[11743] | 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 | .. todo:: |
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| 6 | |
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| 7 | |
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| 8 | |
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| 9 | .. contents:: |
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| 10 | :local: |
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| 11 | |
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| 12 | Starting from an existing configuration |
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| 13 | ======================================= |
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| 14 | |
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| 15 | There are three options to build a new configuration from an existing one. |
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| 16 | |
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| 17 | Option 1: Duplicate an existing configuration |
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| 18 | --------------------------------------------- |
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| 19 | |
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| 20 | The NEMO so-called Reference Configurations cover a number of major features for NEMO setup |
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| 21 | (global, regional, 1D, using embedded zoom with AGRIF...) |
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| 22 | |
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| 23 | One can create a new configuration by duplicating one of the reference configurations |
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| 24 | (``ORCA2_ICE_PISCES`` in the following example) |
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| 25 | |
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| 26 | .. code-block:: console |
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| 27 | |
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| 28 | $ ./makenemo –n 'ORCA2_ICE_PISCES_MINE' -r 'ORCA2_ICE_PISCES' -m 'my_arch' |
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| 29 | |
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| 30 | Option 2: Duplicate with differences |
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| 31 | ------------------------------------ |
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| 32 | |
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| 33 | Create and compile a new configuration based on a reference configuration |
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| 34 | (``ORCA2_ICE_PISCES`` in the following example) but with different pre-processor options. |
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| 35 | For this either add ``add_key`` or ``del_key`` keys as required; e.g. |
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| 36 | |
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| 37 | .. code-block:: console |
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| 38 | |
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[14239] | 39 | $ ./makenemo –n 'ORCA2_ICE_PISCES_MINE' -r 'ORCA2_ICE_PISCES' -m 'my_arch' del_key 'key_xios' add_key 'key_diahth' |
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[11743] | 40 | |
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| 41 | Option 3: Use the SIREN tools to subset an existing model |
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| 42 | --------------------------------------------------------- |
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| 43 | |
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| 44 | Define a regional configuration which is a {sub,super}-set of an existing configuration. |
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| 45 | |
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| 46 | This last option employs the SIREN software tools that are included in the standard distribution. |
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| 47 | The software is written in Fortran 95 and available in the :file:`./tools/SIREN` directory. |
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| 48 | SIREN allows you to create your own regional configuration embedded in a wider one. |
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| 49 | |
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| 50 | SIREN is a set of programs to create all the input files you need to |
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| 51 | run a NEMO regional configuration. |
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| 52 | |
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| 53 | :Demo: Set of GLORYS files (GLObal ReanalYSis on the ORCA025 grid), |
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| 54 | as well as examples of namelists are available `here`_. |
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| 55 | :Doc: :forge:`chrome/site/doc/SIREN/html/index.html` |
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| 56 | :Support: Any questions or comments regarding the use of SIREN should be posted in |
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| 57 | :forge:`the corresponding forum <discussion/forum/2>`. |
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| 58 | |
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| 59 | .. _here: https://prodn.idris.fr/thredds/catalog/ipsl_public/rron463/catalog.html |
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| 60 | |
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[14446] | 61 | Option 4: Use the nesting tools to create embedded zooms or regional configurations from an existing grid |
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| 62 | --------------------------------------------------------------------------------------------------------- |
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| 63 | (see :download:`NESTING README <../../../tools/NESTING/README>`). |
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| 64 | |
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| 65 | |
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[11743] | 66 | Creating a completely new configuration |
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| 67 | ======================================= |
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| 68 | |
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| 69 | From NEMO version 4.0 there are two ways to build configurations from scratch. |
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| 70 | The appropriate method to use depends largely on the target configuration. |
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| 71 | Method 1 is for more complex/realistic global or regional configurations and |
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| 72 | method 2 is intended for simpler, idealised configurations whose |
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| 73 | domains and characteristics can be described in simple geometries and formulae. |
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| 74 | |
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| 75 | Option 1: Create and use a domain configuration file |
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| 76 | ---------------------------------------------------- |
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| 77 | |
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| 78 | This method is used by each of the reference configurations, |
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| 79 | so that downloading their input files linked to their description can help. |
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| 80 | Although starting from scratch, |
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| 81 | it is advisable to create the directory structure to house your new configuration by |
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| 82 | duplicating the closest reference configuration to your target application. |
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| 83 | For example, if your application requires both ocean ice and passive tracers, |
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| 84 | then use the ``ORCA2_ICE_PISCES`` as template, |
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| 85 | and execute following command to build your ``MY_NEW_CONFIG`` configuration: |
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| 86 | |
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| 87 | .. code-block:: sh |
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| 88 | |
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| 89 | $ ./makenemo –n 'MY_NEW_CONFIG' -r 'ORCA2_ICE_PISCES' -m 'my_arch' |
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| 90 | |
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| 91 | where ``MY_NEW_CONFIG`` can be substituted with |
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| 92 | a suitably descriptive name for your new configuration. |
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| 93 | |
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| 94 | The purpose of this step is simply to create and populate the appropriate :file:`WORK`, |
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| 95 | :file:`MY_SRC` and :file:`EXP00` subdirectories for your new configuration. |
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| 96 | Other choices for the base reference configuration might be |
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| 97 | |
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| 98 | :GYRE: If your target application is ocean-only |
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| 99 | :AMM12: If your target application is regional with open boundaries |
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| 100 | |
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| 101 | All the domain information for your new configuration will be contained within |
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| 102 | a netcdf file called :file:`domain_cfg.nc` which you will need to create and |
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| 103 | place in the :file:`./cfgs/MY_NEW_CONFIG/EXP00` sub-directory. |
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| 104 | Firstly though, ensure that your configuration is set to use such a file by checking that |
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| 105 | |
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| 106 | .. code-block:: fortran |
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| 107 | |
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| 108 | ln_read_cfg = .true. |
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| 109 | |
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| 110 | in :file:`./cfgs/MY_NEW_CONFIG/EXP00/namelist_cfg` |
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| 111 | |
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| 112 | Create the :file:`domain_cfg.nc` file which must contain the following fields |
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| 113 | |
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| 114 | .. code-block:: c |
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| 115 | |
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| 116 | /* configuration name, configuration resolution */ |
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| 117 | int ORCA, ORCA_index |
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| 118 | /* lateral global domain b.c. */ |
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[14433] | 119 | int Iperio, Jperio, NFoldT, NFoldF |
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[11743] | 120 | /* flags for z-coord, z-coord with partial steps and s-coord */ |
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| 121 | int ln_zco, ln_zps, ln_sco |
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| 122 | /* flag for ice shelf cavities */ |
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| 123 | int ln_isfcav |
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| 124 | /* geographic position */ |
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| 125 | double glamt, glamu, glamv, glamf |
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| 126 | /* geographic position */ |
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| 127 | double gphit, gphiu, gphiv, gphif |
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| 128 | /* Coriolis parameter (if not on the sphere) */ |
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| 129 | double iff, ff_f, ff_t |
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| 130 | /* horizontal scale factors */ |
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| 131 | double e1t, e1u, e1v, e1f |
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| 132 | /* horizontal scale factors */ |
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| 133 | double e2t, e2u, e2v, e2f |
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| 134 | /* U and V surfaces (if grid size reduction in some straits) */ |
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| 135 | double ie1e2u_v, e1e2u, e1e2v |
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| 136 | /* reference vertical scale factors at T and W points */ |
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| 137 | double e3t_1d, e3w_1d |
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| 138 | /* vertical scale factors 3D coordinate at T,U,V,F and W points */ |
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| 139 | double e3t_0, e3u_0, e3v_0, e3f_0, e3w_0 |
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| 140 | /* vertical scale factors 3D coordinate at UW and VW points */ |
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| 141 | double e3uw_0, e3vw_0 |
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| 142 | /* last wet T-points, 1st wet T-points (for ice shelf cavities) */ |
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| 143 | int bottom_level, top_level |
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| 144 | |
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| 145 | There are two options for creating a :file:`domain_cfg.nc` file: |
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| 146 | |
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| 147 | - Users can use tools of their own choice to build a :file:`domain_cfg.nc` with all mandatory fields. |
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| 148 | - Users can adapt and apply the supplied tool available in :file:`./tools/DOMAINcfg`. |
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| 149 | This tool is based on code extracted from NEMO version 3.6 and will allow similar choices for |
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| 150 | the horizontal and vertical grids that were available internally to that version. |
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| 151 | See :ref:`tools <DOMAINcfg>` for details. |
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| 152 | |
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| 153 | Option 2: Adapt the usr_def configuration module of NEMO for you own purposes |
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| 154 | ----------------------------------------------------------------------------- |
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| 155 | |
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| 156 | This method is intended for configuring easily simple/idealised configurations which |
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| 157 | are often used as demonstrators or for process evaluation and comparison. |
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| 158 | This method can be used whenever the domain geometry has a simple mathematical description and |
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| 159 | the ocean initial state and boundary forcing is described analytically. |
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| 160 | As a start, consider the case of starting a completely new ocean-only test case based on |
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| 161 | the ``LOCK_EXCHANGE`` example. |
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| 162 | |
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| 163 | .. note:: |
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| 164 | |
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| 165 | We probably need an even more basic example than this with only one namelist and |
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| 166 | minimal changes to the usrdef modules |
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| 167 | |
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| 168 | Firstly, construct the directory structure, starting in the :file:`cfgs` directory: |
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| 169 | |
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| 170 | .. code-block:: console |
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| 171 | |
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| 172 | $ ./makenemo -n 'MY_NEW_TEST' -t 'LOCK_EXCHANGE' -m 'my_arch' |
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| 173 | |
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| 174 | where the ``-t`` option has been used to locate the new configuration in |
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| 175 | the :file:`tests` subdirectory |
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| 176 | (it is recommended practice to keep full configurations and idealised cases clearly distinguishable). |
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| 177 | This command will create (amongst others) the following files and directories:: |
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| 178 | |
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| 179 | ./tests/MY_NEW_TEST: |
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| 180 | BLD EXP00 MY_SRC WORK cpp_MY_NEW_TEST.fcm |
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| 181 | |
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| 182 | ./tests/MY_NEW_TEST/EXP00: |
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| 183 | context_nemo.xml domain_def_nemo.xml field_def_nemo-oce.xml file_def_nemo-oce.xml iodef.xml |
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| 184 | namelist_cfg namelist_ref |
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| 185 | |
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| 186 | ./tests/MY_NEW_TEST/MY_SRC: |
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| 187 | usrdef_hgr.F90 usrdef_nam.F90 usrdef_zgr.F90 usrdef_istate.F90 usrdef_sbc.F90 zdfini.F90 |
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| 188 | |
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| 189 | The key to setting up an idealised configuration lies in |
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| 190 | adapting a small set of short Fortran 90 modules which |
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| 191 | should be dropped into the :file:`MY_SRC` directory. |
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| 192 | Here the ``LOCK_EXCHANGE`` example is using 5 such routines but the full set that is available in |
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| 193 | the :file:`src/OCE/USR` directory is:: |
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| 194 | |
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| 195 | ./src/OCE/USR: |
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| 196 | usrdef_closea.F90 usrdef_fmask.F90 usrdef_hgr.F90 usrdef_istate.F90 |
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| 197 | usrdef_nam.F90 usrdef_sbc.F90 usrdef_zgr.F90 |
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| 198 | |
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| 199 | Before discussing these in more detail it is worth noting the various namelist controls that |
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| 200 | engage the different user-defined aspects. |
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| 201 | These controls are set using two new logical switches or are implied by the settings of existing ones. |
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| 202 | For example, the mandatory requirement for an idealised configuration is to provide routines which |
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| 203 | define the horizontal and vertical domains. |
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| 204 | Templates for these are provided in the :file:`usrdef_hgr.F90` and :file:`usrdef_zgr.F90` modules. |
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| 205 | The application of these modules is activated whenever: |
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| 206 | |
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| 207 | .. code-block:: fortran |
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| 208 | |
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| 209 | ln_read_cfg = .false. |
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| 210 | |
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| 211 | in any configuration's :file:`namelist_cfg` file. |
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| 212 | This setting also activates the reading of an optional ``&nam_usrdef`` namelist which can be used to |
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| 213 | supply configuration specific settings. |
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| 214 | These need to be declared and read in the :file:`usrdef_nam.F90` module. |
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| 215 | |
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| 216 | Another explicit control is available in the ``&namsbc`` namelist which |
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| 217 | activates the use of analytical forcing. |
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| 218 | With |
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| 219 | |
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| 220 | .. code-block:: fortran |
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| 221 | |
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| 222 | ln_usr = .true. |
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| 223 | |
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| 224 | Other usrdef modules are activated by less explicit means. |
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| 225 | For example, code in :file:`usrdef_istate.F90` is used to |
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| 226 | define initial temperature and salinity fields if |
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| 227 | |
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| 228 | .. code-block:: fortran |
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| 229 | |
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| 230 | ln_tsd_init = .false. |
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| 231 | |
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| 232 | in the ``&namtsd`` namelist. |
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| 233 | The remaining modules, namely :file:`usrdef_closea.F90` :file:`usrdef_fmask.F90` are specific to |
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| 234 | ORCA configurations and set local variations of some specific fields for |
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| 235 | the various resolutions of the global models. |
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| 236 | They do not need to be considered here in the context of idealised cases but |
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| 237 | it is worth noting that all configuration specific code has now been isolated in the usrdef modules. |
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| 238 | In the case of these last two modules, they are activated only if an ORCA configuration is detected. |
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| 239 | Currently, |
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| 240 | this requires a specific integer variable named ``ORCA`` to be set in a :file:`domain_cfg.nc` file. |
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| 241 | |
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| 242 | .. note:: |
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| 243 | |
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| 244 | This would be less confusing if the ``cn_cfg`` string is read directly as |
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| 245 | a character attribue from the :file:`domain_cfg.nc`. |
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| 246 | |
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| 247 | So, in most cases, the set up of idealised model configurations can be completed by |
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| 248 | copying the template routines from :file:`./src/OCE/USR` into |
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| 249 | your new :file:`./cfgs/MY_NEW_TEST/MY_SRC` directory and |
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| 250 | editing the appropriate modules as needed. |
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| 251 | The default set are those used for the GYRE reference configuration. |
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| 252 | The contents of :file:`MY_SRC` directories from other idealised configurations may provide |
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| 253 | more convenient templates if they share common characteristics with your target application. |
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| 254 | |
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| 255 | Whatever the starting point, |
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| 256 | it should not require too many changes or additional lines of code to produce routines in |
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| 257 | :file:`./src/OCE/USR` that define analytically the domain, |
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| 258 | the initial state and the surface boundary conditions for your new configuration. |
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| 259 | |
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| 260 | To summarize, the base set of modules is: |
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| 261 | |
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| 262 | :usrdef_hgr.F90: Define horizontal grid |
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| 263 | :usrdef_zgr.F90: Define vertical grid |
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| 264 | :usrdef_sbc.F90: Provides at each time-step the surface boundary condition, |
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| 265 | i.e. the momentum, heat and freshwater fluxes |
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| 266 | :usrdef_istate.F90: Defines initialization of the dynamics and tracers |
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| 267 | :usrdef_nam.F90: Configuration-specific namelist processing to |
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| 268 | set any associated run-time parameters |
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| 269 | |
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| 270 | with two specialised ORCA modules |
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| 271 | (not related to idealised configurations but used to isolate configuration specific code that |
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| 272 | is used in ORCA2 reference configurations and established global configurations using |
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| 273 | the ORCA tripolar grid): |
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| 274 | |
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| 275 | :usrdef_fmask.F90: only used in ORCA configurations for |
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| 276 | alteration of f-point land/ocean mask in some straits |
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| 277 | :usrdef_closea.F90: only used in ORCA configurations for |
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| 278 | specific treatments associated with closed seas |
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| 279 | |
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| 280 | From version 4.0, the NEMO release includes a :file:`tests` subdirectory containing available and |
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| 281 | up to date :doc:`test cases <tests>` build by the community. |
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| 282 | These will not be fully supported as are NEMO reference configurations, |
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| 283 | but should provide a source of raw material. |
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