Ignore:
Timestamp:
2018-10-18T12:53:04+02:00 (2 years ago)
Author:
nicolasmartin
Message:

Various modifications related to the setting of a NEMO Quick Start Guide

  • Add missing namelist blocks from ICE and TOP
  • Create a hidden .global.rst to gather common URL links
  • Convert animated gif to frames images for PDF export
  • Place different README.rst appropriately in the code structure and refer to them with symbolic links in doc/rst/source
File:
1 edited

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  • NEMO/trunk/README.rst

    r10187 r10201  
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    52 
     3:Release: |release| 
     4:Date:    |today| 
     5             
    66NEMO for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework of  
    77ocean related engines for oceanographic research, operational oceanography, seasonal forecast and  
    88[paleo]climate studies. 
     9 
     10.. contents:: 
     11   :local: 
    912 
    1013Overview 
     
    1518 
    1619- :rstblue:`OPA` is fundamental to all users by modelling the ocean [thermo]dynamics and  
    17   solving the primitive equations         (``./src/OCE``);  
     20  solving the primitive equations         (``./src/OCE``); :cite:`madec_bk08` 
    1821- :rstgrey:`SI`\ :rstgreysup:`3` for sea-ice simulates ice [thermo]dynamics, brine inclusions and  
    19   subgrid-scale thickness variations      (``./src/ICE``);  
     22  subgrid-scale thickness variations      (``./src/ICE``); :cite:`gmd-8-2991-2015,vancoppenolle200933` 
    2023- :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for the on/offline oceanic tracers transport and  
    21   PISCES for the biogeochemical processes (``./src/MBG``). 
     24  PISCES for the biogeochemical processes (``./src/MBG``). :cite:`gmd-8-2465-2015` 
    2225 
    23 These physical engines are described in their respective reference publications that must be cited for  
     26These physical engines are described in their respective reference publications that must be cited for 
    2427any work related to their use. 
    2528 
     
    3033it offers various features to enable 
    3134 
    32 - 2-way nesting package `AGRIF`_ to create embedded zooms seamlessly 
    33 - Flexible biogeomchemistry with online coarsening and possible integration of a customized model  
    34 - Versatile data assimilation interface with 3 different modules 
    35   (tangent linear, observational operators and increments) 
     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>` 
    3639 
    3740lation a efficient XIOS_ server for outputing diagnostics a coupled via OASIS_ to alternative components or other models to enable Earth system modelling. 
    3841 
    39 | Several builtins configurations are provided to assess the skills and performances of the model which 
    40    can be used as templates for setting up a new configuration (``./cfgs``). 
    41 | The end user could also find some idealised test cases on the web to serve as examples and 
     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 
    4245   to study particular processes (``./tests``). 
    4346 
     
    5154| In any case, both formats are available online: `HTML`_ | `PDF`_ 
    5255 
    53 | Since 2014 the project has a `Special Issue`_ in the Geoscientific Model Development (GMD) open-access journal 
     56| Since 2014 the project has a `Special Issue`_ in the open-access journal Geoscientific Model Development (GMD)  
    5457   from the European Geosciences Union (EGU). 
    5558   The main scope is to collect relevant manuscripts which cover a wide variety of topics like 
    56    process studies, new parameterizations, implementation of new model features and new NEMO configurations. 
     59   process studies, new parameterizations, implementation of new model features and new NEMO configurations. 
    5760| Also it provides a single portal to search, discover and understand about 
    5861   the NEMO modelling framework potential and evolution and to submit their contributions.  
     
    6164===================== 
    6265 
    63 | The NEMO Consortium gathering 6 European institutes organises the sustainable development in order to  
    64    keep a reliable evolving system since 2008. 
     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. 
    6568| It defines the multi-year development strategy which is implemented by the NEMO System Team. 
    6669 
    67 `Working groups`_ are regularly created or resumed to gather the expertise in the NEMO community in order to  
    68 focus the development work on a specific subject or major component of NEMO. 
     70When the need arises, `Working Groups`_ are created or resumed to gather the expertise in the community in order to 
     71focus the development work on a specific subject or major component of the framework. 
    6972 
    70 Definitions 
    71 =========== 
     73How to cite NEMO 
     74================ 
    7275 
    73 AGRIF 
    74    *Adaptive Grid Refinement In Fortran*,  
    75    package for the integration of full adaptive mesh refinement features within  
    76    an existing multidimensional finite difference model 
     76.. bibliography:: references.bib 
     77   :all: 
     78   :style: unsrt 
    7779 
    78 SI\ :sup:`3`\  
    79    *Sea Ice Integrated Initiative*,  
    80    unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 
    81  
    82 OASIS 
    83    *Ocean Atmosphere Sea Ice Soil*,  
    84    coupling software to synchronise numerical codes representing different components of the climate system 
    85  
    86 PISCES 
    87    *Pelagic Interactions Scheme for Carbon and Ecosystem Studies*,  
    88    biogeochemical model simulating marine ecosystems, cycles of carbon and the main nutrients 
    89  
    90 TAM 
    91    *Tangent linear and Adjoint Model*,  
    92    tools to analyse and control the NEMO dynamical core for a wide range of applications such as 
    93    sensitivity analysis, parameter estimation, vectors computation or data assimilation. 
    94  
    95 TOP 
    96    *Tracers in Ocean Paradigm*,  
    97    on/off-line oceanic tracers transport and biogeochemistry models 
    98  
    99 XIOS 
    100    *XML Input Output Server*,  
    101    library dedicated to input/output management of climate code 
    102  
    103 .. _AGRIF:          http://agrif.imag.fr 
    10480.. _HTML:           http://www.nemo-ocean.eu/doc 
    105 .. _NEMO:           http://www.nemo-ocean.eu 
    106 .. _OASIS:          http://verc.enes.org/oasis 
    10781.. _PDF:            http://www.nemo-ocean.eu/wp-content/uploads/NEMO_book.pdf 
    108 .. _Special Issue:  http://www.geosci-model-dev.net/special_issue40.html 
    109 .. _Working groups: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups 
    110 .. _XIOS:           http://forge.ipsl.jussieu.fr/ioserver 
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