Index: NEMO/trunk/README.rst
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+++ NEMO/trunk/README.rst	(revision 10187)
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 .. role:: rstblue
+.. role:: rstgreen
 .. role:: rstgrey
-.. role:: rstgreen
+.. role:: rstgreysup(sup)
 
-================
-NEMO Ocean Model
-================
-
-NEMO_ (Nucleus for European Modelling of the Ocean) is a state-of-the-art modelling framework of 
+NEMO for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework of 
 ocean related engines for oceanographic research, operational oceanography, seasonal forecast and 
 [paleo]climate studies.
 
-The NEMO ocean model has 3 major components:
+Overview
+========
+
+Distributed under CeCILL license (GNU GPL compatible - see ``./LICENSE``),
+the NEMO ocean model has 3 major components:
 
 - :rstblue:`OPA` is fundamental to all users by modelling the ocean [thermo]dynamics and 
-  solving the primitive equations;
-- :rstgrey:`LIM` for sea-ice simulates ice [thermo]dynamics, brine inclusions and 
-  subgrid-scale thickness variations;
-- :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for 
-  the on/offline oceanic tracers transport and PISCES for the biogeochemical processes.
+  solving the primitive equations         (``./src/OCE``); 
+- :rstgrey:`SI`\ :rstgreysup:`3` for sea-ice simulates ice [thermo]dynamics, brine inclusions and 
+  subgrid-scale thickness variations      (``./src/ICE``); 
+- :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for the on/offline oceanic tracers transport and 
+  PISCES for the biogeochemical processes (``./src/MBG``).
 
-These physical engines are described in their respective `reference publications`_.
+These physical engines are described in their respective reference publications that must be cited for 
+any work related to their use.
 
-They are complemented by a 2-way nesting software (AGRIF_) and 
-a versatile data assimilation interface with 3 different modules
-(linear-tangent TAM, observational operators OBS, and increment ASM).
+Applications and capabilities
+=============================
 
-------------
-Applications
-------------
+Not only does the NEMO framework model the ocean circulation,
+it offers various features to enable
 
-| Distributed under CeCILL license (GNU GPL compatible - see ``LICENSE``), 
-  the framework offers several builtins reference configurations to 
-  check your computing architecture and evaluate the model skills and performances (``./cfgs``).
-| The end user could also find some idealized test cases on the web to serve as examples and 
-  to study particular processes.
+- 2-way nesting package `AGRIF`_ to create embedded zooms seamlessly
+- Flexible biogeomchemistry with online coarsening and possible integration of a customized model 
+- Versatile data assimilation interface with 3 different modules
+  (tangent linear, observational operators and increments)
 
-A set of tools is also provided to setup your own configuration and 
-[pre|post]process your data (``./tools``).
+lation a efficient XIOS_ server for outputing diagnostics a coupled via OASIS_ to alternative components or other models to enable Earth system modelling.
 
--------
-Options
--------
+| Several builtins configurations are provided to assess the skills and performances of the model which
+	can be used as templates for setting up a new configuration (``./cfgs``).
+| The end user could also find some idealised test cases on the web to serve as examples and
+	to study particular processes (``./tests``).
 
-For writing diagnostics in a efficient way, NEMO make use of XIOS_ server which 
-controlled the outputs using XML input file.
+A set of tools is also provided to setup your own configuration and [pre|post]process your data (``./tools``).
 
-To enable Earth system modelling, NEMO can be interfaced via 
-OASIS_ coupleur to external components such as atmospheric models or 
-alternative models of sea-ice or biogeochemistry.
+Literature
+==========
 
--------------
-Documentation
--------------
+| The NEMO reference manual and a quick start guide can be generated from Latex and RST source code files
+	(``./doc``), either in PDF or in HTML format, but it might require some additional installations.
+| In any case, both formats are available online: `HTML`_ | `PDF`_
 
-The NEMO reference manual can be generated from the LaTeX source code (``./doc``), 
-either in PDF or in HTML format, but it mights require some additionnal installations.
+| Since 2014 the project has a `Special Issue`_ in the Geoscientific Model Development (GMD) open-access journal
+	from the European Geosciences Union (EGU).
+	The main scope is to collect relevant manuscripts which cover a wide variety of topics like
+   process studies, new parameterizations, implementation of new model features and new NEMO configurations.
+| Also it provides a single portal to search, discover and understand about
+	the NEMO modelling framework potential and evolution and to submit their contributions. 
 
-In any case, both formats are available online on the `NEMO website`__.
-
----------------------
 Community development
----------------------
+=====================
 
 | The NEMO Consortium gathering 6 European institutes organises the sustainable development in order to 
-  keep a reliable evolving system since 2008.
-| It defined the multiyear development strategy which is implemented by the NEMO System Team.
+	keep a reliable evolving system since 2008.
+| It defines the multi-year development strategy which is implemented by the NEMO System Team.
 
---------
-Acronyms
---------
+`Working groups`_ are regularly created or resumed to gather the expertise in the NEMO community in order to 
+focus the development work on a specific subject or major component of NEMO.
+
+Definitions
+===========
 
 AGRIF
- Adaptive Grid Refinement In Fortran
+	*Adaptive Grid Refinement In Fortran*, 
+	package for the integration of full adaptive mesh refinement features within 
+	an existing multidimensional finite difference model
 
-LIM
- Louvain-la-Neuve Ice Model
+SI\ :sup:`3`\ 
+	*Sea Ice Integrated Initiative*, 
+	unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework
 
-OPA
- "Océan PArallélisé" (french)
+OASIS
+	*Ocean Atmosphere Sea Ice Soil*, 
+	coupling software to synchronise numerical codes representing different components of the climate system
 
 PISCES
- Pelagic Interactions Scheme for Carbon and Ecosystem Studies
+	*Pelagic Interactions Scheme for Carbon and Ecosystem Studies*, 
+	biogeochemical model simulating marine ecosystems, cycles of carbon and the main nutrients
 
 TAM
- Tangent Adjoint Model
+	*Tangent linear and Adjoint Model*, 
+	tools to analyse and control the NEMO dynamical core for a wide range of applications such as
+	sensitivity analysis, parameter estimation, vectors computation or data assimilation.
 
 TOP
- Tracers in Ocean Paradigm
+	*Tracers in Ocean Paradigm*, 
+	on/off-line oceanic tracers transport and biogeochemistry models
 
 XIOS
- XML Input Output Server
+	*XML Input Output Server*, 
+	library dedicated to input/output management of climate code
 
-----
-
-.. _AGRIF:                  http://agrif.imag.fr
-.. _Forge:                  http://forge.ipsl.jussieu.fr/nemo
-.. _NEMO:                   http://www.nemo-ocean.eu
-.. _OASIS:                  http://verc.enes.org/oasis
-.. _reference publications: http://www.nemo-ocean.eu/bibliography/documentation
-.. _XIOS:                   http://forge.ipsl.jussieu.fr/ioserver
-
-.. __:  NEMO_
+.. _AGRIF:          http://agrif.imag.fr
+.. _HTML:           http://www.nemo-ocean.eu/doc
+.. _NEMO:           http://www.nemo-ocean.eu
+.. _OASIS:          http://verc.enes.org/oasis
+.. _PDF:            http://www.nemo-ocean.eu/wp-content/uploads/NEMO_book.pdf
+.. _Special Issue:  http://www.geosci-model-dev.net/special_issue40.html
+.. _Working groups: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups
+.. _XIOS:           http://forge.ipsl.jussieu.fr/ioserver
