1 | ***************************** |
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2 | Run a reference configuration |
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3 | ***************************** |
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4 | |
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5 | .. contents:: |
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6 | :local: |
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7 | :depth: 1 |
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8 | |
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9 | Official configurations |
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10 | ======================= |
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11 | |
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12 | | NEMO is distributed with some reference configurations allowing both the user to set up a first application and |
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13 | the developer to validate their developments. |
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14 | | :underline:`The NEMO System Team is in charge of these configurations`. |
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15 | |
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16 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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17 | | | OPA | SI3 | TOP | PISCES | AGRIF | Inputs | |
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18 | +======================+=====+=====+=====+========+=======+===============================+ |
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19 | | `AGRIF_DEMO`_ | X | X | | | X | - `AGRIF_DEMO_v4.0.tar`_ | |
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20 | | | | | | | | - `ORCA2_ICE_v4.0.tar`_ | |
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21 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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22 | | `AMM12`_ | X | | | | | `AMM12_v4.0.tar`_ | |
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23 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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24 | | `C1D_PAPA`_ | X | | | | | `INPUTS_C1D_PAPA_v4.0.tar`_ | |
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25 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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26 | | `GYRE_BFM`_ | X | | X | | | ``-`` | |
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27 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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28 | | `GYRE_PISCES`_ | X | | X | X | | ``-`` | |
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29 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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30 | | `ORCA2_ICE_PISCES`_ | X | X | X | X | | - `ORCA2_ICE_v4.0.tar`_ | |
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31 | | | | | | | | - `INPUTS_PISCES_v4.0.tar`_ | |
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32 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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33 | | `ORCA2_OFF_PISCES`_ | | | X | X | | - `INPUTS_PISCES_v4.0.tar`_ | |
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34 | | | | | | | | - `ORCA2_OFF_v4.0.tar`_ | |
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35 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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36 | | `ORCA2_OFF_TRC`_ | | | X | | | `ORCA2_OFF_v4.0.tar`_ | |
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37 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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38 | | `ORCA2_SAS_ICE`_ | | X | | | | - `ORCA2_ICE_v4.0.tar`_ | |
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39 | | | | | | | | - `INPUTS_SAS_v4.0.tar`_ | |
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40 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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41 | | `SPITZ12`_ | X | X | | | | `SPITZ12_v4.0.tar`_ | |
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42 | +----------------------+-----+-----+-----+--------+-------+-------------------------------+ |
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43 | |
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44 | AGRIF_DEMO |
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45 | ---------- |
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46 | |
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47 | .. image:: _static/AGRIF_DEMO.jpg |
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48 | |
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49 | ``AGRIF_DEMO`` is based on the ``ORCA2_LIM3_PISCES`` global 2° configuration but |
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50 | it includes 3 online nested grids that demonstrate the overall capabilities of AGRIF in a realistic context, |
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51 | including nesting sea ice models. |
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52 | |
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53 | The configuration includes a 1:1 grid in the Pacific and two successively nested grids with odd and |
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54 | even refinement ratios over the Arctic ocean. |
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55 | The finest grid spanning the whole Svalbard archipelago is of particular interest to check that |
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56 | sea ice coupling is done properly. |
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57 | The 1:1 grid, used alone, is used as a benchmark to check that the solution is not corrupted by grid exchanges. |
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58 | |
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59 | Note that since grids interact only at the baroclinic time level, |
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60 | numerically exact results can not be achieved in the 1:1 case. |
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61 | One has to switch to a fully explicit in place of a split explicit free surface scheme in order to |
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62 | retrieve perfect reproducibility. |
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63 | |
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64 | Corresponding ``AGRIF_FixedGrids.in`` file is given by:: |
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65 | |
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66 | 2 |
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67 | 42 82 49 91 1 1 1 |
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68 | 122 153 110 143 4 4 4 |
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69 | 0 |
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70 | 1 |
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71 | 38 80 71 111 3 3 3 |
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72 | 0 |
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73 | |
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74 | AMM12 |
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75 | ----- |
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76 | |
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77 | ``AMM12`` for *Atlantic Margin Model 12kms* is a `regional model`_ covering the Northwest European Shelf domain on |
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78 | a regular lat-lon grid at approximately 12km horizontal resolution. |
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79 | The key ``key_amm_12km`` is used to create the correct dimensions of the AMM domain. |
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80 | |
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81 | | This configuration tests several features of NEMO functionality specific to the shelf seas. |
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82 | | In particular, the AMM uses s-coordinates in the vertical rather than z-coordinates and is forced with |
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83 | tidal lateral boundary conditions using a flather boundary condition from the BDY module (``key_bdy``). |
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84 | |
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85 | The AMM configuration uses the GLS (``key_zdfgls``) turbulence scheme, |
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86 | the VVL non-linear free surface (``key_vvl``) and time-splitting (``key_dynspg_ts``). |
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87 | |
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88 | In addition to the tidal boundary condition, the model may also take open boundary conditions from |
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89 | a North Atlantic model. |
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90 | Boundaries may be completely ommited by removing the BDY key (key_bdy) in ``./cfgs/AMM12/cpp_AMM12_fcm``. |
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91 | |
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92 | Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run. |
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93 | The Baltic boundary is included within the river input file and is specified as a river source. |
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94 | Unlike ordinary river points the Baltic inputs also include salinity and temperature data. |
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95 | |
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96 | C1D_PAPA |
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97 | -------- |
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98 | |
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99 | ``C1D_PAPA`` is a 1D configuration (one water column called NEMO1D, activated with CPP key ``key_c1d``), |
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100 | located at the `PAPA station 145W-50N <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_. |
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101 | |
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102 | | NEMO1D is useful to test vertical physics in NEMO |
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103 | (turbulent closure scheme, solar penetration, interaction ocean/atmosphere.,...) |
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104 | | Size of the horizontal domain is 3x3 grid points. |
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105 | |
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106 | This reference configuration uses a 75 vertical levels grid (1m at the surface), |
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107 | the GLS (key_zdfgls) turbulence scheme with K-epsilon closure and the CORE BULK formulae. |
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108 | The atmospheric forcing comes from ECMWF operational analysis with a modification of the long and short waves flux. |
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109 | This set has been rescaled at a frequency of 1h. 1 year is simulated in outputs, |
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110 | see below (June,15 2010 to June,14 2011) |
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111 | |
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112 | `Reffray 2015`_ describes some tests on vertical physic using this configuration. |
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113 | |
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114 | The inputs tar file includes: |
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115 | |
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116 | - forcing files covering the years 2010 and 2011 (``forcing_PAPASTATION_1h_y201*.nc``) |
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117 | - initialization file for June,15 2010 deduced from observed data and Levitus 2009 climatology |
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118 | (``init_PAPASTATION_m06d15.nc``) |
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119 | - surface chlorophyll file (``chlorophyll_PAPASTATION.nc``) deduced from Seawifs data. |
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120 | |
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121 | GYRE_BFM |
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122 | -------- |
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123 | |
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124 | ``GYRE_BFM`` is the same configuration as `GYRE_PISCES`_, except that PISCES is replaced by |
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125 | BFM biogeochemichal model in coupled mode. |
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126 | |
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127 | GYRE_PISCES |
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128 | ----------- |
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129 | |
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130 | | Idealized configuration representing double gyres in the North hemisphere, Beta-plane with |
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131 | a regular grid spacing at 1° horizontal resolution (and possible use as a benchmark by |
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132 | easily inscreasing grid size), 101 vertical levels, forced with analytical heat, freshwater and |
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133 | wind-stress fields. |
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134 | | This configuration is coupled to `PISCES biogeochemical model`_. |
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135 | |
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136 | Running GYRE as a benchmark |
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137 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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138 | |
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139 | This simple configuration can be used as a benchmark since it is easy to increase resolution |
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140 | (and in this case no physical meaning of outputs): |
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141 | |
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142 | 1. Choose the grid size |
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143 | |
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144 | In ``./cfgs/GYRE/EXP00``, edit your ``namelist_cfg`` file to change the ``jp_cfg``, ``jpi``, ``jpj``, |
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145 | ``jpk`` variables in &namcfg: |
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146 | |
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147 | +------------+---------+---------+---------+------------------+---------------+ |
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148 | | ``jp_cfg`` | ``jpi`` | ``jpj`` | ``jpk`` | Number of points | Equivalent to | |
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149 | +============+=========+=========+=========+==================+===============+ |
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150 | | 1 | 30 | 20 | 101 | 60600 | GYRE 1° | |
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151 | +------------+---------+---------+---------+------------------+---------------+ |
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152 | | 25 | 750 | 500 | 101 | 37875000 | ORCA 1/2° | |
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153 | +------------+---------+---------+---------+------------------+---------------+ |
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154 | | 50 | 1500 | 1000 | 101 | 151500000 | ORCA 1/4° | |
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155 | +------------+---------+---------+---------+------------------+---------------+ |
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156 | | 150 | 4500 | 3000 | 101 | 1363500000 | ORCA 1/12° | |
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157 | +------------+---------+---------+---------+------------------+---------------+ |
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158 | | 200 | 6000 | 4000 | 101 | 2424000000 | ORCA 1/16° | |
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159 | +------------+---------+---------+---------+------------------+---------------+ |
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160 | |
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161 | 2. 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 |
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162 | |
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163 | .. code-block:: fortran |
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164 | |
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165 | nn_bench = 1 ! Bench mode (1/0): CAUTION use zero except for bench |
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166 | |
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167 | 3. 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`) |
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168 | |
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169 | .. code-block:: fortran |
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170 | |
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171 | rn_rdt = 1200. ! time step for the dynamics |
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172 | |
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173 | 4. Optional, in order to increase the number of MPI communication for benchmark purposes: |
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174 | you can change the number of sub-timesteps computed in the time-splitting scheme each iteration. |
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175 | First change the list of active CPP keys for your experiment, |
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176 | in `cfgs/"your configuration name"/cpp_"your configuration name".fcm`: |
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177 | replace ``key_dynspg_flt by key_dynspg_ts`` and recompile/create your executable again |
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178 | |
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179 | .. code-block:: fortran |
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180 | |
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181 | makenemo [...] add_key 'key_dynspg_ts' del_key 'key_dynspg_flt' |
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182 | |
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183 | In your ``namelist_cfg`` file, edit the &namsplit namelist by adding the following line: |
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184 | |
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185 | .. code-block:: fortran |
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186 | |
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187 | nn_baro = 30 ! Number of iterations of barotropic mode/ |
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188 | |
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189 | ``nn_baro = 30`` is a kind of minimum (we usually use 30 to 60). |
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190 | So than increasing the ``nn_baro`` value will increase the number of MPI communications. |
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191 | |
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192 | The GYRE CPP keys, namelists and scripts can be explored in the ``GYRE`` configuration directory |
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193 | (``./cfgs/GYRE`` and ``./cfgs/GYRE/EXP00``). |
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194 | |
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195 | Find monthly mean outputs of 1 year run here: |
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196 | http://prodn.idris.fr/thredds/catalog/ipsl_public/reee451/NEMO_OUT/GYRE/catalog.html |
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197 | |
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198 | ORCA2_ICE_PISCES |
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199 | ---------------- |
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200 | |
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201 | ORCA is the generic name given to global ocean configurations. |
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202 | Its specificity lies on the horizontal curvilinear mesh used to overcome the North Pole singularity found for |
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203 | geographical meshes. |
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204 | SI3 (Sea Ice Integrated Initiative) is a thermodynamic-dynamic sea ice model specifically designed for |
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205 | climate studies. |
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206 | A brief description of the model is given here. |
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207 | |
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208 | :underline:`Space-time domain` |
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209 | |
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210 | The horizontal resolution available through the standard configuration is ORCA2. |
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211 | It is based on a 2 degrees Mercator mesh, (i.e. variation of meridian scale factor as cosinus of the latitude). |
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212 | In the northern hemisphere the mesh has two poles so that the ratio of anisotropy is nearly one everywhere. |
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213 | The mean grid spacing is about 2/3 of the nominal value: for example it is 1.3 degrees for ORCA2. |
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214 | Other resolutions (ORCA4, ORCA05 and ORCA025) are running or under development within specific projects. |
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215 | In the coarse resolution version (i.e. ORCA2 and ORCA4) the meridional grid spacing is increased near |
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216 | the equator to improve the equatorial dynamics. |
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217 | Figures in pdf format of mesh and bathymetry can be found and downloaded here. |
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218 | The sea-ice model runs on the same grid. |
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219 | |
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220 | The vertical domain spreads from the surface to a depth of 5000m. |
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221 | There are 31 levels, with 10 levels in the top 100m. |
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222 | The vertical mesh is deduced from a mathematical function of z ([[AttachmentNum(1)]]). |
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223 | The ocean surface corresponds to the w-level k=1, and the ocean bottom to the w-level k=31. |
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224 | The last T-level (k=31) is thus always in the ground.The depths of the vertical levels and |
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225 | the associated scale factors can be viewed. |
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226 | Higher vertical resolution is used in ORCA025 and ORCA12 (see `DRAKKAR project <http://www.drakkar-ocean.eu>`_). |
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227 | |
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228 | The time step depends on the resolution. It is 1h36' for ORCA2 so that there is 15 time steps in one day. |
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229 | |
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230 | :underline:`Ocean Physics (for ORCA2)` |
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231 | |
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232 | - horizontal diffusion on momentum: the eddy viscosity coefficient depends on the geographical position. |
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233 | It is taken as 40000 $m^2/s$, reduced in the equator regions (2000 $m^2/s$) excepted near the western boundaries. |
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234 | - isopycnal diffusion on tracers: the diffusion acts along the isopycnal surfaces (neutral surface) with |
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235 | a eddy diffusivity coefficient of 2000 $m^2/s$. |
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236 | - Eddy induced velocity parametrization with a coefficient that depends on the growth rate of |
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237 | baroclinic instabilities (it usually varies from 15 $m^2/s$ to 3000 $m^2/s$). |
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238 | - lateral boundary conditions : zero fluxes of heat and salt and no-slip conditions are applied through |
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239 | lateral solid boundaries. |
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240 | - bottom boundary condition : zero fluxes of heat and salt are applied through the ocean bottom. |
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241 | The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes. |
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242 | A linear friction is applied on momentum. |
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243 | - convection: the vertical eddy viscosity and diffusivity coefficients are increased to 1 $m^2/s$ in case of |
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244 | static instability. |
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245 | - forcings: the ocean receives heat, freshwater, and momentum fluxes from the atmosphere and/or the sea-ice. |
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246 | The solar radiation penetrates the top meters of the ocean. |
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247 | The downward irradiance I(z) is formulated with two extinction coefficients [Paulson and Simpson, 1977], |
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248 | whose values correspond to a Type I water in Jerlov's classification (i.e the most transparent water) |
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249 | |
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250 | ORCA2_ICE_PISCES is a reference configuration with the following characteristics: |
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251 | |
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252 | - global ocean configuration |
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253 | - based on a tri-polar ORCA grid, with a 2° horizontal resolution |
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254 | - 31 vertical levels |
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255 | - forced with climatological surface fields |
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256 | - coupled to the sea-ice model SI3. |
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257 | - coupled to TOP passive tracer transport module and `PISCES biogeochemical model`_. |
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258 | |
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259 | :underline:`AGRIF demonstrator` |
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260 | |
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261 | | From the ``ORCA2_ICE_PISCES`` configuration, a demonstrator using AGRIF nesting can be activated. |
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262 | It includes the global ``ORCA2_ICE_PISCES`` configuration and a nested grid in the Agulhas region. |
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263 | | To set up this configuration, after extracting NEMO: |
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264 | |
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265 | - Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated: |
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266 | |
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267 | .. code-block:: console |
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268 | |
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269 | $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif' |
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270 | |
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271 | - Using the ``ORCA2_ICE_PISCES`` input files and namelist, AGRIF test configuration is ready to run |
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272 | |
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273 | :underline:`On-The-Fly Interpolation` |
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274 | |
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275 | | NEMO allows to use the interpolation on the fly option allowing to interpolate input data during the run. |
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276 | If you want to use this option you need files giving informations on weights, which have been created. |
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277 | | You can find at http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/WEIGHTS/catalog.html |
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278 | 2 weights files `bil_weights` for scalar field (bilinear interpolation) and `bic_weights` for |
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279 | vector field (bicubic interpolation). |
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280 | | The data files used are `COREII forcing <http://data1.gdfl.noaa.gov/nomads/forms/mom4/COREv2>`_ extrapolated on |
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281 | continents, ready to be used for on the fly option: |
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282 | `COREII`_ forcing files extrapolated on continents |
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283 | |
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284 | ORCA2_OFF_PISCES |
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285 | ---------------- |
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286 | |
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287 | ``ORCA2_OFF_PISCES`` uses the ORCA2 configuration in which the `PISCES biogeochemical model`_ has been activated in |
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288 | standalone using the dynamical fields that are pre calculated. |
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289 | |
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290 | See `ORCA2_ICE_PISCES`_ for general description of ORCA2. |
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291 | |
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292 | The input files for PISCES are needed, in addition the dynamical fields are used as input. |
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293 | They are coming from a 2000 years of an ORCA2_LIM climatological run using ERA40 atmospheric forcing. |
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294 | |
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295 | ORCA2_OFF_TRC |
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296 | ------------- |
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297 | |
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298 | ``ORCA2_OFF_TRC`` uses the ORCA2_LIM configuration in which the tracer passive transport module TOP has been |
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299 | activated in standalone using the dynamical fields that are pre calculated. |
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300 | |
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301 | See `ORCA2_ICE_PISCES`_ for general description of ORCA2. |
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302 | |
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303 | In ``namelist_top_cfg``, different passive tracers can be activated ( cfc11, cfc12, sf6, c14, age ) or my-trc, |
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304 | a user-defined tracer. |
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305 | |
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306 | The dynamical fields are used as input, they are coming from a 2000 years of an ORCA2_LIM climatological run using |
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307 | ERA40 atmospheric forcing. |
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308 | |
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309 | ORCA2_SAS_ICE |
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310 | ------------- |
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311 | |
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312 | ``ORCA2_SAS_ICE`` is a demonstrator of the SAS ( Stand-alone Surface module ) based on ORCA2_LIM configuration. |
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313 | |
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314 | The standalone surface module allows surface elements such as sea-ice, iceberg drift and surface fluxes to |
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315 | be run using prescribed model state fields. |
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316 | For example, it can be used to inter-compare different bulk formulae or adjust the parameters of |
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317 | a given bulk formula |
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318 | |
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319 | See `ORCA2_ICE_PISCES`_ for general description of ORCA2. |
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320 | |
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321 | Same input files as `ORCA2_ICE_PISCES`_ are needed plus fields from a previous ORCA2_LIM run. |
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322 | |
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323 | More informations on input and configuration files in `NEMO manual`_. |
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324 | |
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325 | SPITZ12 |
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326 | ------- |
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327 | |
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328 | ``SPITZ12`` |
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329 | |
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330 | Unsupported configurations |
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331 | ========================== |
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332 | |
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333 | Other configurations are developed and used by some projects with "NEMO inside", |
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334 | these projects are welcome to publicize it here: http://www.nemo-ocean.eu/projects/add-project |
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335 | |
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336 | :underline:`Obviously these "projects configurations" are not under the NEMO System Team's responsibility`. |
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337 | |
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338 | .. _regional model: http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128 |
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339 | .. _AMM12_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar |
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340 | .. _PISCES biogeochemical model: http://www.geosci-model-dev.net/8/2465/2015 |
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341 | .. _INPUTS_PISCES_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_PISCES_v4.0.tar |
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342 | .. _ORCA2_OFF_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_OFF_v4.0.tar |
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343 | .. _ORCA2_ICE_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar |
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344 | .. _INPUTS_SAS_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar |
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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 |
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346 | .. _Reffray 2015: http://www.geosci-model-dev.net/8/69/2015 |
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347 | .. _COREII: http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html |
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348 | .. _SPITZ12_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar |
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349 | .. _AGRIF_DEMO_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar |
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