Changeset 11751


Ignore:
Timestamp:
2019-10-21T15:58:58+02:00 (11 months ago)
Author:
nicolasmartin
Message:

Review README for tools

Location:
utils/tools
Files:
1 added
1 edited

Legend:

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  • utils/tools/README.rst

    r11736 r11751  
    55.. todo:: 
    66 
    7  
     7   The 'Tools' chapter needs to be enriched 
    88 
    99.. contents:: 
    1010   :local: 
     11   :depth: 1 
    1112 
    1213A set of tools is provided with NEMO to setup user own configuration and (pre|post)process data. 
    1314 
    14 **How to compile a tool** 
     15How to compile a tool 
     16===================== 
    1517 
    1618The tool can be compiled using the maketools script in the tools directory as follows: 
     
    1820.. code-block:: console 
    1921 
    20         $ ./maketools -m '$ARCH' -n '<TOOL_NAME>' 
     22   $ ./maketools -m 'my_arch' -n '<TOOL_NAME>' 
    2123 
    22 where ``$ARCH`` can be selected among available architecture files or providing a user defined one. 
     24where ``my_arch`` can be selected among available architecture files or providing a user defined one. 
     25 
     26List of tools 
     27============= 
    2328 
    2429BDY_TOOLS 
    2530--------- 
    2631 
    27 It contains the utility *bdy_reorder* used to reorder old BDY data files used with previous versions of the model (before 3.4) to make them compatible with NEMO 3.4. 
     32It contains the utility *bdy_reorder* used to reorder old BDY data files used with 
     33previous versions of the model (before 3.4) to make them compatible with NEMO 3.4. 
    2834 
    2935DMP_TOOLS 
    3036--------- 
    3137 
    32 Used to create a netcdf file called ``resto.nc`` containing restoration coefficients for use with the tra_dmp module in NEMO (see `DMP_TOOLS README <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/DMP_TOOLS/README>`_). 
     38Used to create a netcdf file called :file:`resto.nc` containing 
     39restoration coefficients for use with the :file:`tra_dmp` module in NEMO 
     40(see :download:`DMP_TOOLS README <../../../tools/DMP_TOOLS/README>`). 
    3341 
    3442DOMAINcfg 
    3543--------- 
    3644 
    37 This tool allows the creation of a domain configuration file (``domain_cfg.nc``) containing the ocean domain information required to define an ocean configuration from scratch. (see `DOMAINcfg README <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/DOMAINcfg/README>`_). 
     45This tool allows the creation of a domain configuration file (``domain_cfg.nc``) containing 
     46the ocean domain information required to define an ocean configuration from scratch. 
     47(see :download:`DOMAINcfg README <../../../tools/DOMAINcfg/README>`). 
    3848 
    3949GRIDGEN 
    4050------- 
    4151 
    42 A toolbox allowing the creation of regional configurations from curvilinear grid (see `reference guide <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/GRIDGEN/doc_cfg_tools.pdf>`_ ). 
     52A toolbox allowing the creation of regional configurations from curvilinear grid 
     53(see :download:`GRIDGEN documentation <../../../tools/GRIDGEN/doc_cfg_tools.pdf>`). 
    4354 
    4455MISCELLANEOUS 
    4556------------- 
    4657 
    47 The tool allows to create alternative configurations to the community without having to rely on system team sponsorship and support. 
     58The tool allows to create alternative configurations to the community without 
     59having to rely on system team sponsorship and support. 
    4860 
    4961MPP_PREP 
     
    5163 
    5264This tool provides the user with information to choose the best domain decomposition. 
    53 The tool computes the number of water processors for all possible decompositions (up to a maximum number of processors). 
    54 Documentation: `mpp_nc.pdf <http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Users/SetupNewConfiguration/mpp_nc.pdf>`_ 
    55 Tar file     : `mpp_prep-1.0.tar.gz <http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Users/SetupNewConfiguration/mpp_prep-1.0.tar.gz>`_ 
     65The tool computes the number of water processors for all possible decompositions, 
     66up to a maximum number of processors 
     67(see :download:`MPP_PREP documentation <../../../tools/MPP_PREP/mpp_nc.pdf>` and 
     68:download:`MPP_PREP archive <../../../tools/MPP_PREP/mpp_prep-1.0.tar.gz>`). 
    5669 
    5770NESTING 
    5871------- 
    5972 
    60 AGRIF nesting tool allows for the seamless two-way coupling of nested sub-models within the NEMO framework as long as these are defined on subsets of the original root grid. 
    61 It allows to create the grid coordinates, the surface forcing and the initial conditions required by each sub-model when running a NEMO/AGRIF embedded mode (see `NESTING README <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/NESTING/README>`_). 
     73AGRIF nesting tool allows for the seamless two-way coupling of nested sub-models within 
     74the NEMO framework as long as these are defined on subsets of the original root grid. 
     75It allows to create the grid coordinates, the surface forcing and the initial conditions required by 
     76each sub-model when running a NEMO/AGRIF embedded mode 
     77(see :download:`NESTING README <../../../tools/NESTING/README>`). 
    6278 
    6379OBSTOOLS 
    6480-------- 
    6581 
    66 A series of Fortran utilities which are helpful in handling observation files and the feedback file output from the NEMO observation operator. 
    67 Further info are available in the Nemo manual. 
     82A series of Fortran utilities which are helpful in handling observation files and 
     83the feedback file output from the NEMO observation operator. 
     84Further info are available in the :doc:`Nemo manual <cite>`. 
    6885 
    6986REBUILD_NEMO 
    7087------------ 
    7188 
    72 REBUILD_NEMO is a tool to rebuild NEMO output files from multiple processors (mesh_mask, restart or XIOS output files) into one file (see `REBUILD_NEMO README <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/REBUILD_NEMO/README.rst>`_). 
     89REBUILD_NEMO is a tool to rebuild NEMO output files from multiple processors 
     90(mesh_mask, restart or XIOS output files) into one file 
     91(see :download:`REBUILD_NEMO README <../../../tools/REBUILD_NEMO/README.rst>`). 
    7392 
    7493REBUILD 
     
    8099---------- 
    81100 
    82 Offline tool to generate a vertical coordinates input file for use with S coordinates. This has been carried out by copying the model code to an offline tool and then modifying it to suppress the use of 3D arrays (to reduce memory usage). The tool has been created in preparation for the removal of the vertical grid definition from the code. The output file should contain all variables that are necessary to restart the model. 
     101Offline tool to generate a vertical coordinates input file for use with S coordinates. 
     102This has been carried out by copying the model code to an offline tool and then 
     103modifying it to suppress the use of 3D arrays (to reduce memory usage). 
     104The tool has been created in preparation for the removal of the vertical grid definition from 
     105the code. 
     106The output file should contain all variables that are necessary to restart the model. 
    83107 
    84108SECTIONS_DIADCT 
    85109--------------- 
    86110 
    87 When the Transport across sections diagnostic is activated (``key_diadct``), this tool is used to build the binary file containing the pathways between the extremities of each section. 
    88 Further info are available in the Nemo manual. 
     111When the Transport across sections diagnostic is activated (``key_diadct``), 
     112this tool is used to build the binary file containing the pathways between 
     113the extremities of each section. 
     114Further info are available in the :doc:`Nemo manual <cite>`. 
    89115 
    90116SIREN 
    91117----- 
    92118 
    93 SIREN is a configuration management tool to set up regional configurations with NEMO. (see `SIREN README <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/SIREN/README>`_) 
     119SIREN is a configuration management tool to set up regional configurations with NEMO 
     120(see :download:`SIREN README <../../../tools/SIREN/README>`). 
    94121 
    95122WEIGHTS 
    96123------- 
    97124 
    98 This directory contains software for generating and manipulating interpolation weights for use with the Interpolation On the Fly (IOF) option in NEMO v3 onwards. (see `WEIGHTS README <http://forge.ipsl.jussieu.fr/nemo/browser/utils/tools/WEIGHTS/README>`_) 
     125This directory contains software for generating and manipulating interpolation weights for use with 
     126the Interpolation On the Fly (IOF) option in NEMO v3 onwards 
     127(see :download:`WEIGHTS README <../../../tools/WEIGHTS/README>`). 
    99128 
    100129TOYATM 
    101130------ 
    102131 
    103 This directory contains a simplified model that send/receive atmospheric fields to/from NEMO. Used to test the coupling interface. This toy requires OASIS3-MCT to be installed and properly defined in the arch file. 
     132This directory contains a simplified model that send/receive atmospheric fields to/from NEMO. 
     133Used to test the coupling interface. 
     134This toy requires OASIS3-MCT to be installed and properly defined in the arch file. 
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