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This present forge is now archived and remained online for history.
Changeset 10279 for NEMO/trunk – NEMO

Changeset 10279 for NEMO/trunk


Ignore:
Timestamp:
2018-11-07T12:04:15+01:00 (5 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
Location:
NEMO/trunk
Files:
3 added
1 deleted
16 edited
4 moved

Legend:

Unmodified
Added
Removed

  • NEMO/trunk/INSTALL.rst

    r10201 r10279  
    1 ===================== 
     1********************* 
    22Install the framework 
    3 ===================== 
     3********************* 
    44 
    5 .. include:: .global.rst 
    6  
    7 .. contents:: \ 
     5.. contents:: 
    86   :local: 
    97       
    … …  
    2422======================= 
    2523 
    26 Download the source code  
     24Download the source code 
     25------------------------ 
    2726 
    2827.. code:: console 
    … …  
    3130 
    3231Description of directory tree 
    33 ============================= 
     32----------------------------- 
    3433 
    35 +-----------+---------------------------------------------------------------+ 
    36 | Folder    | Purpose                                                       | 
    37 +===========+===============================================================+ 
    38 | ``arch``  | Settings (per architecture-compiler pair)                     | 
    39 +-----------+---------------------------------------------------------------+ 
    40 | ``cfgs``  | Reference configurations                                      | 
    41 +-----------+---------------------------------------------------------------+ 
    42 | ``doc``   | - ``latex``: reference manuals for NEMO, SI\ :sup:`3`\  & TOP | 
    43 |           | - ``rst``:   quick start guide                                | 
    44 +-----------+---------------------------------------------------------------+ 
    45 | ``ext``   | Dependencies included (AGRIF, FCM & IOIPSL)                   | 
    46 +-----------+---------------------------------------------------------------+ 
    47 | ``mk``    | Building  routines                                            | 
    48 +-----------+---------------------------------------------------------------+ 
    49 | ``src``   | Modelling routines                                            | 
    50 |           |                                                               | 
    51 |           | - ``ICE``: SI\ :sup:`3`\ for sea ice                          | 
    52 |           | - ``NST``: AGRIF         for embedded zooms                   | 
    53 |           | - ``OCE``: OPA           for ocean dynamics                   | 
    54 |           | - ``MBG``: TOP           for tracers                          | 
    55 +-----------+---------------------------------------------------------------+ 
    56 | ``tests`` | Test cases                                                    | 
    57 +-----------+---------------------------------------------------------------+ 
    58 | ``tools`` | Utilities to [pre|post]process data                           | 
    59 +-----------+---------------------------------------------------------------+ 
     34+-----------+------------------------------------------------------------+ 
     35| Folder    | Purpose                                                    | 
     36+===========+============================================================+ 
     37| ``arch``  | Settings (per architecture-compiler pair)                  | 
     38+-----------+------------------------------------------------------------+ 
     39| ``cfgs``  | :doc:`Reference configurations <configurations>`           | 
     40+-----------+------------------------------------------------------------+ 
     41| ``doc``   | - ``latex``: reference manuals for |OPA|, |SI3| & |TOP|    | 
     42|           | - ``namelists``: k start guide                             | 
     43|           | - ``rst``:   quick start guide                             | 
     44+-----------+------------------------------------------------------------+ 
     45| ``ext``   | Dependencies included (AGRIF, FCM & IOIPSL)                | 
     46+-----------+------------------------------------------------------------+ 
     47| ``mk``    | Building  routines                                         | 
     48+-----------+------------------------------------------------------------+ 
     49| ``src``   | Modelling routines                                         | 
     50|           |                                                            | 
     51|           | - ``ICE``: |SI3| for sea ice                               | 
     52|           | - ``NST``: AGRIF for embedded zooms                        | 
     53|           | - ``OCE``: |OPA| for ocean dynamics                        | 
     54|           | - ``MBG``: |TOP| for tracers                               | 
     55+-----------+------------------------------------------------------------+ 
     56| ``tests`` | :doc:`Test cases <test_cases>` (unsupported)               | 
     57+-----------+------------------------------------------------------------+ 
     58| ``tools`` | :doc:`Utilities <tools>` to [pre|post]process data         | 
     59+-----------+------------------------------------------------------------+ 
    6060 
    6161Extract and install XIOS 
    … …  
    121121   .. literalinclude:: 
    122122 
    123 ----------------- 
    124123Default behaviour 
    125124----------------- 
    … …  
    128127    If –n option is not specified, ORCA2_LIM is the default configuration used.  
    129128 
    130 ----------------------------- 
    131129Tools used during the process 
    132130----------------------------- 
    … …  
    136134    bld.cfg : FCM rules to compile  
    137135 
    138 -------- 
    139136Examples 
    140137-------- 
    … …  
    163160        echo "./makenemo -n MY_CONFIG -j0 add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" "; 
    164161 
    165 ----------------- 
    166162Running the model 
    167 ----------------- 
     163================= 
    168164 
    169165Once makenemo has run successfully, the opa executable is available in ``CONFIG/MY_CONFIG/EXP00`` 
    … …  
    173169   mpirun -n $NPROCS ./opa    # $NPROCS is the number of processes ; mpirun is your MPI wrapper 
    174170 
    175 -------------------------------------------- 
    176171Viewing and changing list of active CPP keys 
    177 -------------------------------------------- 
     172============================================ 
    178173 
    179174For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in:: 

  • 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. 

  • NEMO/trunk/REFERENCES.bib

    r10201 r10279  
    1 @Book{madec_bk08, 
    2    title = {NEMO ocean engine}, 
    3    publisher = {Note du P\^ole de mod{\'e}lisation, Institut Pierre-Simon Laplace 
    4    (IPSL), France, No 27, ISSN No 1288-1619}, 
    5    year = {2008}, 
    6    author = {G. Madec and NEMO System Team} 
     1@manual{NEMO_manual, 
     2   title={NEMO ocean engine}, 
     3   author={Madec Gurvan and NEMO System Team}, 
     4   organization={NEMO Consortium}, 
     5   journal={Notes du Pôle de modélisation de l\'Institut Pierre-Simon Laplace (IPSL)}, 
     6   number={27}, 
     7   publisher={Zenodo}, 
     8   abstract={The ocean engine of NEMO is a primitive equation model adapted to regional and 
     9   global ocean circulation problems. 
     10   It is intended to be a flexible tool for studying the ocean and its interactions with 
     11   the others components of the earth climate system over a wide range of space and time scales.}, 
     12   doi={10.5281/zenodo.1464816}, 
     13   edition={}, 
     14   year={} 
    715} 
    816 
    9 @Article{gmd-8-2465-2015, 
    10    author = {Aumont, O. and Eth\'e, C. and Tagliabue, A. and Bopp, L. and Gehlen, M.}, 
    11    title = {{PISCES}-v2: an ocean biogeochemical model for carbon and ecosystem studies}, 
    12    journal = {Geoscientific Model Development}, 
    13    volume = {8}, 
    14    year = {2015}, 
    15    number = {8}, 
    16    pages = {2465--2513}, 
    17    doi = {10.5194/gmd-8-2465-2015} 
     17@manual{SI3_manual, 
     18   title={SI³ – Sea Ice modelling Integrated Initiative – The NEMO Sea Ice engine}, 
     19   author={NEMO Sea Ice Working Group}, 
     20   organization={NEMO Consortium}, 
     21   journal={Notes du Pôle de modélisation de l\'Institut Pierre-Simon Laplace (IPSL)}, 
     22   number={31}, 
     23   publisher={Zenodo}, 
     24   abstract={SI³ (Sea Ice modelling Integrated Initiative) is the sea ice engine of NEMO 
     25   (Nucleus for European Modelling of the Ocean). 
     26   It is adapted to regional and global sea ice and climate problems. 
     27   It is intended to be a flexible tool for studying sea ice and its interactions with 
     28   the other components of the Earth System over a wide range of space and time scales. 
     29   SI3 is based on the Arctic Ice Dynamics Joint EXperiment (AIDJEX) framework, 
     30   combining the ice thickness distribution framework, the conservation of horizontal momentum, 
     31   an elastic-viscous plastic rheology, and energy-conserving halo-thermodynamics. 
     32   Prognostic variables are the two-dimensional horizontal velocity field, ice volume, area, enthalpy, 
     33   salt content, snow volume and enthalpy. 
     34   In the horizontal direction, the model uses a curvilinear orthogonal grid. 
     35   In the vertical direction, the model uses equally-spaced layers. 
     36   In thickness space, the model uses thickness categories with prescribed boundaries. 
     37   Various physical and numerical choices are available to describe sea ice physics. 
     38   SI3 is interfaced with the NEMO ocean engine, and, via the OASIS coupler, with 
     39   several atmospheric general circulation models. 
     40   It also supports two-way grid embedding via the AGRIF software.}, 
     41   doi={10.5281/zenodo.1471689}, 
     42   edition={}, 
     43   year={} 
     44} 
     45 
     46@manual{TOP_manual, 
     47   title={TOP – Tracers in Ocean Paradigm – The NEMO Tracers engine}, 
     48   author={NEMO TOP Working Group}, 
     49   organization={NEMO Consortium}, 
     50   journal={Notes du Pôle de modélisation de l\'Institut Pierre-Simon Laplace (IPSL)}, 
     51   number={28}, 
     52   publisher={Zenodo}, 
     53   abstract={}, 
     54   doi={10.5281/zenodo.1471700}, 
     55   edition={}, 
     56   year={} 
    1857} 
    1958 
    … …  
    2867   doi = {10.5194/gmd-8-1245-2015} 
    2968} 
    30  
    31 @Article{gmd-8-2991-2015, 
    32    author = {Rousset, C. and Vancoppenolle, M. and Madec, G. and Fichefet, T. and Flavoni, S. and Barth\'elemy, A. and Benshila, R. and Chanut, J. and Levy, C. and Masson, S. and Vivier, F.}, 
    33    title = {The {L}ouvain-la-{N}euve sea ice model {LIM}3.6: global and regional capabilities}, 
    34    journal = {Geoscientific Model Development}, 
    35    volume = {8}, 
    36    year = {2015}, 
    37    number = {10}, 
    38    pages = {2991--3005}, 
    39    doi = {10.5194/gmd-8-2991-2015} 
    40 } 
    41  
    42 @Article{vancoppenolle200933, 
    43    title = "Simulating the mass balance and salinity of Arctic and Antarctic sea ice. 1. Model description and validation", 
    44    journal = "Ocean Modelling", 
    45    volume = "27", 
    46    number = "1–2", 
    47    pages = "33 - 53", 
    48    year = "2009", 
    49    issn = "1463-5003", 
    50    doi = "10.1016/j.ocemod.2008.10.005", 
    51    author = "Martin Vancoppenolle and Thierry Fichefet and Hugues Goosse and Sylvain Bouillon and Gurvan Madec and Miguel Angel Morales Maqueda", 
    52    keywords = "sea ice, model, thickness, salinity, age, arctic, antarctic" 
    53 } 

  • NEMO/trunk/RELEASE_NOTES.rst

    r10201 r10279  
    1 ====================== 
     1********************** 
    22What's new in NEMO 4.0 
    3 ====================== 
    4  
    5 .. include:: .global.rst 
     3********************** 
    64 
    75.. contents:: 
    … …  
    208206.. _TOP User Quick Guide:        http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide 
    209207 
     208.. The following references should be in the manual bibliographies and referenced via 'bibliography' directive 
    210209.. _Brodeau 2017:                http://doi.org/10.1175/JPO-D-16-0169.1 
    211210.. _Holland 2012:                http://doi.org/10.1175/JCLI-D-11-00078.1 

  • NEMO/trunk/cfgs/AGRIF_DEMO/README.rst

    r10201 r10279  
    1 Embedded zooms with AGRIF 
    2 ========================= 
    3  
    4 .. include:: .global.rst 
     1********************** 
     2Embedded zooms (AGRIF) 
     3********************** 
    54 
    65.. contents:: 
    76   :local: 
    87 
    9 -------- 
    108Overview 
    11 -------- 
     9======== 
    1210 
    1311AGRIF (Adaptive Grid Refinement In Fortran) is a library that allows the seamless space and time refinement over 
    … …  
    1917For a more technical description of the library itself, please refer to http://agrif.imag.fr. 
    2018 
    21 ----------- 
    2219Compilation 
    23 ----------- 
     20=========== 
    2421 
    2522Activating AGRIF requires to append the cpp key ``key_agrif`` at compilation time:  
    … …  
    3431saved arrays may be switched in memory space from one domain to an other. 
    3532 
    36 -------------------------------- 
    3733Definition of the grid hierarchy 
    38 -------------------------------- 
     34================================ 
    3935 
    4036An additional text file ``AGRIF_FixedGrids.in`` is required at run time. 
    … …  
    6864Defining for instance a circumpolar zoom in a global model is therefore not possible.  
    6965 
    70 ------------- 
    7166Preprocessing 
    72 ------------- 
     67============= 
    7368 
    7469Knowing the refinement factors and area, a ``NESTING`` pre-processing tool may help to create needed input files 
    … …  
    7974These correspond to the namelists used to create ``AGRIF_DEMO`` inputs. 
    8075 
    81 ---------------- 
    8276Namelist options 
    83 ---------------- 
     77================ 
    8478 
    8579Each child grid expects to read its own namelist so that different numerical choices can be made 
    … …  
    104982 x refinement factor (from i=1+nbghostcells+1 to i=1+nbghostcells+sponge_area)  
    10599 
    106 ---------- 
    107100References 
    108 ---------- 
     101========== 
    109102 
    110103.. bibliography:: zooms.bib 
    111104   :all: 
    112105   :style: unsrt 
     106   :labelprefix: A 
     107   :keyprefix: a- 

  • NEMO/trunk/cfgs/AGRIF_DEMO/zooms.bib

    r10201 r10279  
    1 @article{DEBREU20121, 
     1@article{DEBREU2012, 
    22   title = "Two-way nesting in split-explicit ocean models: Algorithms, implementation and validation", 
    33   journal = "Ocean Modelling", 
    … …  
    1111} 
    1212 
    13 @article{PENVEN2006157, 
     13@article{PENVEN2006, 
    1414   title = "Evaluation and application of the {ROMS} 1-way embedding procedure to the central california upwelling system", 
    1515   journal = "Ocean Modelling", 
    … …  
    2424} 
    2525 
    26 @article{doi:10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2, 
     26@article{SPALL1991, 
    2727   author = {Spall, Michael A. and Holland, William R.}, 
    2828   title = {A Nested Primitive Equation Model for Oceanic Applications}, 

  • NEMO/trunk/cfgs/README.rst

    r10201 r10279  
    1 ===================== 
    2 Build a configuration 
    3 ===================== 
    4  
    5 .. include:: .global.rst 
     1***************************** 
     2Run a reference configuration 
     3***************************** 
    64 
    75.. contents:: 
    … …  
    97   :depth: 1 
    108       
    11 .. role:: underline  
    12    :class: underline 
    13  
    149Official configurations 
    1510======================= 
    … …  
    4742+----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    4843 
    49 ---------- 
    5044AGRIF_DEMO 
    5145---------- 
    … …  
    7872   0 
    7973 
    80 ----- 
    8174AMM12 
    8275----- 
    … …  
    10194Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    10295 
    103 -------- 
    10496C1D_PAPA 
    10597-------- 
    … …  
    127119- surface chlorophyll file (``chlorophyll_PAPASTATION.nc``) deduced from Seawifs data. 
    128120 
    129 -------- 
    130121GYRE_BFM 
    131122-------- 
    … …  
    134125BFM biogeochemichal model in coupled mode. 
    135126 
    136 ----------- 
    137127GYRE_PISCES 
    138128----------- 
    … …  
    145135 
    146136Running GYRE as a benchmark 
    147 --------------------------- 
     137^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    148138 
    149139This simple configuration can be used as a benchmark since it is easy to increase resolution 
    … …  
    206196http://prodn.idris.fr/thredds/catalog/ipsl_public/reee451/NEMO_OUT/GYRE/catalog.html 
    207197 
    208 ---------------- 
    209198ORCA2_ICE_PISCES 
    210199---------------- 
    … …  
    293282  `COREII`_ forcing files extrapolated on continents 
    294283 
    295 ---------------- 
    296284ORCA2_OFF_PISCES 
    297285---------------- 
    … …  
    305293They are coming from a 2000 years of an ORCA2_LIM climatological run using ERA40 atmospheric forcing. 
    306294 
    307 ------------- 
    308295ORCA2_OFF_TRC 
    309296------------- 
    … …  
    320307ERA40 atmospheric forcing. 
    321308 
    322 ------------- 
    323309ORCA2_SAS_ICE 
    324310------------- 
    … …  
    335321Same input files as `ORCA2_ICE_PISCES`_ are needed plus fields from a previous ORCA2_LIM run. 
    336322 
    337 More informations on input and configuration files in `NEMO Reference manual`_. 
    338  
    339 ------- 
     323More informations on input and configuration files in `NEMO manual`_. 
     324 
    340325SPITZ12 
    341326------- 
    … …  
    358343.. _ORCA2_ICE_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar 
    359344.. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar 
    360 .. _NEMO Reference manual:        http://forge.ipsl.jussieu.fr/nemo/doxygen/index.html?doc=NEMO 
    361345.. _INPUTS_C1D_PAPA_v4.0.tar:     http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar 
    362346.. _Reffray 2015:                 http://www.geosci-model-dev.net/8/69/2015 

  • NEMO/trunk/cfgs/SHARED/README.rst

    r10201 r10279  
    1 Inputs-Outputs with XIOS 
    2 ======================== 
    3  
    4 .. include:: .global.rst 
     1****************** 
     2Diagnostics (XIOS) 
     3****************** 
    54 
    65.. contents:: 
     6   :local: 
    77 
    88| Output of diagnostics in NEMO is usually done using XIOS. 
    … …  
    1010  some simple arithmetic or regridding is carried out in parallel to the NEMO model run. 
    1111| This page gives a basic introduction to using XIOS with NEMO. 
    12   Much more information is available from the XIOS homepage above and from the `Reference Manual`_. 
     12  Much more information is available from the XIOS homepage above and from the `NEMO manual`_. 
    1313 
    1414Use of XIOS for diagnostics is activated using the pre-compiler key ``key_iomput``. 
    1515The default version of XIOS is the 2.0 release.  
    1616 
    17 ------------------------------ 
    1817Extracting and installing XIOS 
    19 ------------------------------ 
     18============================== 
    2019 
    21201. Install the NetCDF4 library. 
    … …  
    2827      $ svn co ​http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.0 xios-2.0 
    2928 
    30    and follow the instructions in `XIOS documentation`_ to compile it. 
    31    If you find problems at this stage, support can be found by subscribing to the `XIOS users mailing list`_ and 
    32    sending a mail message to it.  
     29   and follow the instructions in :xios:`XIOS documentation <wiki/documentation>` to compile it. 
     30   If you find problems at this stage, support can be found by subscribing to the `XIOS mailing list 
     31   <http://forge.ipsl.jussieu.fr/mailman/listinfo.cgi/xios-users>`_ 
     32   and sending a mail message to it.  
    3333 
    34 --------- 
    3534Namelists 
    36 --------- 
     35========= 
    3736 
    3837XIOS is controlled using xml input files that should be copied to your model run directory before 
    … …  
    4746Note that the ``domain_def.xml`` file is also different for XIOS 2.0. 
    4847 
    49 ----- 
    5048Modes 
    51 ----- 
     49===== 
    5250 
    5351Detached Mode 
    … …  
    8179the total number of cores is larger than the number of grid points in the j direction then the model run will fail. 
    8280 
    83 ------------------------------ 
    84 Adding new diagnostics to NEMO 
    85 ------------------------------ 
     81Adding new diagnostics 
     82====================== 
    8683 
    8784If you want to add a NEMO diagnostic to the NEMO code you will need to do the following: 

  • NEMO/trunk/doc/rst/source/NEMO_guide.rst

    r10201 r10279  
    1 .. NEMO documentation master file, created by 
    2    sphinx-quickstart on Tue Oct  9 18:14:01 2018. 
    3    You can adapt this file completely to your liking, but it should at least 
    4    contain the root `toctree` directive. 
    5  
    61################# 
    72Quick Start Guide 
    … …  
    94 
    105.. 
    11    A hidden .global.rst should be included in every subfiles with `include` directive 
    12    It contains a list of common URL links  
    13       
    14 .. include:: .global.rst 
    15  
    16 .. include:: readme.rst 
    17  
    18 Summary 
    19 ======= 
    20  
    21 .. toctree:: 
    22    :maxdepth: 1 
    23    :titlesonly: 
    24  
    25    release_notes.rst 
    26    install.rst 
    27    reference_configurations.rst 
    28    test_cases.rst 
    29    setup_configuration.rst 
    30    interfacing_options.rst 
    31    definitions.rst 
    32  
    33 .. 
    34    For headings markup, this convention is recommended from Python’s Style Guide 
     6   For headings markup, this convention is recommended from Python’s Style Guide 
    357   # with overline, for parts 
    368   * with overline, for chapters 
    … …  
    4012   ", for paragraphs 
    4113 
    42 .. 
    43    Indices and tables 
    44    ================== 
    45    * :ref:`genindex` 
    46    * :ref:`modindex` 
    47    * :ref:`search` 
     14   'global.rst' contains a list of common directives (roles, substitutions and URL links) 
     15   It is loaded for each file thanks to 'rst_epilog' setting in 'conf.py' 
     16 
     17.. toctree:: 
     18   :hidden: 
     19 
     20   release_notes.rst 
     21 
     22.. toctree:: 
     23   :hidden: 
     24   :caption: Getting started 
     25 
     26   install 
     27   configurations 
     28   test_cases 
     29 
     30.. toctree:: 
     31   :hidden: 
     32   :caption: Setup your configuration 
     33 
     34   setup 
     35   diagnostics 
     36   tools 
     37 
     38.. toctree:: 
     39   :hidden: 
     40   :caption: Advanced use 
     41 
     42   zooms 
     43   coarsening 
     44   coupling 
     45   assimilation 
     46   tracers 
     47 
     48.. toctree:: 
     49   :hidden: 
     50   :caption: Glossary 
     51 
     52   definitions 
     53 
     54.. include:: readme.rst 
     55 
     56.. Next headings markup acording to readme.rst 
     57 
     58How to cite NEMO 
     59================ 
     60 
     61.. bibliography:: references.bib 
     62   :all: 
     63   :style: unsrt 
     64   :labelprefix: R 
     65 
     66Disclaimer 
     67========== 
     68 
     69The NEMO source code is freely available and distributed under CeCILL license 
     70(GNU GPL compatible - see ``./LICENSE``). 
     71 
     72You can use, modify and/or redistribute the software under its terms, 
     73but users are provided only with a limited warranty and the software's authors and 
     74the successive licensor's have only limited liability. 

  • NEMO/trunk/doc/rst/source/assimilation.rst

    r10258 r10279  
    1 Data assimilation 
    2 ================= 
    3  
    4 .. include:: .global.rst 
     1************************************** 
     2Data assimilation (OBS/SAO, ASM & TAM) 
     3************************************** 
    54 
    65.. contents:: 
    … …  
    1211- TAM the tangent linear and adjoint model. 
    1312 
    14 Please see the `NEMO reference manual`_ for more details including information about the input file formats and 
     13Please see the `NEMO manual`_ for more details including information about the input file formats and 
    1514the namelist settings. 
    1615 
    17 -------------------------------------- 
    1816Observation and model comparison (OBS) 
    19 -------------------------------------- 
     17====================================== 
    2018 
    2119The observation and model comparison code (OBS) reads in observation files (profile temperature and salinity, 
    … …  
    2826To build with the OBS code active ``key_diaobs`` must be set.  
    2927 
    30 More details in the `NEMO reference manual`_ chapter 12. 
     28More details in the `NEMO manual`_ chapter 12. 
    3129 
    3230Standalone observation operator (SAO) 
    … …  
    4341This is a special version of ``nemogcm.F90`` (which doesn't run the model, but reads in the model fields, and 
    4442observations and runs the OBS code. 
    45 See section 12.4 of the `NEMO reference manual`_. 
     43See section 12.4 of the `NEMO manual`_. 
    4644 
    47 ----------------------------------- 
    4845Apply assimilation increments (ASM) 
    49 ----------------------------------- 
     46=================================== 
    5047 
    5148The ASM code adds the functionality to apply increments to the model variables: 
    … …  
    5653To build the ASM code ``key asminc`` must be set. 
    5754 
    58 More details in the `NEMO reference manual`_ chapter 13. 
     55More details in the `NEMO manual`_ chapter 13. 
    5956 
    60 -------------------------------- 
    6157Tangent linear and adjoint (TAM) 
    62 -------------------------------- 
     58================================ 
    6359 
    6460This is the tangent linear and adjoint code of NEMO which is useful to 4D VAR assimilation. 
    65  
    66 .. _NEMO reference manual: http://doi.org/10.5281/zenodo. 

  • NEMO/trunk/doc/rst/source/conf.py

    r10201 r10279  
    2121 
    2222project = 'NEMO' 
    23 copyright = '2018, NEMO System Team' 
     23copyright = '' 
    2424author = 'NEMO System Team' 
    2525 
    … …  
    3939# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 
    4040# ones. 
    41 extensions = ['sphinxcontrib.bibtex'] 
     41extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex'] 
    4242 
    4343# Add any paths that contain templates here, relative to this directory. 
    … …  
    6363# directories to ignore when looking for source files. 
    6464# This pattern also affects html_static_path and html_extra_path . 
    65 exclude_patterns = [] 
     65exclude_patterns = ['global.rst'] 
    6666 
    6767# The name of the Pygments (syntax highlighting) style to use. 
    … …  
    7474# a list of builtin themes. 
    7575# 
    76 html_theme = 'alabaster' 
     76#html_theme = 'alabaster' 
     77html_theme = 'sphinx_rtd_theme' 
    7778 
    7879# Theme options are theme-specific and customize the look and feel of a theme 
    … …  
    8182# 
    8283html_theme_options = { 
    83     'logo': 'NEMO_grey.png', 
    84     'description': 'Community ocean model for multifarious space and time scales', 
    85     'fixed_sidebar': 'true', 
    86 #    'github_user': 'NEMO-ocean', 
    87 #    'github_repo': 'NEMO-examples', 
    88 #    'github_button': 'true', 
    89 #    'github_banner': 'true' 
     84#  Alabaster theme options 
     85#  'logo': 'NEMO_grey.png', 
     86#  'description': 'Community ocean model for multifarious space and time scales', 
     87#  'fixed_sidebar': True, 
    9088} 
    9189 
    … …  
    162160     'Miscellaneous'), 
    163161] 
     162 
     163 
     164# -- Customisation ----------------------------------------------------------- 
     165 
     166import datetime 
     167year = datetime.date.today().year 
     168copyright = '2008-' + str( year ) + ', NEMO Consortium' 
     169 
     170# Link aliases 
     171extlinks = { 
     172   'doi'    : ('http://doi.org/%s'                       , None), 
     173   'forge'  : ('http://forge.ipsl.jussieu.fr/nemo/%s'    , None), 
     174   'github' : ('http://github.com/%s'                    , None), 
     175   'xios'   : ('http://forge.ipsl.jussieu.fr/ioserver/%s', None), 
     176   'website': ('http://www.nemo-ocean.eu/%s'             , None), 
     177   'zenodo' : ('http://zenodo.org/publication/%s'        , None) 
     178} 
     179 
     180# Include common directives for every rst file 
     181rst_epilog = open('global.rst', 'r').read() 

  • NEMO/trunk/doc/rst/source/coupling.rst

    r10201 r10279  
    1 Coupling with other models (OASIS, SAS, ...) 
    2 ============================================ 
    3  
    4 .. include:: .global.rst 
     1********************** 
     2Coupling (OASIS & SAS) 
     3********************** 
    54 
    65NEMO currently exploits OASIS-3-MCT to implement a generalised coupled interface 

  • NEMO/trunk/doc/rst/source/definitions.rst

    r10201 r10279  
    1 =========== 
     1*********** 
    22Definitions 
    3 =========== 
     3*********** 
    44 
    5 .. include:: .global.rst 
    6  
    7 AGRIF 
     5`AGRIF`_ 
    86   *Adaptive Grid Refinement In Fortran*,  
    97   package for the integration of full adaptive mesh refinement features within  
    … …  
    1412   unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 
    1513 
    16 OASIS 
     14`OASIS`_ 
    1715   *Ocean Atmosphere Sea Ice Soil*,  
    1816   coupling software to synchronise numerical codes representing different components of the climate system 
    … …  
    3129   on/off-line oceanic tracers transport and biogeochemistry models 
    3230 
    33 XIOS 
     31`XIOS`_ 
    3432   *XML Input Output Server*,  
    3533   library dedicated to input/output management of climate code 

  • NEMO/trunk/doc/rst/source/global.rst

    r10277 r10279  
    1 .. Roles (custom styles related to CSS classes) 
     1.. Roles (custom styles related to CSS classes in 'source/_static/style.css') 
    22 
    33.. role:: rstblue 
    … …  
    55.. role:: rstgrey 
    66.. role:: rstgreysup(sup) 
     7.. role:: underline  
     8   :class: underline 
    79 
    8 .. Links 
     10.. Substitutions 
    911 
    10    .. Institutes 
     12.. |OPA| replace:: :rstblue:`NEMO-OPA` 
     13.. |SI3| replace:: :rstgrey:`NEMO-SI`\ :rstgreysup:`3` 
     14.. |TOP| replace:: :rstgreen:`NEMO-TOP/PISCES` 
     15 
     16.. Institutes 
    1117 
    1218.. _CMCC:           http://www.cmcc.it  
    … …  
    1723.. _NERC:           http://nerc.ukri.org 
    1824 
    19    .. Models / Softwares 
     25.. Models / Softwares 
    2026 
    2127.. _AGRIF: http://agrif.imag.fr 
    2228.. _OASIS: http://verc.enes.org/oasis 
     29.. _XIOS:  http://forge.ipsl.jussieu.fr/ioserver 
    2330 
    24    .. NEMO 
     31.. NEMO 
    2532 
    26 .. _NEMO:             http://www.nemo-ocean.eu 
    27 .. _Reference Manual: http://doi.org/10.5281/zenodo.1137733 
    28 .. _Special Issue:    http://www.geosci-model-dev.net/special_issue40.html 
    29 .. _Working Groups:   http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups 
    30  
    31    .. XIOS 
    32  
    33 .. _XIOS:                    http://forge.ipsl.jussieu.fr/ioserver 
    34 .. _XIOS documentation:      http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation 
    35 .. _XIOS users mailing list: http://forge.ipsl.jussieu.fr/mailman/listinfo.cgi/xios-users 
     33.. _NEMO:          http://www.nemo-ocean.eu 
     34.. _NEMO strategy: http://doi.org/10.5281/zenodo.1471663 
     35.. _NEMO guide:    http://doi.org/10.5281/zenodo.1475325 
     36.. _NEMO manual:   http://doi.org/10.5281/zenodo.1464816 
     37.. _SI3 manual:    http://doi.org/10.5281/zenodo.1471689 
     38.. _TOP manual:    http://doi.org/10.5281/zenodo.1471700 

  • NEMO/trunk/doc/rst/source/interfacing_options.rst

    r10201 r10279  
    33=================== 
    44 
    5 .. include:: .global.rst 
    6  
    7 .. contents:: 
     5.. 
     6   contents:: 
    87   :local: 
    98   :depth: 1 
    109 
    1110.. include:: zooms.rst 
     11 
     12.. bibliography:: zooms.bib 
     13   :all: 
     14   :style: unsrt 
     15   :labelprefix: A 
     16   :keyprefix: a- 
    1217 
    1318---- 
    … …  
    2126---- 
    2227 
    23 .. include:: data_assimilation.rst 
     28.. include:: assimilation.rst 
    2429 
    2530---- 

  • 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 

  • NEMO/trunk/src/TOP/README.rst

    r10201 r10279  
    1 TOP interface 
    2 ============= 
    3  
    4 .. include:: .global.rst 
     1********************* 
     2Oceanic tracers (TOP) 
     3********************* 
    54 
    65.. contents:: 
    … …  
    1716up to the full set of equations involving marine biogeochemical cycles. 
    1817 
    19 --------- 
    2018Structure 
    21 --------- 
     19========= 
    2220 
    2321TOP interface has the following location in the source code ``./src/MBG/`` and 
    … …  
    7371   trend computation for tracers 
    7472 
    75 ------------------ 
    7673Synthetic Workflow 
    77 ------------------ 
     74================== 
    7875 
    7976A synthetic description of the TOP interface workflow is given below to summarize the steps involved in 
    … …  
    125122  ↳ call trc_rst_wri, output tracers restart files 
    126123 
    127 --------------------- 
    128124Namelists walkthrough 
    129 --------------------- 
     125===================== 
    130126 
    131127namelist_top 
    … …  
    235231|||| &'''namc14_fcg'''     !  files & dates || 
    236232 
    237 ----------------------------------------------------- 
    238233``MY_TRC`` interface for coupling external BGC models 
    239 ----------------------------------------------------- 
     234===================================================== 
    240235 
    241236The generalized interface is pivoted on MY_TRC module that contains template files to build the coupling between 
    … …  
    277272   if not done elsewhere in the code, using the call to iom_put. 
    278273 
    279 --------------------------------------------------- 
    280274Coupling an external BGC model using NEMO framework 
    281 --------------------------------------------------- 
     275=================================================== 
    282276 
    283277The coupling with an external BGC model through the NEMO compilation framework can be achieved in 

  • NEMO/trunk/tests/README.rst

    r10240 r10279  
    1 ====================== 
     1********************** 
    22Explore the test cases 
    3 ====================== 
     3********************** 
     4 
     5.. contents:: 
     6   :local: 
     7 
     8List 
     9==== 
    410 
    511  The description below is a brief description of the test cases available in NEMO.  
    6   For detailed description and notebook, the reader is directed on the `Github repository`_ 
    7  
    8 .. _Github repository:   https://github.com/sflavoni/NEMO-test-cases/ 
    912 
    1013ICEDYN 
    11 ====== 
     14------ 
    1215   
    1316  This test case illustrates the advection of an ice patch across a East/West and North/South periodic channel.  
    … …  
    1922 
    2023VORTEX 
    21 ====== 
     24------ 
    2225   
    2326  This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom. 
    … …  
    3235 
    3336ISOMIP 
    34 ====== 
     37------ 
    3538 
    3639  The purpose of this test case is to evaluate the impact of various schemes and new development with the iceshelf cavities circulation and melt. 
    … …  
    4346 
    4447LOCK_EXCHANGE 
    45 ============= 
     48------------- 
    4649 
    4750  The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted 
    … …  
    5659 
    5760OVERFLOW 
    58 ======== 
     61-------- 
    5962 
    6063  The OVERFLOW experiment illustrates the impact of different choices of numerical schemes  
    … …  
    6972 
    7073WAD 
    71 === 
     74--- 
    7275 
    7376  A set of simple closed basin geometries for testing the Wetting and drying capabilities.  
    … …  
    8184 
    8285CANAL 
    83 ===== 
     86----- 
    8487 
    8588  East-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex). 
    … …  
    8790  .. image::_static/CANAL_image.gif 
    8891 
    89 ================== 
    9092Compile test cases 
    9193================== 
     94 
    9295The compilation of the test cases is very similar to the manner the reference configurations are compiled. 
    93 If you are not familiar on how to compile NEMO, it is first recomended to read the instruction  
    94 `here <http://forge.ipsl.jussieu.fr/nemo/wiki/Users/ModelInstall>`_ 
     96If you are not familiar on how to compile NEMO, it is first recomended to read :doc:`the instructions <install>` 
    9597 
    9698| In the same manner as the ref. cfg are compiled with '-r' option, test cases can be compile by the use of makenemo with '-a' option. 
    … …  
    99101 
    100102.. code-block:: console 
    101                     
    102         $ ./makenemo -n WAD2 -a WAD -m macport_osx -j 4 
     103  
     104   $ ./makenemo -n WAD2 -a WAD -m macport_osx -j 4 
    103105 
    104 ===================================== 
    105106Run and analyse the test cases 
    106 ===================================== 
     107============================== 
     108 
    107109There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly.  
    108 All the detailed on how to run a specific test cases and Jupyter notebook are available on github `here <https://github.com/sflavoni/NEMO-test-cases>`_. 
     110For detailed description and Jupyter notebook, the reader is directed on 
     111the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_ 
    109112 
    110 ========== 
    111113References 
    112114========== 
    113115 
    114 ..      bibliography:: test_cases.bib 
    115                 :all: 
    116         :style: unsrt 
     116.. bibliography:: test_cases.bib 
     117   :all: 
     118   :style: unsrt 
     119   :labelprefix: T 
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