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doc/rst/source/unpub/doc.rst

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doc/rst/source/unpub/doc.rst

+**Contents**
+
+.. contents::
+   :local:
+
+
+
+
+.. _`Former web platform forge`: https://forge.ipsl.jussieu.fr/nemo
+.. _`NEMO users' guide`: https://sites.nemo-ocean.io/user-guide
+.. _`Migration Guide`: https://sites.nemo-ocean.io/user-guide/migration.html
+.. _`Change list`: https://sites.nemo-ocean.io/user-guide/changes.html
+.. _`Test case repository`: https://github.com/NEMO-ocean/NEMO-examples
+.. _`How to cite`: https://www.nemo-ocean.eu/bibliography/how-to-cite/
+.. _`NEMO forums`: https://nemo-ocean.discourse.group
+.. _`NEMO newsletter`: https://listes.ipsl.fr/sympa/subscribe/nemo-newsletter
+.. _`NEMO publications`: https://www.nemo-ocean.eu/bibliography/publications/add
+.. _`NEMO projects`: https://www.nemo-ocean.eu/projects/add
+.. _`Special Issue`: https://gmd.copernicus.org/articles/special_issue40.html
+.. _`NEMO System Team wiki`: https://forge.nemo-ocean.eu/developers/home/-/wikis/Home
+.. _`NEMO ocean engine`: https://zenodo.org/record/1464816
+.. _`NEMO Tracers engine` : https://zenodo.org/record/1471700
+.. _`NEMO Sea Ice engine`: https://zenodo.org/record/1471689
+
+
+**Welcome to NEMO home page!**
+  
+NEMO (*Nucleus for European Modelling of the Ocean*) is a state-of-the-art modelling
+framework for research activities and forecasting services in ocean and climate sciences,
+developed in a sustainable way by the NEMO European consortium since 2008.
+
+This page intends to help you to get started using the NEMO platform and to introduce you
+to the different levels of information available. It starts here with NEMO release 4.2.0.
+
+Reminder: Our `Former web platform forge`_ (SVN+Trac) contains the previous documentation
+and releases made available from the beginning of the project up to of NEMO 4.0.
+
+Getting started
+===============
+
+Getting your hands on NEMO: the first steps are described in detail in the 
+`NEMO users' guide`_ . This explains how to download the code, build the environment, 
+create the executable, and perform a first integration.
+
+If you are already using a previous release of NEMO, please refer to the 
+`Migration Guide`_ which aims to help you to make the move to 4.2.0.
+
+The above users guides cover in detail what is available from gitlab and supported by NEMO
+System Team. Aside from this web platform, a set of test cases is also available from the
+`Test case repository`_ . These test cases can be useful for students, outreach, and
+exploring specific aspects of NEMO with light configurations. The web page also allows you
+to submit test cases you have developed and want to share with the community. Feel free to
+contribute!
+
+
+Project documentation
+=====================
+
+Reference manuals fully describing NEMO  for the three main component
+
+* |OCE| models the ocean {thermo}dynamics and solves the primitive equations (`./src/OCE <./src/OCE>`_)
+
+* |ICE| simulates sea-ice {thermo}dynamics, brine inclusions and subgrid-scale thickness 
+  variations (`./src/ICE <./src/ICE>`_)
+
+* |MBG| models the {on,off}line oceanic tracers transport and biogeochemical processes 
+  (`./src/TOP <./src/TOP>`_)
+are available from Zenodo:
+
+============ ======================== =====
+ Component    Reference Manual         DOI
+============ ======================== =====
+ |NEMO-OCE|   `NEMO ocean engine`_    .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6334656.svg
+                                         :target: https://doi.org/10.5281/zenodo.6334656                        
+ |NEMO-ICE|   `NEMO Sea Ice engine`_  *not yet available*
+ |NEMO-MBG|   `NEMO Tracers engine`_  .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg
+                                         :target: https://doi.org/10.5281/zenodo.1471700
+============ ======================== =====
+
+These reference manuals are the publications that should be cited in your own
+publications. Please visit `How to cite`_? for details.
+
+New features of 4.2.0 release are described in the `Change list`_ section of the `NEMO users' guide`_
+
+
+Asking questions, and exchanging information
+============================================
+- Register once for all and use the `NEMO forums`_ on discourse to share and discuss with the NEMO community.
+
+- Register once for all and receive by mail the `NEMO newsletter`_ : recommended for all
+  users to receive the major announcements from the project (new releases, open meetings and
+  main informations). Low traffic: about ten messages a year.
+
+
+Contributing to NEMO visibility: projects and publications
+==========================================================
+Please help us justifying the NEMO development efforts by
+
+-  Adding your publications using NEMO and its outputs to the `NEMO publications`_ page
+
+-  Describing your project using NEMO on the `NEMO projects`_ page
+
+NEMO also has a `Special Issue`_ in the open-access journal
+Geoscientific Model Development (GMD) from the European Geosciences Union
+The main scope is to collect relevant manuscripts covering various topics and
+to provide a single portal to assess the model potential and evolution.
+
+
+
+Contributing to NEMO development
+================================
+
+NEMO strives to be written in a way which allows the easy incorporation of developments.
+You are welcome to contribute to the development of the NEMO Shared reference.  NEMO
+development is driven by  NEMO Consortium planning and producing NEMO's sustainable
+development in order to keep a reliable evolving framework.  Development is organised and
+scheduled through a five years development strategy, Working groups and the activities of
+the development team (named NEMO System Team) in a yearly workplan. More information is
+available on the `NEMO System Team wiki`_
+
+
+Disclaimer
+==========
+
+The NEMO source code is freely available and distributed under
+`CeCILL v2.0 license <./LICENSE>`_ (GNU GPL compatible).
+
+You can use, modify and/or redistribute the software under its terms,
+but users are provided only with a limited warranty and the software's authors and
+the successive licensor's have only limited liability.

doc/rst/source/zooms.bib

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doc/rst/source/zooms.bib

+
+@article{         debreu.marchesiello.ea_OM12,
+  title         = "Two-way nesting in split-explicit ocean models:
+                  Algorithms, implementation and validation",
+  pages         = "1--21",
+  journal       = "Ocean Modelling",
+  volume        = "49-50",
+  author        = "Debreu, Laurent and Marchesiello, Patrick and Penven,
+                  Pierrick and Cambon, Gildas",
+  year          = "2012",
+  month         = "Jun",
+  publisher     = "Elsevier BV",
+  issn          = "1463-5003",
+  doi           = "10.1016/j.ocemod.2012.03.003"
+}
+
+@article{         penven.debreu.ea_OM06,
+  title         = "Evaluation and application of the ROMS 1-way embedding
+                  procedure to the central california upwelling system",
+  pages         = "157--187",
+  journal       = "Ocean Modelling",
+  volume        = "12",
+  number        = "1-2",
+  author        = "Penven, Pierrick and Debreu, Laurent and Marchesiello,
+                  Patrick and McWilliams, James C.",
+  year          = "2006",
+  month         = "Jan",
+  publisher     = "Elsevier BV",
+  issn          = "1463-5003",
+  doi           = "10.1016/j.ocemod.2005.05.002"
+}
+
+@article{         spall.holland_JPO91,
+  title         = "A Nested Primitive Equation Model for Oceanic
+                  Applications",
+  pages         = "205--220",
+  journal       = "Journal of Physical Oceanography",
+  volume        = "21",
+  number        = "2",
+  author        = "Spall, Michael A. and Holland, William R.",
+  year          = "1991",
+  month         = "Feb",
+  publisher     = "American Meteorological Society",
+  issn          = "1520-0485",
+  doi           = "10.1175/1520-0485(1991)021<0205:anpemf>2.0.co;2"
+}

doc/rst/source/zooms.rst

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doc/rst/source/zooms.rst

+**************
+Embedded zooms
+**************
+
+.. todo::
+
+
+
+.. contents::
+   :local:
+
+Overview
+========
+
+AGRIF (Adaptive Grid Refinement In Fortran) is a library that
+allows the seamless space and time refinement over rectangular regions in NEMO.
+Refinement factors can be odd or even (usually lower than 5 to maintain stability).
+Interaction between grid is "two-ways" in the sense that
+the parent grid feeds the child grid open boundaries and
+the child grid provides volume averages of prognostic variables once
+a given number of time step is completed.
+These pages provide guidelines how to use AGRIF in NEMO.
+For a more technical description of the library itself, please refer to AGRIF_.
+
+Compilation
+===========
+
+Activating AGRIF requires to append the cpp key ``key_agrif`` at compilation time:
+
+.. code-block:: sh
+
+   ./makenemo [...] add_key 'key_agrif'
+
+Although this is transparent to users,
+the way the code is processed during compilation is different from the standard case:
+a preprocessing stage (the so called ``conv`` program) translates the actual code so that
+saved arrays may be switched in memory space from one domain to an other.
+
+Definition of the grid hierarchy
+================================
+
+An additional text file :file:`AGRIF_FixedGrids.in` is required at run time.
+This is where the grid hierarchy is defined.
+An example of such a file, here taken from the ``ICEDYN`` test case, is given below
+
+.. literalinclude:: ../../../tests/ICE_AGRIF/EXPREF/AGRIF_FixedGrids.in
+
+The first line indicates the number of zooms (1).
+The second line contains the starting and ending indices in both directions on the root grid
+(``imin=34 imax=63 jmin=34 jmax=63``) followed by the space and time refinement factors (3 3 3).
+The last line is the number of child grid nested in the refined region (0).
+A more complex example with telescoping grids can be found below and
+in the :file:`AGRIF_DEMO` reference configuration directory.
+
+.. todo::
+
+   Add some plots here with grid staggering and positioning?
+
+When creating the nested domain, one must keep in mind that
+the child domain is shifted toward north-east and
+depends on the number of ghost cells as illustrated by
+the *attempted* drawing below for ``nbghostcells=1`` and ``nbghostcells=3``.
+The grid refinement is 3 and ``nxfin`` is the number of child grid points in i-direction.
+
+.. image:: _static/agrif_grid_position.jpg
+
+Note that rectangular regions must be defined so that they are connected to a single parent grid.
+Hence, defining overlapping grids with the same refinement ratio will not work properly,
+boundary data exchange and update being only performed between root and child grids.
+Use of east-west periodic or north-fold boundary conditions is not allowed in child grids either.
+Defining for instance a circumpolar zoom in a global model is therefore not possible.
+
+Preprocessing
+=============
+
+Knowing the refinement factors and area,
+a ``NESTING`` pre-processing tool may help to create needed input files
+(mesh file, restart, climatological and forcing files).
+The key is to ensure volume matching near the child grid interface,
+a step done by invoking the :file:`Agrif_create_bathy.exe` program.
+You may use the namelists provided in the :file:`NESTING` directory as a guide.
+These correspond to the namelists used to create ``AGRIF_DEMO`` inputs.
+
+Namelist options
+================
+
+Each child grid expects to read its own namelist so that different numerical choices can be made
+(these should be stored in the form :file:`1_namelist_cfg`, :file:`2_namelist_cfg`, etc...
+according to their rank in the grid hierarchy).
+Consistent time steps and number of steps with the chosen time refinement have to be provided.
+Specific to AGRIF is the following block:
+
+.. literalinclude:: ../../namelists/namagrif
+   :language: fortran
+
+where sponge layer coefficients have to be chosen according to the child grid mesh size.
+The sponge area is hard coded in NEMO and applies on the following grid points:
+2 x refinement factor (from ``i=1+nbghostcells+1`` to ``i=1+nbghostcells+sponge_area``)
+
+.. rubric:: References
+
+.. bibliography:: zooms.bib
+   :all:
+   :style: unsrt
+   :labelprefix: A
+   :keyprefix: a-