1 | ****************************** |
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2 | Setting up a new configuration |
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3 | ****************************** |
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4 | |
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5 | .. contents:: |
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6 | |
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7 | Starting from an existing configuration |
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8 | ======================================= |
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9 | |
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10 | There are three options to build a new configuration from an existing one: |
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11 | |
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12 | Option 1: Duplicate an existing configuration |
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13 | --------------------------------------------- |
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14 | |
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15 | The NEMO so-called Reference Configurations cover a number of major features for NEMO setup |
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16 | (global, regional, 1D, using embeded zoom with AGRIF...) |
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17 | |
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18 | One can create a new configuration by duplicating one of the reference configurations |
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19 | (``ORCA2_LIM3_PISCES`` in the following example) |
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20 | |
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21 | .. code-block:: sh |
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22 | |
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23 | makenemo –n 'ORCA2_LIM3_PISCES_MINE' -r 'ORCA2_LIM3_PISCES' |
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24 | |
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25 | Option 2: Duplicate with differences |
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26 | ------------------------------------ |
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27 | |
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28 | Create and compile a new configuration based on a reference configuration |
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29 | (``ORCA2_LIM3_PISCES`` in the following example) but with different pre-processor options. |
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30 | For this either add ``add_key`` or ``del_key`` keys as required; e.g. |
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31 | |
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32 | .. code-block:: sh |
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33 | |
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34 | makenemo –n 'ORCA2_LIM3_PISCES_MINE' -r 'ORCA2_LIM3_PISCES' del_key 'key_iomput' add_key 'key_xios' |
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35 | |
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36 | Option 3: Use the SIREN tools to subset an existing model |
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37 | --------------------------------------------------------- |
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38 | |
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39 | Define a regional configuration which is a sub- or super-set of an existing configuration. |
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40 | |
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41 | This last option employs the SIREN software tools that are included in the standard distribution. |
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42 | The software is written in Fortran 95 and available in the ``./tools/SIREN`` directory. |
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43 | SIREN allows you to create your own regional configuration embedded in a wider one. |
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44 | |
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45 | SIREN is a set of programs to create all the input files you need to run a NEMO regional configuration. |
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46 | As a basic demonstrator, a set of GLORYS files (GLObal ReanalYSis on the ORCA025 grid), |
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47 | as well as examples of namelists are available `here`_. |
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48 | |
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49 | `SIREN documentation`_ |
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50 | |
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51 | Any questions or comments regarding the use of SIREN should be posted in `the corresponding forum`_. |
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52 | |
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53 | Creating a completely new configuration |
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54 | ======================================= |
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55 | |
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56 | From NEMO version 4.0 there are two ways to build configurations from scratch. |
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57 | The appropriate method to use depends largely on the target configuration. |
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58 | Method 1 is for more complex/realistic global or regional configurations and |
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59 | method 2 is intended for simpler, idealised configurations whose |
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60 | domains and characteristics can be described in simple geometries and formulae. |
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61 | |
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62 | Option 1: Create and use a domain configuration file |
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63 | ---------------------------------------------------- |
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64 | |
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65 | This method is used by each of the reference configurations, |
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66 | so that downloading their input files linked to their description can help. |
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67 | Although starting from scratch it is advisable to create the directory structure to house your new configuration by |
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68 | duplicating the closest reference configuration to your target application. |
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69 | For example, if your application requires both ocean ice and passive tracers, |
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70 | then use the ``ORCA2_LIM3_PISCES`` as template, |
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71 | and execute following command to build your ``MY_NEW_CONFIG`` configuration: |
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72 | |
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73 | .. code-block:: sh |
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74 | |
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75 | makenemo –n 'MY_NEW_CONFIG' -r 'ORCA2_LIM3_PISCES' |
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76 | |
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77 | where ``MY_NEW_CONFIG`` can be substituted with a suitably descriptive name for your new configuration. |
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78 | |
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79 | The purpose of this step is simply to create and populate the appropriate ``WORK``, ``MY_SRC`` and |
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80 | ``EXP00`` subdirectories for your new configuration. |
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81 | Other choices for the base reference configuration might be |
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82 | |
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83 | - ``GYRE`` - If your target application is ocean-only |
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84 | - ``AMM12`` - If your target application is regional with open boundaries |
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85 | |
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86 | All the domain information for your new configuration will be contained within |
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87 | a netcdf file called ``domain_cfg.nc`` which you will need to create and |
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88 | place in the ``./cfgs/MY_NEW_CONFIG/EXP00`` sub-directory. |
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89 | Firstly though, ensure that your configuration is set to use such a file by checking that |
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90 | |
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91 | .. code-block:: fortran |
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92 | |
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93 | ln_read_cfg = .true. |
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94 | |
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95 | in ``./cfgs/MY_NEW_CONFIG/EXP00/namelist_cfg`` |
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96 | |
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97 | Create the domain_cfg.nc file which must contain the following fields |
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98 | |
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99 | .. code-block:: c++ |
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100 | |
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101 | int ORCA, ORCA_index /* configuration name, configuration resolution */ |
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102 | int jpiglo, jpjglo, jpkglo /* global domain sizes */ |
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103 | int jperio /* lateral global domain b.c. */ |
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104 | int ln_zco, ln_zps, ln_sco /* flags for z-coord, z-coord with partial steps and s-coord */ |
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105 | int ln_isfcav /* flag for ice shelf cavities */ |
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106 | double glamt, glamu, glamv, glamf /* geographic position */ |
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107 | double gphit, gphiu, gphiv, gphif /* geographic position */ |
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108 | double iff, ff_f, ff_t /* Coriolis parameter (if not on the sphere) */ |
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109 | double e1t, e1u, e1v, e1f /* horizontal scale factors */ |
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110 | double e2t, e2u, e2v, e2f /* horizontal scale factors */ |
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111 | double ie1e2u_v, e1e2u, e1e2v /* U and V surfaces (if grid size reduction in some straits) */ |
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112 | double e3t_1d, e3w_1d /* reference vertical scale factors at T and W points */ |
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113 | double e3t_0, e3u_0, e3v_0, e3f_0, e3w_0 /* vertical scale factors 3D coordinate at T,U,V,F and W points */ |
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114 | double e3uw_0, e3vw_0 /* vertical scale factors 3D coordinate at UW and VW points */ |
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115 | int bottom_level, top_level /* last wet T-points, 1st wet T-points (for ice shelf cavities) */ |
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116 | |
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117 | There are two options for creating a domain_cfg.nc file: |
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118 | |
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119 | - Users can use tools of their own choice to build a ``domain_cfg.nc`` with all mandatory fields. |
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120 | - Users can adapt and apply the supplied tool available in ``./tools/DOMAINcfg``. |
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121 | This tool is based on code extracted from NEMO version 3.6 and will allow similar choices for |
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122 | the horizontal and vertical grids that were available internally to that version. |
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123 | See ``./tools/DOMAINcfg/README`` for details. |
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124 | |
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125 | Option 2: Adapt the usr_def configuration module of NEMO for you own purposes |
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126 | ----------------------------------------------------------------------------- |
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127 | |
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128 | This method is intended for configuring easily simple/idealised configurations which |
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129 | are often used as demonstrators or for process evaluation and comparison. |
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130 | This method can be used whenever the domain geometry has a simple mathematical description and |
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131 | the ocean initial state and boundary forcing is described analytically. |
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132 | As a start, consider the case of starting a completely new ocean-only test case based on |
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133 | the ``LOCK_EXCHANGE`` example. |
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134 | [Note: we probably need an even more basic example than this with only one namelist and |
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135 | minimal changes to the usrdef modules] |
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136 | |
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137 | Firstly, construct the directory structure, starting in the ``cfgs`` directory: |
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138 | |
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139 | .. code-block:: sh |
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140 | |
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141 | ./makenemo -n 'MY_NEW_TEST' -t 'LOCK_EXCHANGE' |
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142 | |
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143 | where the ``-t`` option has been used to locate the new configuration in the ``tests`` subdirectory |
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144 | (it is recommended practice to keep full configurations and idealised cases clearly distinguishable). |
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145 | This command will have created (amongst others) the following files and directories:: |
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146 | |
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147 | ./tests/MY_NEW_TEST: |
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148 | BLD MY_SRC cpp_MY_NEW_TEST.fcm |
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149 | EXP00 WORK |
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150 | # |
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151 | ./tests/MY_NEW_TEST/EXP00: |
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152 | context_nemo.xml domain_def_nemo.xml |
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153 | field_def_nemo-opa.xml file_def_nemo-opa.xml |
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154 | iodef.xml |
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155 | namelist_cfg |
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156 | namelist_ref |
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157 | # |
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158 | ./tests/MY_NEW_TEST/MY_SRC: |
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159 | usrdef_hgr.F90 usrdef_nam.F90 usrdef_zgr.F90 |
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160 | usrdef_istate.F90 usrdef_sbc.F90 zdfini.F90 |
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161 | |
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162 | The key to setting up an idealised configuration lies in adapting a small set of short Fortran 90 modules which |
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163 | should be dropped into the ``MY_SRC`` directory. |
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164 | Here the ``LOCK_EXCHANGE`` example is using 5 such routines but the full set that is available in |
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165 | the ``src/OCE/USR`` directory is:: |
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166 | |
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167 | ./src/OCE/USR: |
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168 | usrdef_closea.F90 usrdef_istate.F90 usrdef_zgr.F90 |
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169 | usrdef_fmask.F90 usrdef_nam.F90 |
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170 | usrdef_hgr.F90 usrdef_sbc.F90 |
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171 | |
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172 | Before discussing these in more detail it is worth noting the various namelist controls that |
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173 | engage the different user-defined aspects. |
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174 | These controls are set using two new logical switches or are implied by the settings of existing ones. |
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175 | For example, the mandatory requirement for an idealised configuration is to provide routines which |
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176 | define the horizontal and vertical domains. |
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177 | Templates for these are provided in the ``usrdef_hgr.F90`` and ``usrdef_zgr.F90`` modules. |
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178 | The application of these modules is activated whenever: |
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179 | |
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180 | .. code-block:: fortran |
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181 | |
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182 | ln_read_cfg = .false. |
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183 | |
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184 | in any configuration's ``namelist_cfg`` file. |
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185 | This setting also activates the reading of an optional ``nam_usrdef`` namelist which can be used to |
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186 | supply configuration specific settings. |
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187 | These need to be declared and read in the ``usrdef_nam.F90`` module. |
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188 | |
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189 | Another explicit control is available in the ``namsbc`` namelist which activates the use of analytical forcing. |
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190 | With |
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191 | |
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192 | .. code-block:: fortran |
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193 | |
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194 | ln_usr = .true. |
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195 | |
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196 | Other usrdef modules are activated by less explicit means. |
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197 | For example, code in ``usrdef_istate.F90`` is used to define initial temperature and salinity fields if |
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198 | |
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199 | .. code-block:: fortran |
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200 | |
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201 | ln_tsd_init = .false. |
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202 | |
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203 | in the ``namtsd`` namelist. |
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204 | The remaining modules, namely:: |
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205 | |
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206 | usrdef_closea.F90 usrdef_fmask.F90 |
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207 | |
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208 | are specific to ORCA configurations and set local variations of some specific fields for |
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209 | the various resolutions of the global models. |
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210 | They do not need to be considered here in the context of idealised cases but it is worth noting that all |
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211 | configuration specific code has now been isolated in the usrdef modules. |
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212 | In the case of these last two modules, they are activated only if an ORCA configuration is detected. |
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213 | Currently this requires a specific integer variable named ``ORCA`` to be set in a ``domain_cfg.nc`` file. |
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214 | [Note: this would be less confusing if the cn_cfg string is read directly as a character attribue from |
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215 | the ``domain_cfg.nc`` ] |
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216 | |
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217 | So, in most cases, the set up of idealised model configurations can be completed by |
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218 | copying the template routines from ``./src/OCE/USR`` into |
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219 | your new ``./cfgs/MY_NEW_TEST/MY_SRC`` directory and editing the appropriate modules as needed. |
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220 | The default set are those used for the GYRE reference configuration. |
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221 | The contents of ``MY_SRC`` directories from other idealised configurations may provide more convenient templates if |
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222 | they share common characteristics with your target application. |
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223 | |
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224 | Whatever the starting point it should not require too many changes or additional lines of code to |
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225 | produce routines in ``./src/OCE/USR`` that define analytically the domain, |
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226 | the initial state and the surface boundary conditions for your new configuration. |
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227 | |
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228 | To summarize, the base set of modules is: |
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229 | |
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230 | - ``usrdef_hgr.F90`` : define horizontal grid |
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231 | - ``usrdef_zgr.F90`` : define vertical grid |
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232 | - ``usrdef_sbc.F90`` : provides at each time-step the surface boundary condition, i.e. the momentum, heat and freshwater fluxes |
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233 | - ``usrdef_istate.F90``: defines initialization of the dynamics and tracers |
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234 | - ``usrdef_nam.F90`` : configuration-specific namelist processing to set any associated run-time parameters |
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235 | |
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236 | with two specialised ORCA modules |
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237 | (not related to idealised configurations but used to isolate configuration specific code that is used in |
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238 | ORCA2 reference configurations and established global configurations using the ORCA tripolar grid): |
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239 | |
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240 | - ``usrdef_fmask.F90`` : only used in ORCA CONFIGURATIONS for alteration of f-point land/ocean mask in some straits |
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241 | - ``usrdef_closea.F90``: only used in ORCA CONFIGURATIONS for specific treatments associated with closed seas |
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242 | |
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243 | From version 4.0, the NEMO release includes a ``tests`` subdirectory containing available and |
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244 | up to date test cases build by the community. |
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245 | These will not be fully supported as is NEMO reference but should provide a source of raw material. |
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246 | |
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247 | .. _here: http://prodn.idris.fr/thredds/catalog/ipsl_public/rron463/catalog.html?dataset=DatasetScanipsl_public/rron463/INPUT_SIREN.tar |
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248 | .. _the corresponding forum: http://forge.ipsl.jussieu.fr/nemo/discussion/forum/2 |
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249 | .. _SIREN documentation: http://forge.ipsl.jussieu.fr/nemo/doxygen/index.html |
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