| 1 | ***** |
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| 2 | Tools |
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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 | The 'Tools' chapter needs to be enriched |
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| 8 | |
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| 9 | .. contents:: |
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| 10 | :local: |
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| 11 | :depth: 1 |
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| 12 | |
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| 13 | A set of tools is provided with NEMO to setup user own configuration and (pre|post)process data. |
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| 14 | |
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| 15 | How to compile a tool |
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| 16 | ===================== |
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| 17 | |
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| 18 | The tool can be compiled using the maketools script in the tools directory as follows: |
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| 19 | |
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| 20 | .. code-block:: console |
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| 21 | |
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| 22 | $ ./maketools -m 'my_arch' -n '<TOOL_NAME>' |
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| 23 | |
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| 24 | where ``my_arch`` can be selected among available architecture files or providing a user defined one. |
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| 25 | |
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| 26 | List of tools |
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| 27 | ============= |
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| 28 | |
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| 29 | BDY_TOOLS |
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| 30 | --------- |
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| 31 | |
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| 32 | It contains the utility *bdy_reorder* used to reorder old BDY data files used with |
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| 33 | previous versions of the model (before 3.4) to make them compatible with NEMO 3.4. |
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| 34 | |
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| 35 | DMP_TOOLS |
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| 36 | --------- |
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| 37 | |
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| 38 | Used to create a netcdf file called :file:`resto.nc` containing |
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| 39 | restoration coefficients for use with the :file:`tra_dmp` module in NEMO |
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| 40 | (see :download:`DMP_TOOLS README <../../../tools/DMP_TOOLS/README>`). |
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| 41 | |
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| 42 | DOMAINcfg |
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| 43 | --------- |
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| 44 | |
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| 45 | This tool allows the creation of a domain configuration file (``domain_cfg.nc``) containing |
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| 46 | the ocean domain information required to define an ocean configuration from scratch. |
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| 47 | (see :download:`DOMAINcfg README <../../../tools/DOMAINcfg/README>`). |
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| 48 | |
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| 49 | GRIDGEN |
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| 50 | ------- |
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| 51 | |
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| 52 | A toolbox allowing the creation of regional configurations from curvilinear grid |
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| 53 | (see :download:`GRIDGEN documentation <../../../tools/GRIDGEN/doc_cfg_tools.pdf>`). |
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| 54 | |
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| 55 | MISCELLANEOUS |
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| 56 | ------------- |
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| 57 | |
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| 58 | The tool allows to create alternative configurations to the community without |
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| 59 | having to rely on system team sponsorship and support. |
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| 60 | |
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| 61 | MPP_PREP |
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| 62 | -------- |
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| 63 | |
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| 64 | This tool provides the user with information to choose the best domain decomposition. |
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| 65 | The tool computes the number of water processors for all possible decompositions, |
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| 66 | up to a maximum number of processors |
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| 67 | (see :download:`MPP_PREP documentation <../../../tools/MPP_PREP/mpp_nc.pdf>` and |
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| 68 | :download:`MPP_PREP archive <../../../tools/MPP_PREP/mpp_prep-1.0.tar.gz>`). |
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| 69 | |
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| 70 | NESTING |
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| 71 | ------- |
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| 72 | |
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| 73 | AGRIF nesting tool allows for the seamless two-way coupling of nested sub-models within |
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| 74 | the NEMO framework as long as these are defined on subsets of the original root grid. |
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| 75 | It allows to create the grid coordinates, the surface forcing and the initial conditions required by |
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| 76 | each sub-model when running a NEMO/AGRIF embedded mode |
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| 77 | (see :download:`NESTING README <../../../tools/NESTING/README>`). |
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| 78 | |
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| 79 | OBSTOOLS |
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| 80 | -------- |
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| 81 | |
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| 82 | A series of Fortran utilities which are helpful in handling observation files and |
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| 83 | the feedback file output from the NEMO observation operator. |
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| 84 | Further info are available in the :doc:`Nemo manual <cite>`. |
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| 85 | |
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| 86 | REBUILD_NEMO |
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| 87 | ------------ |
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| 88 | |
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| 89 | REBUILD_NEMO is a tool to rebuild NEMO output files from multiple processors |
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| 90 | (mesh_mask, restart or XIOS output files) into one file |
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| 91 | (see :download:`REBUILD_NEMO README <../../../tools/REBUILD_NEMO/README.rst>`). |
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| 92 | |
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| 93 | REBUILD |
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| 94 | ------- |
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| 95 | |
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| 96 | It contains the old version of REBUILD_NEMO tool based on the IOIPSL code. |
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| 97 | |
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| 98 | SCOORD_GEN |
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| 99 | ---------- |
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| 100 | |
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| 101 | Offline tool to generate a vertical coordinates input file for use with S coordinates. |
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| 102 | This has been carried out by copying the model code to an offline tool and then |
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| 103 | modifying it to suppress the use of 3D arrays (to reduce memory usage). |
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| 104 | The tool has been created in preparation for the removal of the vertical grid definition from |
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| 105 | the code. |
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| 106 | The output file should contain all variables that are necessary to restart the model. |
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| 107 | |
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| 108 | SECTIONS_DIADCT |
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| 109 | --------------- |
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| 110 | |
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| 111 | When the Transport across sections diagnostic is activated (``key_diadct``), |
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| 112 | this tool is used to build the binary file containing the pathways between |
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| 113 | the extremities of each section. |
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| 114 | Further info are available in the :doc:`Nemo manual <cite>`. |
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| 115 | |
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| 116 | SIREN |
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| 117 | ----- |
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| 118 | |
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| 119 | SIREN is a configuration management tool to set up regional configurations with NEMO |
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| 120 | (see :download:`SIREN README <../../../tools/SIREN/README>`). |
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| 121 | |
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| 122 | WEIGHTS |
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| 123 | ------- |
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| 124 | |
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| 125 | This directory contains software for generating and manipulating interpolation weights for use with |
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| 126 | the Interpolation On the Fly (IOF) option in NEMO v3 onwards |
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| 127 | (see :download:`WEIGHTS README <../../../tools/WEIGHTS/README>`). |
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| 128 | |
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| 129 | TOYATM |
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| 130 | ------ |
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| 131 | |
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| 132 | This directory contains a simplified model that send/receive atmospheric fields to/from NEMO. |
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| 133 | Used to test the coupling interface. |
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| 134 | This toy requires OASIS3-MCT to be installed and properly defined in the arch file. |
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