6, c14) and water age module (age). See ``namelist_top_cfg`` to inspect the selection of each component with the dedicated logical keys.
186
187Pre-calculated dynamical fields are provided to NEMO using the namelist ``&namdta_dyn``  in ``namelist_cfg``, in this case with a 5 days frequency (120 hours):
188
189.. code-block:: fortran
190
191  !-----------------------------------------------------------------------
192  &namdta_dyn    !   offline ocean input files                            (OFF_SRC only)
193  !-----------------------------------------------------------------------
194     ln_dynrnf       =  .false.    !  runoffs option enabled (T) or not (F)
195     ln_dynrnf_depth =  .false.    !  runoffs is spread in vertical (T) or not (F)
196     cn_dir      = './'      !  root directory for the ocean data location
197     !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
198     !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask !
199     !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   !
200     sn_tem      = 'dyna_grid_T'           ,       120         , 'votemper'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
201     sn_sal      = 'dyna_grid_T'           ,       120         , 'vosaline'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
202     sn_mld      = 'dyna_grid_T'           ,       120         , 'somixhgt'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
203     sn_emp      = 'dyna_grid_T'           ,       120         , 'sowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
204     sn_fmf      = 'dyna_grid_T'           ,       120         , 'iowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
205     sn_ice      = 'dyna_grid_T'           ,       120         , 'soicecov'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
206     sn_qsr      = 'dyna_grid_T'           ,       120         , 'soshfldo'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
207     sn_wnd      = 'dyna_grid_T'           ,       120         , 'sowindsp'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
208     sn_uwd      = 'dyna_grid_U'           ,       120         , 'uocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
209     sn_vwd      = 'dyna_grid_V'           ,       120         , 'vocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
210     sn_wwd      = 'dyna_grid_W'           ,       120         , 'wocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
211     sn_avt      = 'dyna_grid_W'           ,       120         , 'voddmavs'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
212     sn_ubl      = 'dyna_grid_U'           ,       120         , 'sobblcox'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
213     sn_vbl      = 'dyna_grid_V'           ,       120         , 'sobblcoy'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
214  /
215
216Input dynamical fields for this configuration (ORCA2_OFF_v4.0.tar_) comes from a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing.
217
218Note that, this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that model mesh is not varying in time and it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that requires the provision of bbl coefficients through ``sn_ubl`` and ``sn_vbl`` fields.
219
220It is also possible to activate PISCES model (see ORCA2_OFF_PISCES_) or a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` (and adaptation of :forge:`browser/NEMO/trunk/src/TOP/MY_TRC` routines).
221
222In addition, the offline module (OFF) allows for the provision of further fields:
223
2241. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and by including an input datastream similarly to the following:
225
226.. code-block:: fortran
227
228     sn_rnf      = 'dyna_grid_T'           ,       120         , 'sorunoff'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
229
2302. **VVL dynamical fields**, in the case input data were produced by a dyamical core using variable volume (``ln_linssh = .false.``) it necessary to provide also diverce and E-P at before timestep by including input datastreams similarly to the following
231
232.. code-block:: fortran
233
234     sn_div       = 'dyna_grid_T'           ,       120         ,    'e3t'     ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
235     sn_empb      = 'dyna_grid_T'           ,       120         , 'sowaflupb'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
236
237
238More details can be found by inspecting the offline data manager at :forge:`browser/NEMO/trunk/src/OFF/dtadyn.F90`
239
240
241ORCA2_SAS_ICE
242-------------
243
244ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and it relies on ORCA2 global ocean configuration (see `ORCA2_ICE_PISCES`_ for general description).
245
246The standalone surface module allows surface elements such as sea-ice, iceberg drift, and surface fluxes to be run using prescribed model state fields.
247It can profitably be used to compare different bulk formulae or adjust the parameters of a given bulk formula.
248
249More informations about SAS can be found in NEMO manual.
250
251SPITZ12
252-------
253
254SPITZ12 is a regional configuration around the Svalbard archipelago at 1/12° of horizontal resolution and 75 vertical levels. See `Rousset et al. (2015) <https://www.geosci-model-dev.net/8/2991/2015/>`_ for more details.
255
256This configuration references to year 2002, with atmospheric forcing provided every 2 hours using NCAR bulk formulae, while lateral boundary conditions for dynamical fields have 3 days time frequency.
257
258
259.. _AGRIF_DEMO_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar
260.. _AMM12_v4.0.tar:               http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar
261.. _PISCES biogeochemical model:  http://www.geosci-model-dev.net/8/2465/2015
262.. _INPUTS_PISCES_v4.0.tar:       http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_PISCES_v4.0.tar
263.. _ORCA2_OFF_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_OFF_v4.0.tar
264.. _ORCA2_ICE_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar
265.. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar
266.. _INPUTS_C1D_PAPA_v4.0.tar:     http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar
267.. _SPITZ12_v4.0.tar:             http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar
268
269.. _COREII:                       http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html
270
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