Ignore:
Timestamp:
2018-11-07T12:04:15+01:00 (3 years ago)
Author:
nicolasmartin
Message:

Various improvments for quick start guide

  • implementation of Rtd theme (Read the Docs) with custom layout and style file
  • add reviewed BibTeX entries for NEMO references with DOI (manuals, guide, development strategy)
  • enhancement of bibliography management and configuration file for guide building
  • standardisation of headings markup
  • numerous edits
File:
1 edited

Legend:

Unmodified
Added
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  • NEMO/trunk/src/OCE/CRS/README.rst

    r10201 r10279  
     1********************************** 
    12On line biogeochemistry coarsening 
    2 ================================== 
    3  
    4 .. include:: .global.rst 
     3********************************** 
    54 
    65.. contents:: 
    76   :local: 
    87 
    9 .. role:: underline  
    10    :class: underline 
    11  
    12 ------------ 
    138Presentation 
    14 ------------ 
     9============ 
    1510 
    1611A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed. 
     
    2015A presentation is available [attachment:crs_wiki_1.1.pdf​ here], where the methodology is presented. 
    2116 
    22 ----------------------------------------------------- 
    2317What is available and working for now in this version 
    24 ----------------------------------------------------- 
     18===================================================== 
    2519 
    2620[To be completed] 
    2721 
    28 ---------------------------------------------- 
    2922Description of the successful validation tests 
    30 ---------------------------------------------- 
     23============================================== 
    3124 
    3225[To be completed] 
    3326 
    34 ------------------------------------------------------------------ 
    3527What is not working yet with on line coarsening of biogeochemistry 
    36 ------------------------------------------------------------------ 
     28================================================================== 
    3729 
    3830[To be completed] 
     
    4032''should include precise explanation on MPI decomposition problems too'' 
    4133 
    42 --------------------------------------------- 
    4334How to set up and use on line biogeochemistry 
    44 --------------------------------------------- 
     35============================================= 
    4536 
    46 :underline:`How to activate coarsening?` 
     37Extract the on line biogeochemistry branch 
     38------------------------------------------ 
     39 
     40To get the appropriate source code with the on line coarsening of biogeochemistry feature: 
     41 
     42.. code-block:: console 
     43 
     44   $ svn co https://forge.ipsl.jussieu.fr/nemo/browser/NEMO/branches/2018/dev_r5003_MERCATOR6_CRS 
     45 
     46 
     47How to activate coarsening? 
     48--------------------------- 
    4749 
    4850To activate the coarsening, ``key_crs`` should be added to list of CPP keys. 
     
    8385  so only works when ``key_top`` is in the cpp list and eventually ``key_pisces`` or ``key_my_trc``. 
    8486 
    85 :underline:`Choice of operator to coarsene KZ` 
     87Choice of operator to coarsene KZ 
     88--------------------------------- 
    8689 
    8790A sensiblity test has been done with an Age tracer to compare the different operators. 
     
    9093Some results can be found [xxx here] 
    9194 
    92 :underline:`Example of xml files to output coarsened variables with XIOS` 
     95Example of xml files to output coarsened variables with XIOS 
     96------------------------------------------------------------ 
    9397 
    9498In the [attachment:iodef.xml iodef.xml]  file, a "nemo" context is defined and 
     
    98102the associated variable are listed in [attachment:file_crs_def.xml file_crs_def.xml ]. 
    99103 
    100 :underline:`Passive tracers tracers initial conditions` 
     104Passive tracers tracers initial conditions 
     105------------------------------------------ 
    101106 
    102107When initial conditions are provided in NetCDF files, the field might be: 
     
    132137         cn_dir        =  './'      !  root directory for the location of the data files 
    133138 
    134 :underline:`PISCES forcing files` 
     139PISCES forcing files 
     140-------------------- 
    135141 
    136142They might be on the coarsened grid. 
    137143 
    138 :underline:`Perspectives` 
     144Perspectives 
     145============ 
    139146 
    140147For the future, a few options are on the table to implement coarsening for biogeochemistry in 4.0 and 
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