[11735] | 1 | ******************************** |
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| 2 | Run the Reference configurations |
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| 3 | ******************************** |
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[10186] | 4 | |
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[11734] | 5 | .. todo:: |
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| 6 | |
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| 7 | Lack of illustrations for ref. cfgs, and more generally in the guide. |
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| 8 | |
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[10605] | 9 | NEMO is distributed with a set of reference configurations allowing both |
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| 10 | the user to set up his own first applications and |
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| 11 | the developer to test/validate his NEMO developments (using SETTE package). |
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[10186] | 12 | |
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[11734] | 13 | .. contents:: |
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| 14 | :local: |
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| 15 | :depth: 1 |
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| 16 | |
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[10605] | 17 | .. attention:: |
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[10186] | 18 | |
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[10605] | 19 | Concerning the configurations, |
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| 20 | the NEMO System Team is only in charge of the so-called reference configurations described below. |
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| 21 | |
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| 22 | .. hint:: |
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| 23 | |
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| 24 | Configurations developed by external research projects or initiatives that |
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| 25 | make use of NEMO are welcome to be publicized through the website by |
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| 26 | filling up the form :website:`to add an associated project<projects/add>`. |
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| 27 | |
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| 28 | How to compile an experiment from a reference configuration |
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| 29 | =========================================================== |
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| 30 | |
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[11743] | 31 | To compile the ORCA2_ICE_PISCES_ reference configuration using :file:`makenemo`, |
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[11734] | 32 | one should use the following, by selecting among available architecture file or |
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| 33 | providing a user defined one: |
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[10605] | 34 | |
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| 35 | .. code-block:: console |
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[11708] | 36 | |
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[11734] | 37 | $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my_arch' -j '4' |
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[10605] | 38 | |
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| 39 | A new ``EXP00`` folder will be created within the selected reference configurations, |
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[11734] | 40 | namely ``./cfgs/ORCA2_ICE_PISCES/EXP00``. |
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| 41 | It will be necessary to uncompress the archives listed in the above table for |
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| 42 | the given reference configuration that includes input & forcing files. |
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[10605] | 43 | |
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| 44 | Then it will be possible to launch the execution of the model through a runscript |
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| 45 | (opportunely adapted to the user system). |
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[11708] | 46 | |
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[10605] | 47 | List of Configurations |
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| 48 | ====================== |
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| 49 | |
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[11734] | 50 | All forcing files listed below in the table are available from |DOI data|_ |
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[10605] | 51 | |
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[11734] | 52 | =================== === === === === === ================================== |
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| 53 | Configuration Component(s) Archives (input & forcing files) |
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| 54 | ------------------- ------------------- ---------------------------------- |
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| 55 | Name O S T P A |
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| 56 | =================== === === === === === ================================== |
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| 57 | AGRIF_DEMO_ X X X AGRIF_DEMO_v4.0.tar, |
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| 58 | ORCA2_ICE_v4.0.tar |
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| 59 | AMM12_ X AMM12_v4.0.tar |
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| 60 | C1D_PAPA_ X INPUTS_C1D_PAPA_v4.0.tar |
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| 61 | GYRE_BFM_ X X *none* |
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| 62 | GYRE_PISCES_ X X X *none* |
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| 63 | ORCA2_ICE_PISCES_ X X X X ORCA2_ICE_v4.0.tar, |
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| 64 | INPUTS_PISCES_v4.0.tar |
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| 65 | ORCA2_OFF_PISCES_ X X ORCA2_OFF_v4.0.tar, |
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| 66 | INPUTS_PISCES_v4.0.tar |
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| 67 | ORCA2_OFF_TRC_ X ORCA2_OFF_v4.0.tar |
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| 68 | ORCA2_SAS_ICE_ X ORCA2_ICE_v4.0.tar, |
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| 69 | INPUTS_SAS_v4.0.tar |
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| 70 | SPITZ12_ X X SPITZ12_v4.0.tar |
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| 71 | =================== === === === === === ================================== |
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[10605] | 72 | |
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[11734] | 73 | .. admonition:: Legend for component combination |
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[10186] | 74 | |
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[11734] | 75 | O for OCE, S for SI\ :sup:`3`, T for TOP, P for PISCES and A for AGRIF |
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| 76 | |
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[10541] | 77 | AGRIF_DEMO |
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| 78 | ---------- |
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[10186] | 79 | |
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[10605] | 80 | ``AGRIF_DEMO`` is based on the ``ORCA2_ICE_PISCES`` global configuration at 2° of resolution with |
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| 81 | the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF in |
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| 82 | a realistic context (including the nesting of sea ice models). |
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[10541] | 83 | |
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[10605] | 84 | The configuration includes a 1:1 grid in the Pacific and two successively nested grids with |
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| 85 | odd and even refinement ratios over the Arctic ocean, |
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| 86 | with the finest grid spanning the whole Svalbard archipelago that is of |
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| 87 | particular interest to test sea ice coupling. |
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[10541] | 88 | |
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[11734] | 89 | .. image:: _static/AGRIF_DEMO_no_cap.jpg |
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| 90 | :scale: 66% |
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| 91 | :align: center |
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| 92 | |
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[10605] | 93 | The 1:1 grid can be used alone as a benchmark to check that |
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[11708] | 94 | the model solution is not corrupted by grid exchanges. |
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[10605] | 95 | Note that since grids interact only at the baroclinic time level, |
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| 96 | numerically exact results can not be achieved in the 1:1 case. |
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[11734] | 97 | Perfect reproducibility is obtained only by switching to a fully explicit setup instead of |
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| 98 | a split explicit free surface scheme. |
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[10541] | 99 | |
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[10186] | 100 | AMM12 |
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| 101 | ----- |
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| 102 | |
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[10605] | 103 | ``AMM12`` stands for *Atlantic Margin Model at 12 km* that is |
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| 104 | a regional configuration covering the Northwest European Shelf domain on |
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| 105 | a regular horizontal grid of ~12 km of resolution (see :cite:`ODEA2012`). |
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[10186] | 106 | |
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[11734] | 107 | .. image:: _static/AMM_domain.png |
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| 108 | :align: center |
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| 109 | |
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[11708] | 110 | This configuration allows to tests several features of NEMO specifically addressed to the shelf seas. |
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[10605] | 111 | In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme, |
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| 112 | tidal lateral boundary conditions using a flather scheme (see more in ``BDY``). |
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[10541] | 113 | Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``. |
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[10186] | 114 | |
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[10605] | 115 | Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run |
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| 116 | (``AMM12_v4.0.tar``). |
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[10186] | 117 | |
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[10605] | 118 | Note that, the Baltic boundary is included within the river input file and is specified as a river source, |
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| 119 | but unlike ordinary river points the Baltic inputs also include salinity and temperature data. |
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[10186] | 120 | |
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| 121 | C1D_PAPA |
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| 122 | -------- |
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| 123 | |
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[11734] | 124 | .. figure:: _static/Papa2015.jpg |
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| 125 | :height: 225px |
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| 126 | :align: left |
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[10186] | 127 | |
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[11734] | 128 | ``C1D_PAPA`` is a 1D configuration for the `PAPA station`_ located in |
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| 129 | the northern-eastern Pacific Ocean at 50.1°N, 144.9°W. |
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| 130 | See :gmd:`Reffray et al. (2015) <8/69/2015>` for the description of |
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| 131 | its physical and numerical turbulent-mixing behaviour. |
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[10186] | 132 | |
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[11734] | 133 | | The water column setup, called NEMO1D, is activated with |
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| 134 | the inclusion of the CPP key ``key_c1d`` and |
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| 135 | has a horizontal domain of 3x3 grid points. |
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| 136 | | This reference configuration uses 75 vertical levels grid (1m at the surface), |
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| 137 | GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae. |
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| 138 | |
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[10605] | 139 | Data provided with ``INPUTS_C1D_PAPA_v4.0.tar`` file account for: |
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[10186] | 140 | |
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[11734] | 141 | - :file:`forcing_PAPASTATION_1h_y201[0-1].nc`: |
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| 142 | ECMWF operational analysis atmospheric forcing rescaled to 1h |
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| 143 | (with long and short waves flux correction) for years 2010 and 2011 |
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| 144 | - :file:`init_PAPASTATION_m06d15.nc`: Initial Conditions from |
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| 145 | observed data and Levitus 2009 climatology |
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| 146 | - :file:`chlorophyll_PAPASTATION.nc`: surface chlorophyll file from Seawifs data |
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[10186] | 147 | |
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| 148 | GYRE_BFM |
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| 149 | -------- |
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| 150 | |
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[11734] | 151 | ``GYRE_BFM`` shares the same physical setup of GYRE_PISCES_, |
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| 152 | but NEMO is coupled with the `BFM`_ biogeochemical model as described in ``./cfgs/GYRE_BFM/README``. |
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[10186] | 153 | |
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| 154 | GYRE_PISCES |
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| 155 | ----------- |
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| 156 | |
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[10605] | 157 | ``GYRE_PISCES`` is an idealized configuration representing a Northern hemisphere double gyres system, |
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| 158 | in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels, |
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| 159 | with PISCES BGC model :cite:`gmd-8-2465-2015`. |
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[11708] | 160 | Analytical forcing for heat, freshwater and wind-stress fields are applied. |
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[10186] | 161 | |
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[11734] | 162 | This configuration acts also as demonstrator of the **user defined setup** |
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| 163 | (``ln_read_cfg = .false.``) and grid setting are handled through |
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| 164 | the ``&namusr_def`` controls in :file:`namelist_cfg`: |
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[10186] | 165 | |
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[10605] | 166 | .. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg |
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| 167 | :language: fortran |
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[11734] | 168 | :lines: 35-41 |
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[10186] | 169 | |
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[10605] | 170 | Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and |
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| 171 | vertical levels are set by ``jpkglo``. |
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[11734] | 172 | The specific code changes can be inspected in :file:`./src/OCE/USR`. |
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[10186] | 173 | |
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[11734] | 174 | .. rubric:: Running GYRE as a benchmark |
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[10186] | 175 | |
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[11734] | 176 | | This simple configuration can be used as a benchmark since it is easy to increase resolution, |
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| 177 | with the drawback of getting results that have a very limited physical meaning. |
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| 178 | | GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE`` |
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| 179 | (integer multiplier scaling factor), as described in the following table: |
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[10186] | 180 | |
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[11734] | 181 | =========== ============ ============ ============ =============== |
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| 182 | ``nn_GYRE`` ``jpiglo`` ``jpjglo`` ``jpkglo`` Equivalent to |
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| 183 | =========== ============ ============ ============ =============== |
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| 184 | 1 30 20 31 GYRE 1° |
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| 185 | 25 750 500 101 ORCA 1/2° |
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| 186 | 50 1500 1000 101 ORCA 1/4° |
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| 187 | 150 4500 3000 101 ORCA 1/12° |
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| 188 | 200 6000 4000 101 ORCA 1/16° |
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| 189 | =========== ============ ============ ============ =============== |
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[10186] | 190 | |
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[11734] | 191 | | Note that, it is necessary to set ``ln_bench = .true.`` in ``&namusr_def`` to |
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| 192 | avoid problems in the physics computation and that |
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| 193 | the model timestep should be adequately rescaled. |
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| 194 | | For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, |
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| 195 | the timestep ``rn_rdt`` should be set to 1200 seconds |
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| 196 | Differently from previous versions of NEMO, the code uses by default the time-splitting scheme and |
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| 197 | internally computes the number of sub-steps. |
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[10186] | 198 | |
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| 199 | ORCA2_ICE_PISCES |
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| 200 | ---------------- |
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| 201 | |
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[10605] | 202 | ``ORCA2_ICE_PISCES`` is a reference configuration for the global ocean with |
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| 203 | a 2°x2° curvilinear horizontal mesh and 31 vertical levels, |
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| 204 | distributed using z-coordinate system and with 10 levels in the top 100m. |
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| 205 | ORCA is the generic name given to global ocean Mercator mesh, |
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| 206 | (i.e. variation of meridian scale factor as cosinus of the latitude), |
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| 207 | with two poles in the northern hemisphere so that |
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| 208 | the ratio of anisotropy is nearly one everywhere |
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[10186] | 209 | |
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[11734] | 210 | This configuration uses the three components |
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[10186] | 211 | |
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[11734] | 212 | - |OCE|, the ocean dynamical core |
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| 213 | - |ICE|, the thermodynamic-dynamic sea ice model. |
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| 214 | - |MBG|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015` |
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[10186] | 215 | |
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[10541] | 216 | All components share the same grid. |
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[10605] | 217 | The model is forced with CORE-II normal year atmospheric forcing and |
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| 218 | it uses the NCAR bulk formulae. |
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[10186] | 219 | |
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[11734] | 220 | .. rubric:: Ocean Physics |
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[10186] | 221 | |
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[11734] | 222 | :horizontal diffusion on momentum: |
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| 223 | the eddy viscosity coefficient depends on the geographical position. |
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| 224 | It is taken as 40000 m\ :sup:`2`/s, reduced in the equator regions (2000 m\ :sup:`2`/s) |
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| 225 | excepted near the western boundaries. |
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| 226 | :isopycnal diffusion on tracers: |
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| 227 | the diffusion acts along the isopycnal surfaces (neutral surface) with |
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| 228 | an eddy diffusivity coefficient of 2000 m\ :sup:`2`/s. |
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| 229 | :Eddy induced velocity parametrization: |
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| 230 | With a coefficient that depends on the growth rate of baroclinic instabilities |
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| 231 | (it usually varies from 15 m\ :sup:`2`/s to 3000 m\ :sup:`2`/s). |
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| 232 | :lateral boundary conditions: |
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| 233 | Zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries. |
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| 234 | :bottom boundary condition: |
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| 235 | Zero fluxes of heat and salt are applied through the ocean bottom. |
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| 236 | The Beckmann [19XX] simple bottom boundary layer parameterization is applied along |
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| 237 | continental slopes. |
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| 238 | A linear friction is applied on momentum. |
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| 239 | :convection: |
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| 240 | The vertical eddy viscosity and diffusivity coefficients are increased to 1 m\ :sup:`2`/s in |
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| 241 | case of static instability. |
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[14446] | 242 | :time step: is 5400sec (1h30') so that there is 16 time steps in one day. |
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[10605] | 243 | |
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[10186] | 244 | ORCA2_OFF_PISCES |
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| 245 | ---------------- |
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| 246 | |
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[10605] | 247 | ``ORCA2_OFF_PISCES`` shares the same general offline configuration of ``ORCA2_ICE_TRC``, |
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| 248 | but only PISCES model is an active component of TOP. |
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[10186] | 249 | |
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| 250 | ORCA2_OFF_TRC |
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| 251 | ------------- |
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| 252 | |
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[11734] | 253 | | ``ORCA2_OFF_TRC`` is based on the ORCA2 global ocean configuration |
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| 254 | (see ORCA2_ICE_PISCES_ for general description) along with |
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| 255 | the tracer passive transport module (TOP), |
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| 256 | but dynamical fields are pre-calculated and read with specific time frequency. |
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| 257 | | This enables for an offline coupling of TOP components, |
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| 258 | here specifically inorganic carbon compounds (CFC11, CFC12, SF6, C14) and water age module (age). |
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| 259 | See :file:`namelist_top_cfg` to inspect the selection of |
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| 260 | each component with the dedicated logical keys. |
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[10186] | 261 | |
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[10605] | 262 | Pre-calculated dynamical fields are provided to NEMO using |
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[11734] | 263 | the namelist ``&namdta_dyn`` in :file:`namelist_cfg`, |
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[10605] | 264 | in this case with a 5 days frequency (120 hours): |
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[10186] | 265 | |
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[11734] | 266 | .. literalinclude:: ../../namelists/namdta_dyn |
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[10605] | 267 | :language: fortran |
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[10186] | 268 | |
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[11734] | 269 | Input dynamical fields for this configuration (:file:`ORCA2_OFF_v4.0.tar`) comes from |
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[10605] | 270 | a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing. |
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[10541] | 271 | |
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[11734] | 272 | | Note that, |
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| 273 | this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that |
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| 274 | model mesh is not varying in time and |
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| 275 | it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that |
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| 276 | requires the provision of BBL coefficients through ``sn_ubl`` and ``sn_vbl`` fields. |
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| 277 | | It is also possible to activate PISCES model (see ``ORCA2_OFF_PISCES``) or |
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| 278 | a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` |
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| 279 | (and adaptation of ``./src/TOP/MY_TRC`` routines). |
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[10541] | 280 | |
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| 281 | In addition, the offline module (OFF) allows for the provision of further fields: |
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| 282 | |
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[10605] | 283 | 1. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and |
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| 284 | by including an input datastream similarly to the following: |
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[10541] | 285 | |
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[11734] | 286 | .. code-block:: fortran |
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[10541] | 287 | |
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[11734] | 288 | sn_rnf = 'dyna_grid_T', 120, 'sorunoff' , .true., .true., 'yearly', '', '', '' |
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[10541] | 289 | |
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[11734] | 290 | 2. **VVL dynamical fields**, in the case input data were produced by a dyamical core using |
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| 291 | variable volume (``ln_linssh = .false.``) |
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| 292 | it is necessary to provide also diverce and E-P at before timestep by |
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[10605] | 293 | including input datastreams similarly to the following |
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[10541] | 294 | |
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[11734] | 295 | .. code-block:: fortran |
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[10541] | 296 | |
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[11734] | 297 | sn_div = 'dyna_grid_T', 120, 'e3t' , .true., .true., 'yearly', '', '', '' |
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| 298 | sn_empb = 'dyna_grid_T', 120, 'sowaflupb', .true., .true., 'yearly', '', '', '' |
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[10541] | 299 | |
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[10605] | 300 | More details can be found by inspecting the offline data manager in |
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[11734] | 301 | the routine :file:`./src/OFF/dtadyn.F90`. |
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[10541] | 302 | |
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[10186] | 303 | ORCA2_SAS_ICE |
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| 304 | ------------- |
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| 305 | |
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[11734] | 306 | | ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and |
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| 307 | it relies on ORCA2 global ocean configuration (see ORCA2_ICE_PISCES_ for general description). |
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| 308 | | The standalone surface module allows surface elements such as sea-ice, iceberg drift, and |
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| 309 | surface fluxes to be run using prescribed model state fields. |
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| 310 | It can profitably be used to compare different bulk formulae or |
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| 311 | adjust the parameters of a given bulk formula. |
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[10186] | 312 | |
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[11734] | 313 | More informations about SAS can be found in :doc:`NEMO manual <cite>`. |
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[10186] | 314 | |
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| 315 | SPITZ12 |
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| 316 | ------- |
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| 317 | |
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[10605] | 318 | ``SPITZ12`` is a regional configuration around the Svalbard archipelago |
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| 319 | at 1/12° of horizontal resolution and 75 vertical levels. |
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[11734] | 320 | See :gmd:`Rousset et al. (2015) <8/2991/2015>` for more details. |
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[10186] | 321 | |
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[10605] | 322 | This configuration references to year 2002, |
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| 323 | with atmospheric forcing provided every 2 hours using NCAR bulk formulae, |
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| 324 | while lateral boundary conditions for dynamical fields have 3 days time frequency. |
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[10186] | 325 | |
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[11723] | 326 | .. rubric:: References |
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[10186] | 327 | |
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[11723] | 328 | .. bibliography:: cfgs.bib |
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[10605] | 329 | :all: |
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| 330 | :style: unsrt |
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| 331 | :labelprefix: C |
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