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1REFERENCE CONFIGURATIONS
2========================
3
4NEMO 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).
5*The NEMO System Team is in charge only for these configurations.*
6
7Configurations 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>`_
8
9Available Configurations
10------------------------
11====================== ===== ===== ===== ======== ======= ================================================
12 Configuration                     Component(s)                            Input & Forcing File(s)
13---------------------- ---------------------------------- ------------------------------------------------
14 Name                   OPA   SI3   TOP   PISCES   AGRIF
15====================== ===== ===== ===== ======== ======= ================================================
16 AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar_, ORCA2_ICE_v4.0.tar_
17 AMM12_                  X                                 AMM12_v4.0.tar_
18 C1D_PAPA_               X                                 INPUTS_C1D_PAPA_v4.0.tar_
19 GYRE_BFM_               X           X                     *none*
20 GYRE_PISCES_            X           X      X              *none*
21 ORCA2_ICE_PISCES_       X     X     X      X              ORCA2_ICE_v4.0.tar_, INPUTS_PISCES_v4.0.tar_
22 ORCA2_OFF_PISCES_                   X      X              ORCA2_OFF_v4.0.tar_, INPUTS_PISCES_v4.0.tar_
23 ORCA2_OFF_TRC_                      X                     ORCA2_OFF_v4.0.tar_
24 ORCA2_SAS_ICE_                X                           ORCA2_ICE_v4.0.tar_, INPUTS_SAS_v4.0.tar_
25 SPITZ12_                X     X                           SPITZ12_v4.0.tar_
26====================== ===== ===== ===== ======== ======= ================================================
27
28**How to compile an experiment from a reference configuration**
29
30A 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:
31
32
33.. code-block:: console
34               
35        $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4'
36
37A 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.
38
39Then it will be possible to launch the execution of the model through a runscript (opportunely adapted to the user system).
40
41AGRIF_DEMO
42----------
43
44AGRIF_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).
45
46The 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.
47
48The 1:1 grid can be used alone as a benchmark to check that the model solution is not corrupted by grid exchanges.
49Note 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.
50
51AMM12
52-----
53
54AMM12 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>`_).
55
56This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.
57In particular, AMM12  accounts for vertical s-coordinates system, GLS turbulence scheme, tidal lateral boundary conditions using a flather scheme (see more in BDY).
58Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.
59
60Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run (AMM12_v4.0.tar_).
61
62Note 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.
63
64C1D_PAPA
65--------
66
67C1D_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.
68
69The 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.
70
71This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae.
72Data provided with INPUTS_C1D_PAPA_v4.0.tar_ file account for :
73
74- ``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
75- ``init_PAPASTATION_m06d15.nc`` : Initial Conditions from observed data and Levitus 2009 climatology
76- ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data
77
78
79GYRE_BFM
80--------
81
82GYRE_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 :trac:`source:/NEMO/trunk/cfgs/GYRE_BFM/README`.
83
84
85GYRE_PISCES
86-----------
87
88GYRE_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. 
89
90This 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:
91
92.. code-block:: fortran
93
94  !-----------------------------------------------------------------------
95  &namusr_def    !   GYRE user defined namelist
96  !-----------------------------------------------------------------------
97     nn_GYRE     =     1     !  GYRE resolution [1/degrees]
98     ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
99     jpkglo      =    31     !  number of model levels
100  /
101
102Note 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 :trac:`source:/NEMO/trunk/src/OCE/USR` 
103
104**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.
105
106GYRE 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:
107
108=========== ========= ========== ============ ===================
109``nn_GYRE``  *jpiglo*  *jpjglo*   ``jpkglo``   **Equivalent to**
110=========== ========= ========== ============ ===================
111 1           30        20         31           GYRE 1°
112 25          750       500        101          ORCA 1/2°
113 50          1500      1000       101          ORCA 1/4°
114 150         4500      3000       101          ORCA 1/12°
115 200         6000      4000       101          ORCA 1/16°
116=========== ========= ========== ============ ===================
117
118Note 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.
119
120For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, the timestep should be set to 1200 seconds
121
122.. code-block:: fortran
123   
124   rn_rdt      = 1200.     !  time step for the dynamics
125
126Differently from previous versions of NEMO, the code uses by default  the time-splitting scheme and internally computes the number of sub-steps.
127
128
129ORCA2_ICE_PISCES
130----------------
131
132ORCA2_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.
133ORCA 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
134
135In this configuration, the ocean dynamical core  is coupled to 
136
137- **ICE**, namely SI3 (Sea Ice Integrated Initiative) a thermodynamic-dynamic sea ice model specifically designed for climate studies.
138- **TOP**, passive tracer transport module and `PISCES biogeochemical model`_
139
140All components share the same grid.
141
142The model is forced with CORE-II normal year atmospheric forcing and it uses the NCAR bulk formulae.
143
144**Ocean Physics configuration**
145
146- *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.
147- *isopycnal diffusion on tracers*: the diffusion acts along the isopycnal surfaces (neutral surface) with an eddy diffusivity coefficient of 2000 m^2/s.
148- *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).
149- *lateral boundary conditions* : zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries.
150- *bottom boundary condition* : zero fluxes of heat and salt are applied through the ocean bottom.
151  The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes.
152  A linear friction is applied on momentum.
153- *convection*: the vertical eddy viscosity and diffusivity coefficients are increased to 1 m^2/s in case of static instability.
154- *time step* is 5760sec (1h36') so that there is 15 time steps in one day.
155
156
157
158**AGRIF demonstrator**
159
160From the ORCA2_ICE_PISCES configuration, a demonstrator using AGRIF nesting can be activated that includes a nested grid in the Agulhas region.
161
162To set up this configuration, after extracting NEMO:
163
164Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated:
165
166.. code-block:: console
167               
168        $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif'
169
170By using the input files and namelists for ORCA2_ICE_PISCES, the AGRIF test configuration is ready to run.
171
172
173ORCA2_OFF_PISCES
174----------------
175
176ORCA2_OFF_PISCES  shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP.
177
178
179ORCA2_OFF_TRC
180-------------
181
182ORCA2_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.
183
184This 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.
185
186Pre-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):
187
188.. code-block:: fortran
189
190  !-----------------------------------------------------------------------
191  &namdta_dyn    !   offline ocean input files                            (OFF_SRC only)
192  !-----------------------------------------------------------------------
193     ln_dynrnf       =  .false.    !  runoffs option enabled (T) or not (F)
194     ln_dynrnf_depth =  .false.    !  runoffs is spread in vertical (T) or not (F)
195     cn_dir      = './'      !  root directory for the ocean data location
196     !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
197     !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask !
198     !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   !
199     sn_tem      = 'dyna_grid_T'           ,       120         , 'votemper'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
200     sn_sal      = 'dyna_grid_T'           ,       120         , 'vosaline'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
201     sn_mld      = 'dyna_grid_T'           ,       120         , 'somixhgt'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
202     sn_emp      = 'dyna_grid_T'           ,       120         , 'sowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
203     sn_fmf      = 'dyna_grid_T'           ,       120         , 'iowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
204     sn_ice      = 'dyna_grid_T'           ,       120         , 'soicecov'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
205     sn_qsr      = 'dyna_grid_T'           ,       120         , 'soshfldo'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
206     sn_wnd      = 'dyna_grid_T'           ,       120         , 'sowindsp'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
207     sn_uwd      = 'dyna_grid_U'           ,       120         , 'uocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
208     sn_vwd      = 'dyna_grid_V'           ,       120         , 'vocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
209     sn_wwd      = 'dyna_grid_W'           ,       120         , 'wocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
210     sn_avt      = 'dyna_grid_W'           ,       120         , 'voddmavs'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
211     sn_ubl      = 'dyna_grid_U'           ,       120         , 'sobblcox'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
212     sn_vbl      = 'dyna_grid_V'           ,       120         , 'sobblcoy'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
213  /
214
215Input 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.
216
217Note 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.
218
219It 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 :trac:`source:/NEMO/trunk/src/TOP/MY_TRC` routines).
220
221In addition, the offline module (OFF) allows for the provision of further fields:
222
2231. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and by including an input datastream similarly to the following:
224
225.. code-block:: fortran
226
227     sn_rnf      = 'dyna_grid_T'           ,       120         , 'sorunoff'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
228
2292. **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
230
231.. code-block:: fortran
232
233     sn_div       = 'dyna_grid_T'           ,       120         ,    'e3t'     ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
234     sn_empb      = 'dyna_grid_T'           ,       120         , 'sowaflupb'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
235
236
237More details can be found by inspecting the offline data manager at :trac:`source:/NEMO/trunk/src/OFF/dtadyn.F90`
238
239
240ORCA2_SAS_ICE
241-------------
242
243ORCA2_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).
244
245The standalone surface module allows surface elements such as sea-ice, iceberg drift, and surface fluxes to be run using prescribed model state fields.
246It can profitably be used to compare different bulk formulae or adjust the parameters of a given bulk formula.
247
248More informations about SAS can be found in NEMO manual.
249
250SPITZ12
251-------
252
253SPITZ12 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.
254
255This 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.
256
257
258.. _AGRIF_DEMO_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar
259.. _AMM12_v4.0.tar:               http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar
260.. _PISCES biogeochemical model:  http://www.geosci-model-dev.net/8/2465/2015
261.. _INPUTS_PISCES_v4.0.tar:       http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_PISCES_v4.0.tar
262.. _ORCA2_OFF_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_OFF_v4.0.tar
263.. _ORCA2_ICE_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar
264.. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar
265.. _INPUTS_C1D_PAPA_v4.0.tar:     http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar
266.. _SPITZ12_v4.0.tar:             http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar
267
268.. _COREII:                       http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html
269
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