1 | ******************************** |
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2 | Run the Reference configurations |
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3 | ******************************** |
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4 | |
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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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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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12 | |
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13 | .. contents:: |
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14 | :local: |
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15 | :depth: 1 |
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16 | |
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17 | .. attention:: |
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18 | |
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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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31 | To compile the ORCA2_ICE_PISCES_ reference configuration using :file:`makenemo`, |
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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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34 | |
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35 | .. code-block:: console |
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36 | |
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37 | $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my_arch' -j '4' |
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38 | |
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39 | A new ``EXP00`` folder will be created within the selected reference configurations, |
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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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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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46 | |
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47 | List of Configurations |
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48 | ====================== |
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49 | |
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50 | All forcing files listed below in the table are available from |DOI data|_ |
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51 | |
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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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72 | |
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73 | .. admonition:: Legend for component combination |
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74 | |
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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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77 | AGRIF_DEMO |
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78 | ---------- |
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79 | |
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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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83 | |
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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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88 | |
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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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93 | The 1:1 grid can be used alone as a benchmark to check that |
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94 | the model solution is not corrupted by grid exchanges. |
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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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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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99 | |
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100 | AMM12 |
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101 | ----- |
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102 | |
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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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106 | |
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107 | .. image:: _static/AMM_domain.png |
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108 | :align: center |
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109 | |
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110 | This configuration allows to tests several features of NEMO specifically addressed to the shelf seas. |
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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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113 | Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``. |
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114 | |
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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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117 | |
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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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120 | |
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121 | C1D_PAPA |
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122 | -------- |
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123 | |
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124 | .. figure:: _static/Papa2015.jpg |
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125 | :height: 225px |
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126 | :align: left |
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127 | |
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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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132 | |
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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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139 | Data provided with ``INPUTS_C1D_PAPA_v4.0.tar`` file account for: |
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140 | |
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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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147 | |
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148 | GYRE_BFM |
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149 | -------- |
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150 | |
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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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153 | |
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154 | GYRE_PISCES |
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155 | ----------- |
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156 | |
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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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160 | Analytical forcing for heat, freshwater and wind-stress fields are applied. |
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161 | |
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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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165 | |
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166 | .. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg |
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167 | :language: fortran |
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168 | :lines: 35-41 |
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169 | |
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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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172 | The specific code changes can be inspected in :file:`./src/OCE/USR`. |
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173 | |
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174 | .. rubric:: Running GYRE as a benchmark |
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175 | |
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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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180 | |
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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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190 | |
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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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198 | |
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199 | ORCA2_ICE_PISCES |
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200 | ---------------- |
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201 | |
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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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209 | |
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210 | This configuration uses the three components |
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211 | |
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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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215 | |
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216 | All components share the same grid. |
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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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219 | |
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220 | .. rubric:: Ocean Physics |
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221 | |
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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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242 | :time step: is 5760sec (1h36') so that there is 15 time steps in one day. |
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243 | |
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244 | ORCA2_OFF_PISCES |
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245 | ---------------- |
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246 | |
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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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249 | |
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250 | ORCA2_OFF_TRC |
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251 | ------------- |
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252 | |
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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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261 | |
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262 | Pre-calculated dynamical fields are provided to NEMO using |
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263 | the namelist ``&namdta_dyn`` in :file:`namelist_cfg`, |
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264 | in this case with a 5 days frequency (120 hours): |
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265 | |
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266 | .. literalinclude:: ../../namelists/namdta_dyn |
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267 | :language: fortran |
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268 | |
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269 | Input dynamical fields for this configuration (:file:`ORCA2_OFF_v4.0.tar`) comes from |
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270 | a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing. |
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271 | |
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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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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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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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285 | |
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286 | .. code-block:: fortran |
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287 | |
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288 | sn_rnf = 'dyna_grid_T', 120, 'sorunoff' , .true., .true., 'yearly', '', '', '' |
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289 | |
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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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293 | including input datastreams similarly to the following |
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294 | |
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295 | .. code-block:: fortran |
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296 | |
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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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299 | |
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300 | More details can be found by inspecting the offline data manager in |
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301 | the routine :file:`./src/OFF/dtadyn.F90`. |
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302 | |
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303 | ORCA2_SAS_ICE |
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304 | ------------- |
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305 | |
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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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312 | |
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313 | More informations about SAS can be found in :doc:`NEMO manual <cite>`. |
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314 | |
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315 | SPITZ12 |
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316 | ------- |
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317 | |
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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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320 | See :gmd:`Rousset et al. (2015) <8/2991/2015>` for more details. |
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321 | |
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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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325 | |
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326 | .. rubric:: References |
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327 | |
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328 | .. bibliography:: cfgs.bib |
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329 | :all: |
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330 | :style: unsrt |
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331 | :labelprefix: C |
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