Changeset 5920b7f in flex_extract.git for For_developers


Ignore:
Timestamp:
May 30, 2020, 9:35:50 AM (4 years ago)
Author:
anphi <anne.philipp@…>
Branches:
master, ctbto, dev
Children:
a9d33f6
Parents:
550435b
Message:

New compilation of Sphinx after extensive review in language/content/understanding

Location:
For_developers/Sphinx/source
Files:
13 edited

Legend:

Unmodified
Added
Removed

  • For_developers/Sphinx/source/Documentation/Api/api_fortran.rst

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    1 **************************************
     1******************************************************
    22Auto-generated documentation for the Fortran programme
    3 **************************************
     3******************************************************
    44
    55.. contents::

  • For_developers/Sphinx/source/Documentation/Api/api_python.rst

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    1 *************************************
     1***************************************************
    22Auto-generated documentation for the Python scripts
    3 *************************************
     3***************************************************
    44
    55.. contents::

  • For_developers/Sphinx/source/Documentation/Input/compilejob.rst

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    1 ********************************************
     1*********************************************
    22The compilation job script ``compilejob.ksh``
    3 ********************************************
     3*********************************************
    44
    55The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.

  • For_developers/Sphinx/source/Documentation/Input/examples.rst

    rf20342a r5920b7f  
    3636        CONTROL_OD.OPER.FC.twicedaily.3hourly
    3737
     38.. todo::
     39
    3840   #PS some information to be added.
    3941 

  • For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst

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    1 **************************************
     1****************************************
    22The Fortran makefile for ``calc_etadot``
    3 **************************************
     3****************************************
    44
    55.. _ref-convert:

  • For_developers/Sphinx/source/Documentation/Input/jobscript.rst

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    1 *************************
     1**************************
    22The job script ``job.ksh``
    3 *************************
     3**************************
    44
    55The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
    … …  
    2020
    2121What does the job script do?
    22 ---------------------------
     22----------------------------
    2323
    2424 #. It sets necessary batch system parameters.

  • For_developers/Sphinx/source/Documentation/Input/run.rst

    rf20342a r5920b7f  
    1515
    1616Submission parameters
    17 --------------------
     17---------------------
    1818
    1919
    … …  
    3434
    3535
    36 .. _ref-install-script:
     36
    3737       
    3838Usage of ``submit.py`` (optional)

  • For_developers/Sphinx/source/Documentation/output.rst

    rf20342a r5920b7f  
    205205
    206206This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
    207 #PS NEEDS MORE DESCRIPTION
     207
     208.. todo::
     209
     210        #PS NEEDS MORE DESCRIPTION
    208211
    209212

  • For_developers/Sphinx/source/Documentation/vertco.rst

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    2121   
    2222Calculation of the vertical velocity from the horizontal wind using the continuity equation
    23 ===================================================================================
     23===========================================================================================
    2424
    2525The vertical velocity in the ECMWF's eta vertical coordinate system is computed by the Fortran program ``calc_etadot``, using the continuity equation and thereby ensuring mass-consistent 3D wind fields. A detailed description of ``calc_etadot`` can be found in the
    … …  
    4242   
    4343Calculation of the vertical velocity from the pre-calculated MARS parameter 77
    44 ======================================================================
     44==============================================================================
    4545
    4646Since November 2008, the parameter 77 (deta/dt) is stored in ``MARS`` on full model levels. ``FLEXTRA``/``FLEXPART`` in its current version requires ``deta/dt`` on model half levels, multiplied by ``dp/deta``. In ``flex_extract``, the program ``calc_etadot`` assumes that parameter 77 is available if the ``CONTROL`` parameter ``ETA`` is set to 1.

  • For_developers/Sphinx/source/Ecmwf/hintsecmwf.rst

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    99
    1010How can I find out what data are available?
    11 ==========================================
     11===========================================
    1212
    1313Go to the `Web Interface for accessing member-state data sets <http://apps.ecmwf.int/archive-catalogue/>`_

  • For_developers/Sphinx/source/index.rst

    ra14839a r5920b7f  
    7878          <ul>
    7979            <li><a href="Developers/gen_docu.html">Updateing the documentation</a></li>
    80 <!--           <li><a href=""></a><Placeholder></li>
    81             <li><a href=""></a><Placeholder></li>-->
     80            <li><a href=""></a><Placeholder></li>
     81            <li><a href=""></a><Placeholder></li>
    8282          </ul>
    8383        </td>

  • For_developers/Sphinx/source/quick_start.rst

    r550435b r5920b7f  
    337337----------------
    338338
    339 This data set provides the output of the real-time atmospheric model runs in high resolution, including 10-day forecasts. The model undergoes frequent adaptations and improvements. Thus, retrieving data from this dataset requires extra attention in selecting correct settings of the parameters. See :ref:`ref-tab-dataset-cmp` for the most important parameters.
     339This data set provides the output of the real-time atmospheric model runs in high resolution, including 10-day forecasts. The model undergoes frequent adaptations and improvements. Thus, retrieving data from this dataset requires extra attention in selecting correct settings of the parameters. See :ref:`[Table of datasets]<ref-tab-dataset-cmp>` for the most important parameters.
    340340Currently, fields can be retrieved at 1 h temporal resolution by filling the gaps between analysis fields with 1-hourly forecast fields. Since 4 June 2008, the eta coordinate vertical velocity is directly available from MARS, therefore ``ETA`` should be set to ``1`` to save computation time. The horizontal resolution can be up to ``0.1°`` and in combination with ``137`` vertical levels can lead to problems in terms of job duration and disk space quota.
    341341It is recommended to submit such high resolution cases as single day retrievals (see ``JOB_CHUNK`` parameter in ``run.sh`` script) to avoid job failures due to exceeding limits.   
    … …  
    405405    If set to ``1``, all temporary files are preserved. Otherwise, everything except the final output files will be deleted.
    406406request
    407     This produces an extra *csv* file ``mars_requests.csv`` where the content of each MARS request submitted within the job is stored, which is useful for debugging and documentation.
    408 Possible values are 0 for normal data retrieval, 1 for not retrieving data and just writing out the MARS requests, and 2 to retrieve data and write out requests.
     407    This produces an extra *csv* file ``mars_requests.csv`` where the content of each MARS request submitted within the job is stored, which is useful for debugging and documentation. Possible values are 0 for normal data retrieval, 1 for not retrieving data and just writing out the MARS requests, and 2 to retrieve data and write out requests.
    409408mailfail
    410409    As a default, e-mails are sent to the mail address defined for the ECMWF user account. It is possible to overwrite this by specifying one or more e-mail addresses (comma-separated list). In order to include the e-mail associated with the user account, add ``${USER}`` to the list.
    … …  
    418417    The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
    419418    The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
    420 # needs to be rephrased
     419   
     420    .. todo::
     421
     422            #PS needs to be rephrased
    421423
    422424    .. code-block:: bash
    … …  
    431433Vertical velocity           
    432434    The vertical velocity for ``FLEXPART`` is not directly available from MARS and has to be calculated.
    433     There are several options for this, and the following parameters are responsible for the selection. See :doc:`Documentation/vertco` for a detailed explanation. Using ``ETADIFF 1``, ``OMEGA 1`` and ``OMEGADIFF 1`` is recommended for debugging and testing only.
    434   Usually, one has to decide between ``GAUSS 1`` and ``ETA 1``. ``GAUSS 1`` means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. ``ETA 1`` means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use ``ETA 1`` where possible, as there is a substantial computational overhead for solving the continuity equation.
     435    There are several options for this, and the following parameters are responsible for the selection.                 See :doc:`Documentation/vertco` for a detailed explanation. Using ``ETADIFF 1``, ``OMEGA 1`` and ``OMEGADIFF 1`` is recommended for debugging and testing only.
     436    Usually, one has to decide between ``GAUSS 1`` and ``ETA 1``. ``GAUSS 1`` means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. ``ETA 1`` means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use ``ETA 1`` where possible, as there is a substantial computational overhead for solving the continuity equation.
    435437
    436438    .. code-block:: bash
    … …  
    448450    The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
    449451    After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
    450 #PS shouldn't we explain how to define a domain??
     452   
     453        .. todo::
     454               
     455                #PS shouldn't we explain how to define a domain??
     456               
    451457    The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and  `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
    452458   
    … …  
    466472    Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME``  the forecast starting time, and  ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
    467473   
     474        .. todo::
     475
     476                #PS for which application would this be typical?
     477           
    468478    .. code-block:: bash
    469479       :caption: Example setting for the definition of flux fields.
    470 #PS for which application would this be typical?
     480
    471481   
    472482        DTIME 3

  • For_developers/Sphinx/source/todo.rst

    rba99230 r5920b7f  
    77
    88.. todolist::
     9
     10
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