Changeset 11707


Ignore:
Timestamp:
2019-10-16T11:05:06+02:00 (11 months ago)
Author:
nicolasmartin
Message:

Review of the rst content
In short, new citations.rst to have a distinct page for NEMO references and
an update of the global directives

Location:
NEMO/trunk/doc/rst
Files:
1 added
5 edited
1 moved

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/doc/rst/README.rst

    r10991 r11707  
    33********************** 
    44 
    5 | The NEMO guide is made up of several files written in `ReStructuredText <http://docutils.sourceforge.net/rst.html>`_ (`.rst` extension), a WYSIWYG markup language used in the Python community, and scattered all over the NEMO sources. 
     5| The NEMO guide is made up of several files written in 
     6  `ReStructuredText <http://docutils.sourceforge.net/rst.html>`_ (`.rst` extension), 
     7  a WYSIWYG markup language used in the Python community, and scattered all over the NEMO sources. 
    68| You can view them one by one in plain text from `./source` folder, or export all to a user-friendly guide under `./build` (only HTML format at the moment, PDF expected later). 
    79 
  • NEMO/trunk/doc/rst/source/NEMO_guide.rst

    r10602 r11707  
    4444   :caption: Miscellaneous 
    4545 
     46   citations 
    4647   contributing 
    4748   release_notes 
    48    Glossary<definitions> 
     49   glossary 
    4950 
    5051.. include:: readme.rst 
    5152 
    5253.. Next headings markup acording to readme.rst 
    53  
    54 References 
    55 ========== 
    56  
    57 .. bibliography:: references.bib 
    58    :all: 
    59    :style: unsrt 
    60    :labelprefix: R 
    6154 
    6255Disclaimer 
  • NEMO/trunk/doc/rst/source/_static/style.css

    r10279 r11707  
    1 .rstblue               { color: blue    ; } 
    2 .rstgrey , .rstgreysup { color: grey    ; } 
    3 .rstgreen              { color: seagreen; } 
     1.blue            { color: blue    ; } 
     2.grey , .greysup { color: grey    ; } 
     3.green           { color: seagreen; } 
    44 
    55.logo { filter: invert(1) !important; } 
  • NEMO/trunk/doc/rst/source/data_assimilation.rst

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    77 
    88The assimilation interface to NEMO is split into three modules. 
    9 - OBS for the observation operator 
    10 - ASM for the application of increments and model bias correction (based on the assimilation increments). 
    11 - TAM the tangent linear and adjoint model. 
    129 
    13 Please see the `NEMO manual`_ for more details including information about the input file formats and 
     10- ``OBS`` for the observation operator 
     11- ``ASM`` for the application of increments and model bias correction 
     12  (based on the assimilation increments). 
     13- ``TAM`` the tangent linear and adjoint model. 
     14 
     15Please see |DOI man OCE|_ for more details including information about the input file formats and 
    1416the namelist settings. 
    1517 
    16 Observation and model comparison (OBS) 
    17 ====================================== 
     18Observation and model comparison (``OBS``) 
     19========================================== 
    1820 
    19 The observation and model comparison code (OBS) reads in observation files (profile temperature and salinity, 
    20 sea surface temperature, sea level anomaly, sea ice concentration, and velocity) and 
    21 calculates an interpolated model equivalent value at the observation location and nearest model timestep. 
     21The observation and model comparison code (OBS) reads in observation files 
     22(profile temperature and salinity, sea surface temperature, sea level anomaly, sea ice concentration, 
     23and velocity) and calculates an interpolated model equivalent value at 
     24the observation location and nearest model timestep. 
    2225The resulting data are saved in a feedback file (or files). 
    2326The code was originally developed for use with the NEMOVAR data assimilation code, but 
    2427can be used for validation or verification of model or any other data assimilation system. 
    2528This is all controlled by the namelist. 
    26 To build with the OBS code active ``key_diaobs`` must be set.  
     29To build with the OBS code active ``key_diaobs`` must be set. 
    2730 
    28 More details in the `NEMO manual`_ chapter 12. 
     31More details in |DOI man OCE|_ "Observation and Model Comparison (``OBS``)" chapter. 
    2932 
    30 Standalone observation operator (SAO) 
    31 ------------------------------------- 
     33Standalone observation operator (``SAO``) 
     34----------------------------------------- 
    3235 
    3336The OBS code can also be run after a model run using saved NEMO model data. 
     
    3942Then include ``SAO`` at the end of the relevant line in ``cfg.txt`` file. 
    4043Then recompile with the replacement main program in ``./src/SAO``. 
    41 This is a special version of ``nemogcm.F90`` (which doesn't run the model, but reads in the model fields, and 
    42 observations and runs the OBS code. 
    43 See section 12.4 of the `NEMO manual`_. 
     44This is a special version of ``nemogcm.F90`` (which doesn't run the model, 
     45but reads in the model fields, and observations and runs the OBS code. 
     46See "Standalone observation operator (``SAO``)" section in |DOI man OCE|_. 
    4447 
    45 Apply assimilation increments (ASM) 
    46 =================================== 
     48Apply assimilation increments (``ASM``) 
     49======================================= 
    4750 
    4851The ASM code adds the functionality to apply increments to the model variables: 
    4952temperature, salinity, sea surface height, velocity and sea ice concentration. 
    50 These are read into the model from a NetCDF file which may be produced by separate data assimilation code. 
     53These are read into the model from a NetCDF file which 
     54may be produced by separate data assimilation code. 
    5155The code can also output model background fields which are used as an input to data assimilation code. 
    52 This is all controlled by the namelist nam_asminc. 
     56This is all controlled by the namelist ``&nam_asminc``. 
    5357To build the ASM code ``key asminc`` must be set. 
    5458 
    55 More details in the `NEMO manual`_ chapter 13. 
     59More details in |DOI man OCE|_ "Apply Assimilation Increments (``ASM``)" chapter. 
    5660 
    57 Tangent linear and adjoint (TAM) 
    58 ================================ 
     61Tangent linear and adjoint (``TAM``) 
     62==================================== 
    5963 
    6064This is the tangent linear and adjoint code of NEMO which is useful to 4D VAR assimilation. 
  • NEMO/trunk/doc/rst/source/global.rst

    r10605 r11707  
    11.. Roles (custom styles related to CSS classes in 'source/_static/style.css') 
    22 
    3 .. role:: rstblue 
    4 .. role:: rstgreen 
    5 .. role:: rstgrey 
    6 .. role:: rstgreysup(sup) 
    7 .. role:: underline  
    8    :class: underline 
     3.. role:: blue 
     4.. role:: green 
     5.. role:: grey 
     6.. role:: greysup(sup) 
     7.. role: underline 
     8..   :class: underline 
    99 
    1010.. Substitutions 
    1111 
    12 .. |OPA| replace:: :rstblue:`NEMO-OPA` 
    13 .. |SI3| replace:: :rstgrey:`NEMO-SI`\ :rstgreysup:`3` 
    14 .. |TOP| replace:: :rstgreen:`NEMO-TOP/PISCES` 
     12.. |NEMO-OCE| replace:: :blue:`NEMO-OCE (Ocean dynamics)` 
     13.. |NEMO-ICE| replace:: :grey:`NEMO-SI`\ :greysup:`3`\ :grey:`(Sea Ice)` 
     14.. |NEMO-MBG| replace:: :green:`NEMO-TOP/PISCES (Biogeochemistry)` 
    1515 
    16 .. Institutes 
     16.. External links 
    1717 
    18 .. _CMCC:           https://www.cmcc.it  
    19 .. _CNRS:           https://www.cnrs.fr 
    20 .. _Mercator Ocean: https://www.mercator-ocean.fr 
    21 .. _Met Office:     https://www.metoffice.gov.uk 
    22 .. _MOI:            https://www.mercator-ocean.fr 
    23 .. _NERC:           https://nerc.ukri.org 
     18   .. Consortium institutes 
    2419 
    25 .. Models / Softwares 
     20.. _CMCC:       https://www.cmcc.it 
     21.. _CNRS:       https://www.cnrs.fr 
     22.. _Met Office: https://www.metoffice.gov.uk 
     23.. _MOI:        https://www.mercator-ocean.fr 
     24.. _NERC:       https://nerc.ukri.org 
     25 
     26   .. Models / Libraries / Dependencies 
    2627 
    2728.. _AGRIF:  http://agrif.imag.fr 
    28 .. _FCM:    https://metomi.github.io/fcm/doc/ 
     29.. _FCM:    https://metomi.github.io/fcm 
    2930.. _IOIPSL: https://forge.ipsl.jussieu.fr/igcmg/browser/IOIPSL 
     31.. _NEMO:   https://www.nemo-ocean.eu 
    3032.. _OASIS:  https://portal.enes.org/oasis 
     33.. _XIOS:   https://forge.ipsl.jussieu.fr/ioserver 
    3134 
    32 .. NEMO 
     35   .. Misc. 
    3336 
    34 .. _NEMO:          https://www.nemo-ocean.eu 
    35 .. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663 
    36 .. _NEMO guide:    :samp: https://doi.org/10.5281/zenodo.1475325 
    37 .. _NEMO manual:   https://doi.org/10.5281/zenodo.1464816 
    38 .. _SI3 manual:    :samp: https://doi.org/10.5281/zenodo.1471689 
    39 .. _TOP manual:    :samp: https://doi.org/10.5281/zenodo.1471700 
     37.. _EGU: http://www.egu.eu 
     38.. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html 
     39 
     40.. DOI 
     41 
     42   .. Publications (`:samp:` to deactivate link for unpublished documents) 
     43 
     44.. _DOI man   OCE:        https://doi.org/10.5281/zenodo.1464816 
     45.. _DOI man   ICE: :samp: https://doi.org/10.5281/zenodo.1471689 
     46.. _DOI man   MBG: :samp: https://doi.org/10.5281/zenodo.1471700 
     47.. _DOI strt  gui: :samp: https://doi.org/10.5281/zenodo.1475325 
     48.. _DOI dev  stgy:        https://doi.org/10.5281/zenodo.1471663 
     49 
     50   .. Badges (same labels as previously, substitution to link images) 
     51 
     52.. |DOI man   OCE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg 
     53.. |DOI man   ICE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg 
     54.. |DOI man   MBG| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg 
     55.. |DOI strt  gui| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg 
  • NEMO/trunk/doc/rst/source/glossary.rst

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    1 *********** 
    2 Definitions 
    3 *********** 
     1******** 
     2Glossary 
     3******** 
    44 
    55`AGRIF`_ 
    6    *Adaptive Grid Refinement In Fortran*,  
    7    package for the integration of full adaptive mesh refinement features within  
     6   *Adaptive Grid Refinement In Fortran*, 
     7   package for the integration of full adaptive mesh refinement features within 
    88   an existing multidimensional finite difference model 
    99 
    10 SI\ :sup:`3`\  
    11    *Sea Ice Integrated Initiative*,  
     10SI\ :sup:`3`\ 
     11   *Sea Ice Integrated Initiative*, 
    1212   unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 
    1313 
    1414`OASIS`_ 
    15    *Ocean Atmosphere Sea Ice Soil*,  
     15   *Ocean Atmosphere Sea Ice Soil*, 
    1616   coupling software to synchronise numerical codes representing different components of the climate system 
    1717 
    1818PISCES 
    19    *Pelagic Interactions Scheme for Carbon and Ecosystem Studies*,  
     19   *Pelagic Interactions Scheme for Carbon and Ecosystem Studies*, 
    2020   biogeochemical model simulating marine ecosystems, cycles of carbon and the main nutrients 
    2121 
    2222TAM 
    23    *Tangent linear and Adjoint Model*,  
     23   *Tangent linear and Adjoint Model*, 
    2424   tools to analyse and control the NEMO dynamical core for a wide range of applications such as 
    2525   sensitivity analysis, parameter estimation, vectors computation or data assimilation. 
    2626 
    2727TOP 
    28    *Tracers in Ocean Paradigm*,  
     28   *Tracers in Ocean Paradigm*, 
    2929   on/off-line oceanic tracers transport and biogeochemistry models 
    3030 
    3131`XIOS`_ 
    32    *XML Input Output Server*,  
     32   *XML Input Output Server*, 
    3333   library dedicated to input/output management of climate code 
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