Ignore:
Timestamp:
2018-11-07T12:04:15+01:00 (2 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

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  • NEMO/trunk/README.rst

    r10201 r10279  
    1 .. include:: .global.rst 
    2  
     1:Authors: NEMO System Team 
    32:Release: |release| 
    43:Date:    |today| 
    5              
    6 NEMO for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework of  
    7 ocean related engines for oceanographic research, operational oceanography, seasonal forecast and  
    8 [paleo]climate studies. 
     4 
     5`NEMO`_ for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework for 
     6research activities and forecasting services in ocean and climate sciences. 
    97 
    108.. contents:: 
     
    1412======== 
    1513 
    16 Distributed under CeCILL license (GNU GPL compatible - see ``./LICENSE``), 
    17 the NEMO ocean model has 3 major components: 
     14The NEMO ocean model has 3 major components: 
    1815 
    19 - :rstblue:`OPA` is fundamental to all users by modelling the ocean [thermo]dynamics and  
    20   solving the primitive equations         (``./src/OCE``); :cite:`madec_bk08` 
    21 - :rstgrey:`SI`\ :rstgreysup:`3` for sea-ice simulates ice [thermo]dynamics, brine inclusions and  
    22   subgrid-scale thickness variations      (``./src/ICE``); :cite:`gmd-8-2991-2015,vancoppenolle200933` 
    23 - :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for the on/offline oceanic tracers transport and  
    24   PISCES for the biogeochemical processes (``./src/MBG``). :cite:`gmd-8-2465-2015` 
     16- |OPA| models the ocean [thermo]dynamics and solves the primitive equations 
     17  (``./src/OCE``) :cite:`NEMO_manual`; 
     18- |SI3| simulates ice [thermo]dynamics, brine inclusions and subgrid-scale thickness variations 
     19  (``./src/ICE``) :cite:`SI3_manual`; 
     20- |TOP| models the [on|off]line oceanic tracers transport and the biogeochemical processes 
     21  (``./src/MBG``) :cite:`TOP_manual`. 
    2522 
    26 These physical engines are described in their respective reference publications that must be cited for 
     23These physical core engines are described in their respective <reference publications> that must be cited for 
    2724any work related to their use. 
    2825 
     
    3330it offers various features to enable 
    3431 
    35 - 2-way nesting package `AGRIF`_ to create :doc:`embedded zooms <zooms>` seamlessly 
    36 - Flexible biogeochemistry with :doc:`online coarsening <coarsening>` and 
    37   opportunity to integrate an :doc:`alternative model <tracers>` 
    38 - Versatile :doc:`data assimilation interface <data_assimilation>` 
     32- Create :doc:`embedded zooms <zooms>` seamlessly with 2-way nesting package `AGRIF`_. 
     33- :doc:`Low cost biogeochemistry <coarsening>` and :doc:`alternative model opportunity <tracers>`. 
     34- Versatile :doc:`assimilation <assimilation>`. 
     35- :doc:`Output diagnostics <diagnostics>` with `XIOS`_ server. 
     36- :doc:`Coupling <coupling>` via `OASIS`_ for Earth system modelling. 
    3937 
    40 lation a efficient XIOS_ server for outputing diagnostics a coupled via OASIS_ to alternative components or other models to enable Earth system modelling. 
    41  
    42 | Several :doc:`builtins configurations <reference_configurations>` are provided to assess the skills and 
    43    performances of the model which can be used as templates for setting up a new configuration (``./cfgs``). 
    44 | The end user could also find some :doc:`idealised test cases <test_cases>` on the web to serve as examples and 
     38| Several :doc:`builtins configurations <configurations>` are provided to assess the skills and performances of 
     39   the model which can be used as templates for :doc:`setting up a new configuration <setup>` (``./cfgs``). 
     40| The end user could also find some :doc:`idealised test cases <test_cases>` online to serve as templates and 
    4541   to study particular processes (``./tests``). 
    4642 
    47 A set of tools is also provided to setup your own configuration and [pre|post]process your data (``./tools``). 
     43A set of :doc:`utilities <tools>` is also provided to [pre|post]process your data (``./tools``). 
    4844 
    4945Literature 
    5046========== 
    5147 
    52 | The NEMO reference manual and a quick start guide can be generated from Latex and RST source code files 
    53    (``./doc``), either in PDF or in HTML format, but it might require some additional installations. 
    54 | In any case, both formats are available online: `HTML`_ | `PDF`_ 
     48:doc:`install` 
    5549 
    56 | Since 2014 the project has a `Special Issue`_ in the open-access journal Geoscientific Model Development (GMD)  
    57    from the European Geosciences Union (EGU). 
    58    The main scope is to collect relevant manuscripts which cover a wide variety of topics like 
    59    process studies, new parameterizations, implementation of new model features and new NEMO configurations. 
    60 | Also it provides a single portal to search, discover and understand about 
    61    the NEMO modelling framework potential and evolution and to submit their contributions.  
     50The reference documentation is archived online 
     51 
     52+-------+-------------------+----------------+ 
     53|       | Reference manual  | |NEMO manual|_ | 
     54| |OPA| +-------------------+----------------+ 
     55|       | Quick start guide | |NEMO guide|_  | 
     56+-------+-------------------+----------------+ 
     57| |SI3|                     | |SI3 manual|_  | 
     58+---------------------------+----------------+ 
     59| |TOP|                     | |TOP manual|_  | 
     60+---------------------------+----------------+ 
     61 
     62.. |NEMO manual| image:: http://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg 
     63.. |NEMO guide|  image:: http://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg 
     64.. |SI3 manual|  image:: http://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg 
     65.. |TOP manual|  image:: http://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg 
     66 
     67| Reference manuals and quick start guide can be build from source and exported to HTML or PDF (``./doc``). 
     68| In any case, one can find them online: 
     69 
     70Since 2014 the project has a `Special Issue <http://www.geosci-model-dev.net/special_issue40.html>`_ in 
     71the open-access journal Geoscientific Model Development (GMD) from the European Geosciences Union (EGU). 
     72The main scope is to collect relevant manuscripts covering various topics and to provide a single portal to 
     73assess the model potential and evolution. 
     74 
     75Used by a wide audience, numerous :website:`associated projects <projects>` have been carried out and 
     76extensive :website:`bibliography <bibliography/publications>` published. 
    6277 
    6378Community development 
    6479===================== 
    6580 
    66 | The NEMO Consortium gathering 6 European institutes (`CMCC`_, `CNRS`_, `MOI`_, `Met Office`_ and `NERC`_) 
    67    organises the sustainable development in order to keep a reliable evolving system since 2008. 
    68 | It defines the multi-year development strategy which is implemented by the NEMO System Team. 
     81| The NEMO Consortium pulling together 5 European institutes (`CMCC`_, `CNRS`_, `MOI`_, `Met Office`_ and `NERC`_) 
     82   plans the sustainable development in order to keep a reliable evolving framework since 2008. 
     83| It defines the |NEMO strategy|_ which is implemented by the System Team on 
     84   a yearly basis in order to release a new version almost every four years. 
    6985 
    70 When the need arises, `Working Groups`_ are created or resumed to gather the expertise in the community in order to 
    71 focus the development work on a specific subject or major component of the framework. 
     86.. |NEMO strategy| replace:: multi-year development strategy 
    7287 
    73 How to cite NEMO 
    74 ================ 
    75  
    76 .. bibliography:: references.bib 
    77    :all: 
    78    :style: unsrt 
    79  
    80 .. _HTML:           http://www.nemo-ocean.eu/doc 
    81 .. _PDF:            http://www.nemo-ocean.eu/wp-content/uploads/NEMO_book.pdf 
     88When the need arises, :forge:`working groups <wiki/WorkingGroups>` are created or resumed to 
     89gather the community expertise for advising on the development activities. 
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