diff --git a/Documentation/html/Developers/gen_docu.html b/Documentation/html/Developers/gen_docu.html index 2d111da9bc64ea27151afb25cd953681f1b0cebe..90ca8931e4f9edbb345156b58c23550049429e07 100644 --- a/Documentation/html/Developers/gen_docu.html +++ b/Documentation/html/Developers/gen_docu.html @@ -8,7 +8,7 @@ <meta name="viewport" content="width=device-width, initial-scale=1.0"> - <title>Update Documentation — flex_extract 7.1 alpha documentation</title> + <title>Updating the documentation — flex_extract 7.1 alpha documentation</title> @@ -95,9 +95,9 @@ <li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li> <li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li> <li class="toctree-l1 current"><a class="reference internal" href="../dev_guide.html">Developer Guide</a><ul class="current"> -<li class="toctree-l2 current"><a class="current reference internal" href="#">Update Documentation</a><ul> -<li class="toctree-l3"><a class="reference internal" href="#additional-software">Additional Software</a></li> -<li class="toctree-l3"><a class="reference internal" href="#online-documentation-with-sphinx">Online-documentation with Sphinx</a><ul> +<li class="toctree-l2 current"><a class="current reference internal" href="#">Updating the documentation</a><ul> +<li class="toctree-l3"><a class="reference internal" href="#additional-software">Additional software</a></li> +<li class="toctree-l3"><a class="reference internal" href="#on-line-documentation-with-sphinx">On-line documentation with Sphinx</a><ul> <li class="toctree-l4"><a class="reference internal" href="#sequence-diagramms">Sequence diagramms</a></li> <li class="toctree-l4"><a class="reference internal" href="#block-diagramms">Block diagramms</a></li> </ul> @@ -157,7 +157,7 @@ <li><a href="../dev_guide.html">Developer Guide</a> »</li> - <li>Update Documentation</li> + <li>Updating the documentation</li> <li class="wy-breadcrumbs-aside"> @@ -176,12 +176,12 @@ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div itemprop="articleBody"> - <div class="section" id="update-documentation"> -<h1>Update Documentation<a class="headerlink" href="#update-documentation" title="Permalink to this headline">¶</a></h1> + <div class="section" id="updating-the-documentation"> +<h1>Updating the documentation<a class="headerlink" href="#updating-the-documentation" title="Permalink to this headline">¶</a></h1> <p>UNDER CONSTRUCTION</p> <div class="section" id="additional-software"> -<h2>Additional Software<a class="headerlink" href="#additional-software" title="Permalink to this headline">¶</a></h2> -<p>Developers working on <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> should make extensive use of the prepared test cases, unit tests and update the documentation. For this, some additional software is necessary:</p> +<h2>Additional software<a class="headerlink" href="#additional-software" title="Permalink to this headline">¶</a></h2> +<p>Developers working on <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> should make extensive use of the prepared test cases and unit tests, and should also update the documentation. For this, some additional software is necessary:</p> <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>pip install pylint pip install pytest pip install mock @@ -195,14 +195,14 @@ pip install pycallgraph </pre></div> </div> </div> -<div class="section" id="online-documentation-with-sphinx"> -<h2>Online-documentation with Sphinx<a class="headerlink" href="#online-documentation-with-sphinx" title="Permalink to this headline">¶</a></h2> -<p>Use the scriot <code class="docutils literal notranslate"><span class="pre">gen_docu.sh</span></code> to generate an update of the online documentation of the python component.</p> -<p>It uses <code class="docutils literal notranslate"><span class="pre">pyreverse</span></code> to generate a class and a package diagram with graphviz and overwrites the old files in the developers directory. -<code class="docutils literal notranslate"><span class="pre">pyreverse</span></code> creates <code class="docutils literal notranslate"><span class="pre">dot</span></code> files and with the <code class="docutils literal notranslate"><span class="pre">dot</span></code> program of the <code class="docutils literal notranslate"><span class="pre">graphviz</span></code> software the <code class="docutils literal notranslate"><span class="pre">png</span></code> files are created. Everything happens in the Python source directory before moving them finally to the <code class="docutils literal notranslate"><span class="pre">For_developers</span></code> directory. The Sphinx source code has a <code class="docutils literal notranslate"><span class="pre">_files</span></code> directory which contains links to these <code class="docutils literal notranslate"><span class="pre">png</span></code> files and therefore they should not be renamed.</p> +<div class="section" id="on-line-documentation-with-sphinx"> +<h2>On-line documentation with Sphinx<a class="headerlink" href="#on-line-documentation-with-sphinx" title="Permalink to this headline">¶</a></h2> +<p>Use the script <code class="docutils literal notranslate"><span class="pre">gen_docu.sh</span></code> to generate an update of the on-line documentation of the Python component.</p> +<p>It uses <code class="docutils literal notranslate"><span class="pre">pyreverse</span></code> to generate class and package diagrams with <code class="docutils literal notranslate"><span class="pre">graphviz</span></code> and overwrites the old files in the developers directory. +<code class="docutils literal notranslate"><span class="pre">pyreverse</span></code> creates <code class="docutils literal notranslate"><span class="pre">dot</span></code> files, and with the <code class="docutils literal notranslate"><span class="pre">dot</span></code> program of the <code class="docutils literal notranslate"><span class="pre">graphviz</span></code> software, the <code class="docutils literal notranslate"><span class="pre">png</span></code> files are created. Everything happens in the Python source directory before moving them finally to the <code class="docutils literal notranslate"><span class="pre">For_developers</span></code> directory. The Sphinx source code has a <code class="docutils literal notranslate"><span class="pre">_files</span></code> directory which contains links to these <code class="docutils literal notranslate"><span class="pre">png</span></code> files and therefore they should not be renamed.</p> <div class="section" id="sequence-diagramms"> <h3>Sequence diagramms<a class="headerlink" href="#sequence-diagramms" title="Permalink to this headline">¶</a></h3> -<p>You might need to adapt the fonts path for the diagrams to a true type font. Currently it is set to:</p> +<p>You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to:</p> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Fontpath for seqdiag (truetype font)</span> <span class="nv">seqdiag_fontpath</span> <span class="o">=</span> <span class="s1">'/usr/share/fonts/dejavu/DejaVuSerif.ttf'</span> </pre></div> @@ -210,7 +210,7 @@ pip install pycallgraph </div> <div class="section" id="block-diagramms"> <h3>Block diagramms<a class="headerlink" href="#block-diagramms" title="Permalink to this headline">¶</a></h3> -<p>You might need to adapt the fonts path for the diagrams to a true type font. Currently it is set to:</p> +<p>You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to:</p> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Fontpath for blockdiag (truetype font)</span> <span class="nv">blockdiag_fontpath</span> <span class="o">=</span> <span class="s1">'/usr/share/fonts/dejavu/DejaVuSerif.ttf'</span> </pre></div> diff --git a/Documentation/html/Documentation/Api/api_fortran.html b/Documentation/html/Documentation/Api/api_fortran.html index 850bec622499a72cb76cefc79af44ea21299748b..1ed5ca1d74329ff5c4048805a10703f317425798 100644 --- a/Documentation/html/Documentation/Api/api_fortran.html +++ b/Documentation/html/Documentation/Api/api_fortran.html @@ -183,8 +183,7 @@ <div class="section" id="fortran-s-auto-generated-documentation"> <h1>Fortran’s Auto Generated Documentation<a class="headerlink" href="#fortran-s-auto-generated-documentation" title="Permalink to this headline">¶</a></h1> -<p>Link to other documentation!</p> -<p>…. f:autoprogram:: preconvert</p> +<p><a class="reference external" href="Fortran/index.html">Fortran API</a></p> <div class="toctree-wrapper compound"> </div> </div> diff --git a/Documentation/html/Documentation/Api/api_python.html b/Documentation/html/Documentation/Api/api_python.html index 51fcfcc162c61aa2436fb1b282509f57a80c8617..eeac6d609f9af8e67fc978acdd80101aaf1c433e 100644 --- a/Documentation/html/Documentation/Api/api_python.html +++ b/Documentation/html/Documentation/Api/api_python.html @@ -220,14 +220,14 @@ <span id="install"></span><h3><a class="toc-backref" href="#id4">install</a><a class="headerlink" href="#module-install" title="Permalink to this headline">¶</a></h3> <p>This script installs the flex_extract program.</p> <p>Depending on the selected installation environment (locally or on the -ECMWF server ecgate or cca) the program extracts the commandline +ECMWF server ecgate or cca) the program extracts the command line arguments and the CONTROL file parameter and prepares the corresponding environment. -The necessary files are collected in a tar-ball and placed -at the target location. There its untared, the environment variables will -be set and the Fortran code will be compiled. -If the ECMWF environment is selected a job script is prepared and submitted -for the remaining configurations after putting the tar-ball to the +The necessary files are collected in a tar ball and placed +at the target location. There, is is untared, the environment variables are +set, and the Fortran code is compiled. +If the ECMWF environment is selected, a job script is prepared and submitted +for the remaining configurations after putting the tar ball on the target ECMWF server.</p> <p>Type: install.py –help to get information about command line parameters. @@ -235,8 +235,8 @@ Read the documentation for usage instructions.</p> <dl class="function"> <dt id="install.check_install_conditions"> <code class="sig-prename descclassname">install.</code><code class="sig-name descname">check_install_conditions</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/install.html#check_install_conditions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.check_install_conditions" title="Permalink to this definition">¶</a></dt> -<dd><p>Checks a couple of necessary attributes and conditions -for the installation such as if they exist and contain values. +<dd><p>Checks necessary attributes and conditions +for the installation, e.g. whether they exist and contain values. Otherwise set default values.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> @@ -262,7 +262,7 @@ build files (e.g. *.o, *.mod and CONVERT2)</p> <dt id="install.get_install_cmdline_args"> <code class="sig-prename descclassname">install.</code><code class="sig-name descname">get_install_cmdline_args</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/install.html#get_install_cmdline_args"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.get_install_cmdline_args" title="Permalink to this definition">¶</a></dt> <dd><p>Decomposes the command line arguments and assigns them to variables. -Apply default values for non mentioned arguments.</p> +Apply default values for arguments not present.</p> <dl class="field-list simple"> <dt class="field-odd">Returns</dt> <dd class="field-odd"><p><strong>args</strong> – Contains the commandline arguments from script/program call.</p> @@ -288,8 +288,8 @@ command line.</p> <dl class="function"> <dt id="install.install_via_gateway"> <code class="sig-prename descclassname">install.</code><code class="sig-name descname">install_via_gateway</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/install.html#install_via_gateway"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.install_via_gateway" title="Permalink to this definition">¶</a></dt> -<dd><p>Prepare data transfer to remote gate and submit a job script which will -install everything on the remote gate.</p> +<dd><p>Prepare data transfer to remote gateway and submit a job script which will +install everything on the remote gateway.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>c</strong> (<a class="reference internal" href="#ControlFile.ControlFile" title="ControlFile.ControlFile"><em>ControlFile</em></a>) – Contains all the parameters of CONTROL file and @@ -314,8 +314,8 @@ is stored in a new file “job.temp” in the python directory.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> -<li><p><strong>makefile</strong> (<em>str</em>) – Name of the makefile which should be used to compile FORTRAN -CONVERT2 program.</p></li> +<li><p><strong>makefile</strong> (<em>str</em>) – Name of the makefile which should be used to compile the Fortran +program.</p></li> <li><p><strong>ecuid</strong> (<em>str</em>) – The user id on ECMWF server.</p></li> <li><p><strong>ecgid</strong> (<em>str</em>) – The group id on ECMWF server.</p></li> <li><p><strong>fp_root</strong> (<em>str</em>) – Path to the root directory of FLEXPART environment or flex_extract @@ -381,8 +381,8 @@ environment.</p></li> <code class="sig-prename descclassname">install.</code><code class="sig-name descname">mk_tarball</code><span class="sig-paren">(</span><em class="sig-param">tarball_path</em>, <em class="sig-param">target</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/install.html#mk_tarball"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#install.mk_tarball" title="Permalink to this definition">¶</a></dt> <dd><p>Creates a tarball with all necessary files which need to be sent to the installation directory. -It does not matter if this is local or remote. -Collects all python files, the Fortran source and makefiles, +It does not matter whether this is local or remote. +Collects all Python files, the Fortran source and makefiles, the ECMWF_ENV file, the CONTROL files as well as the template files.</p> <dl class="field-list simple"> @@ -2273,23 +2273,23 @@ they can be deleted.</p> <h2><a class="toc-backref" href="#id12">Modules</a><a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h2> <div class="section" id="module-get_mars_data"> <span id="get-mars-data"></span><h3><a class="toc-backref" href="#id13">get_mars_data</a><a class="headerlink" href="#module-get_mars_data" title="Permalink to this headline">¶</a></h3> -<p>This script extracts MARS data from ECMWF servers.</p> +<p>This script extracts MARS data from ECMWF.</p> <p>At first, the necessary parameters from command line and CONTROL files are extracted. They define the data set to be extracted from MARS.</p> <p>This file can also be imported as a module and contains the following functions:</p> <blockquote> <div><ul class="simple"> -<li><p>main - the main function of the script</p></li> -<li><p>get_mars_data - overall control of ECMWF data retrievment</p></li> +<li><p>main - the main function of the script</p></li> +<li><p>get_mars_data - overall control of ECMWF data retrievment</p></li> <li><p>write_reqheader - writes the header into the mars_request file</p></li> -<li><p>mk_server - creates the server connection to ECMWF servers</p></li> -<li><p>mk_dates - defines the start and end date</p></li> -<li><p>remove_old - deletes old retrieved grib files</p></li> -<li><p>do_retrievement - creates individual retrievals</p></li> +<li><p>mk_server - creates the server connection to ECMWF servers</p></li> +<li><p>mk_dates - defines the start and end date</p></li> +<li><p>remove_old - deletes old retrieved grib files</p></li> +<li><p>do_retrieval - creates individual retrievals</p></li> </ul> </div></blockquote> -<p>Type: get_mars_data.py –help +<p>Type get_mars_data.py –help to get information about command line parameters. Read the documentation for usage instructions.</p> <dl class="function"> @@ -2315,7 +2315,7 @@ Read the documentation for usage instructions.</p> <dl class="function"> <dt id="get_mars_data.do_retrievement"> <code class="sig-prename descclassname">get_mars_data.</code><code class="sig-name descname">do_retrievement</code><span class="sig-paren">(</span><em class="sig-param">c</em>, <em class="sig-param">server</em>, <em class="sig-param">start</em>, <em class="sig-param">end</em>, <em class="sig-param">delta_t</em>, <em class="sig-param">fluxes=False</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/get_mars_data.html#do_retrievement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.do_retrievement" title="Permalink to this definition">¶</a></dt> -<dd><p>Divides the complete retrieval period in smaller chunks and +<dd><p>Divides the total retrieval period into smaller chunks and retrieves the data from MARS.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> @@ -2325,8 +2325,7 @@ command line.</p></li> <li><p><strong>server</strong> (<em>ECMWFService</em><em> or </em><em>ECMWFDataServer</em>) – The server connection to ECMWF.</p></li> <li><p><strong>start</strong> (<em>datetime</em>) – The start date of the retrieval.</p></li> <li><p><strong>end</strong> (<em>datetime</em>) – The end date of the retrieval.</p></li> -<li><p><strong>delta_t</strong> (<em>datetime</em>) – Delta_t + 1 is the maximal time period of a single -retrieval.</p></li> +<li><p><strong>delta_t</strong> (<em>datetime</em>) – Delta_t + 1 is the maximum time period of a single retrieval.</p></li> <li><p><strong>fluxes</strong> (<em>boolean</em><em>, </em><em>optional</em>) – Decides if the flux parameters are to be retrieved or the rest of the parameter list. Default value is False.</p></li> @@ -2338,9 +2337,9 @@ Default value is False.</p></li> <dl class="function"> <dt id="get_mars_data.get_mars_data"> <code class="sig-prename descclassname">get_mars_data.</code><code class="sig-name descname">get_mars_data</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/get_mars_data.html#get_mars_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.get_mars_data" title="Permalink to this definition">¶</a></dt> -<dd><p>Retrieves the EC data needed for a FLEXPART simulation.</p> -<p>Start and end dates for retrieval period is set. Retrievals -are divided into smaller periods if necessary and datechunk parameter +<dd><p>Retrieves the ECMWF data required for a FLEXPART simulation.</p> +<p>Start and end dates for retrieval period are set. Retrievals +are divided into shorter periods if necessary and if datechunk parameter is set.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> @@ -2353,20 +2352,20 @@ command line.</p> <dl class="function"> <dt id="get_mars_data.main"> <code class="sig-prename descclassname">get_mars_data.</code><code class="sig-name descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/get_mars_data.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.main" title="Permalink to this definition">¶</a></dt> -<dd><p>Controls the program to get data out of mars.</p> -<p>This is done if it is called directly from command line. -Then it also takes program call arguments and control file input.</p> +<dd><p>Controls the program to retrieve data from MARS.</p> +<p>This is done if called directly from command line. +Then, arguments and control file are taken as input.</p> </dd></dl> <dl class="function"> <dt id="get_mars_data.mk_dates"> <code class="sig-prename descclassname">get_mars_data.</code><code class="sig-name descname">mk_dates</code><span class="sig-paren">(</span><em class="sig-param">c</em>, <em class="sig-param">fluxes</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/get_mars_data.html#mk_dates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.mk_dates" title="Permalink to this definition">¶</a></dt> -<dd><p>Prepares start and end date depending on flux or non flux data.</p> -<p>If forecast for maximum one day (upto 24h) are to be retrieved, then +<dd><p>Prepares start and end date depending on flux or non-flux type of data.</p> +<p>If forecasts for a maximum of one day (24 h) are to be retrieved, then collect accumulation data (flux data) with additional days in the -beginning and at the end (used for complete disaggregation of +beginning and at the end (needed for complete disaggregation of original period)</p> -<p>If forecast data longer than 24h are to be retrieved, then +<p>If forecast data for more than +24 h are to be retrieved, then collect accumulation data (flux data) with the exact start and end date (disaggregation will be done for the exact time period with boundary conditions)</p> @@ -2396,10 +2395,11 @@ Default value is False.</p></li> <dl class="function"> <dt id="get_mars_data.mk_server"> <code class="sig-prename descclassname">get_mars_data.</code><code class="sig-name descname">mk_server</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/get_mars_data.html#mk_server"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.mk_server" title="Permalink to this definition">¶</a></dt> -<dd><p>Creates a server connection with available python API.</p> -<p>Which API is used depends on availability and the dataset to be retrieved. -The CDS API is used for ERA5 dataset no matter if the user is a member or -a public user. ECMWF WebAPI is used for all other available datasets.</p> +<dd><p>Creates a server connection with available Python API.</p> +<p>The API selected depends on availability and the data set to be retrieved. +The CDS API is used for ERA5 data, no matter whether the user is a +member-state or a public user. +ECMWF WebAPI is used for all other available datasets.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>c</strong> (<a class="reference internal" href="#ControlFile.ControlFile" title="ControlFile.ControlFile"><em>ControlFile</em></a>) – Contains all the parameters of CONTROL file and @@ -2422,8 +2422,8 @@ matching the pattern.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> -<li><p><strong>pattern</strong> (<em>str</em>) – The sub string pattern which identifies the files to be deleted.</p></li> -<li><p><strong>inputdir</strong> (<em>str</em><em>, </em><em>optional</em>) – Path to the directory where the retrieved data is stored.</p></li> +<li><p><strong>pattern</strong> (<em>str</em>) – The substring pattern which identifies the files to be deleted.</p></li> +<li><p><strong>inputdir</strong> (<em>str</em><em>, </em><em>optional</em>) – Path to the directory where the retrieved data are stored.</p></li> </ul> </dd> </dl> @@ -2432,10 +2432,10 @@ matching the pattern.</p> <dl class="function"> <dt id="get_mars_data.write_reqheader"> <code class="sig-prename descclassname">get_mars_data.</code><code class="sig-name descname">write_reqheader</code><span class="sig-paren">(</span><em class="sig-param">marsfile</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/get_mars_data.html#write_reqheader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#get_mars_data.write_reqheader" title="Permalink to this definition">¶</a></dt> -<dd><p>Writes header with column names into mars request file.</p> +<dd><p>Writes header with column names into MARS request file.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> -<dd class="field-odd"><p><strong>marsfile</strong> (<em>str</em>) – Path to the mars request file.</p> +<dd class="field-odd"><p><strong>marsfile</strong> (<em>str</em>) – Path to the MARS request file.</p> </dd> </dl> </dd></dl> @@ -2446,9 +2446,9 @@ matching the pattern.</p> <p>This script prepares the final version of the grib files which are then used by FLEXPART.</p> <p>It converts the bunch of grib files extracted via get_mars_data before, -by doing the necessary conversion to get consistent grids or the +by doing the necessary conversion to obtain consistent grids or the disaggregation of flux data. Finally, the data fields are combined -in files per available hour with the naming convention xxYYMMDDHH, +in files per hour available with the naming convention xxYYMMDDHH, where xx should be 2 arbitrary letters (mostly xx is chosen to be “EN”).</p> <p>This file can also be imported as a module which then contains the following functions:</p> @@ -2464,19 +2464,18 @@ Read the documentation for usage instructions.</p> <dl class="function"> <dt id="prepare_flexpart.main"> <code class="sig-prename descclassname">prepare_flexpart.</code><code class="sig-name descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/prepare_flexpart.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#prepare_flexpart.main" title="Permalink to this definition">¶</a></dt> -<dd><p>Controls the program to prepare flexpart input files from mars data.</p> -<p>This is done if it is called directly from command line. -Then it also takes program call arguments and control file input.</p> +<dd><p>Controls the program to prepare FLEXPART input files from MARS data.</p> +<p>This is done if called directly from the command line. +Then, arguments and control file are taken as input.</p> </dd></dl> <dl class="function"> <dt id="prepare_flexpart.prepare_flexpart"> <code class="sig-prename descclassname">prepare_flexpart.</code><code class="sig-name descname">prepare_flexpart</code><span class="sig-paren">(</span><em class="sig-param">ppid</em>, <em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/prepare_flexpart.html#prepare_flexpart"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#prepare_flexpart.prepare_flexpart" title="Permalink to this definition">¶</a></dt> -<dd><p>Converts the mars data into flexpart ready input files.</p> -<p>Specific data fields are converted to a different grid and the flux -data are going to be disaggregated. The data fields are collected by -hour and stored in a file with a specific FLEXPART relevant naming -convention.</p> +<dd><p>Converts the MARS data into files ready as input for FLEXPART.</p> +<p>Certain fields are converted to a different grid and the flux +data are disaggregated. Fields are collected by hour and stored in a file +with a specific naming convention.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> @@ -2498,7 +2497,7 @@ command line.</p></li> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">clean_up</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#clean_up"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.clean_up" title="Permalink to this definition">¶</a></dt> <dd><p>Remove files from the intermediate directory (inputdir).</p> <p>It keeps the final FLEXPART input files if program runs without -ECMWF Api and keywords “ectrans” or “ecstorage” are set to “1”.</p> +ECMWF API and keywords “ectrans” or “ecstorage” are set to “1”.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>c</strong> (<a class="reference internal" href="#ControlFile.ControlFile" title="ControlFile.ControlFile"><em>ControlFile</em></a>) – Contains all the parameters of CONTROL file and @@ -2510,18 +2509,17 @@ command line.</p> <dl class="function"> <dt id="tools.execute_subprocess"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">execute_subprocess</code><span class="sig-paren">(</span><em class="sig-param">cmd_list</em>, <em class="sig-param">error_msg='SUBPROCESS FAILED!'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#execute_subprocess"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.execute_subprocess" title="Permalink to this definition">¶</a></dt> -<dd><p>Executes a command line instruction via a subprocess.</p> +<dd><p>Executes a command via a subprocess.</p> <p>Error handling is done if an error occures.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> -<dd class="field-odd"><p><strong>cmd_list</strong> (<em>list of str</em>) – A list of the components for the command line execution. Each -list entry is a single part of the command which is seperated from -the rest by a blank space. -E.g. [‘mv’, file1, file2]</p> +<dd class="field-odd"><p><strong>cmd_list</strong> (<em>list of str</em>) – A list of the components for the command line execution. +They will be concatenated with blank space for the command +to be submitted, like [‘mv’, file1, file2] for mv file1 file2.</p> </dd> <dt class="field-even">Returns</dt> -<dd class="field-even"><p><strong>error_msg</strong> – The possible error message if the subprocess failed. -By default it will just tell “SUBPROCESS FAILED!”.</p> +<dd class="field-even"><p><strong>error_msg</strong> – Error message if the subprocess fails. +By default it will just say “SUBPROCESS FAILED!”.</p> </dd> <dt class="field-odd">Return type</dt> <dd class="field-odd"><p>str, optional</p> @@ -2554,10 +2552,10 @@ the temporary times which were used for processing reasons.</p></li> <dt id="tools.get_cmdline_args"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">get_cmdline_args</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#get_cmdline_args"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_cmdline_args" title="Permalink to this definition">¶</a></dt> <dd><p>Decomposes the command line arguments and assigns them to variables. -Apply default values for non mentioned arguments.</p> +Apply default values for arguments not present.</p> <dl class="field-list simple"> <dt class="field-odd">Returns</dt> -<dd class="field-odd"><p><strong>args</strong> – Contains the commandline arguments from script/program call.</p> +<dd class="field-odd"><p><strong>args</strong> – Contains the command line arguments from the script / program call.</p> </dd> <dt class="field-even">Return type</dt> <dd class="field-even"><p>Namespace</p> @@ -2568,7 +2566,7 @@ Apply default values for non mentioned arguments.</p> <dl class="function"> <dt id="tools.get_dimensions"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">get_dimensions</code><span class="sig-paren">(</span><em class="sig-param">info</em>, <em class="sig-param">purefc</em>, <em class="sig-param">dtime</em>, <em class="sig-param">index_vals</em>, <em class="sig-param">start_date</em>, <em class="sig-param">end_date</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#get_dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_dimensions" title="Permalink to this definition">¶</a></dt> -<dd><p>This function specifies the correct dimensions for x, y and t.</p> +<dd><p>This function specifies the correct dimensions for x, y, and t.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> @@ -2580,7 +2578,7 @@ Apply default values for non mentioned arguments.</p> <li><p><strong>purefc</strong> (<em>int</em>) – Switch for definition of pure forecast mode or not.</p></li> <li><p><strong>dtime</strong> (<em>str</em>) – Time step in hours.</p></li> <li><p><strong>index_vals</strong> (<em>list of list of str</em>) – Contains the values from the keys used for a distinct selection -of grib messages in processing the grib files. +of GRIB messages in processing the grib files. Content looks like e.g.: index_vals[0]: (‘20171106’, ‘20171107’, ‘20171108’) ; date index_vals[1]: (‘0’, ‘1200’, ‘1800’, ‘600’) ; time @@ -2601,9 +2599,9 @@ index_vals[2]: (‘0’, ‘12’, ‘3’, ‘6’, ‘9’) ; stepRange</p></l <dl class="function"> <dt id="tools.get_informations"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">get_informations</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#get_informations"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_informations" title="Permalink to this definition">¶</a></dt> -<dd><p>Gets basic information from an example grib file.</p> -<p>These information are important for later use and the -initialization of numpy arrays for data storing.</p> +<dd><p>Extracts basic information from a sample grib file.</p> +<p>This information is needed for later use and the +initialization of numpy arrays where data are stored.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>filename</strong> (<em>str</em>) – Name of the file which will be opened to extract basic information.</p> @@ -2624,7 +2622,8 @@ initialization of numpy arrays for data storing.</p> <dl class="function"> <dt id="tools.get_list_as_string"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">get_list_as_string</code><span class="sig-paren">(</span><em class="sig-param">list_obj</em>, <em class="sig-param">concatenate_sign='</em>, <em class="sig-param">'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#get_list_as_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.get_list_as_string" title="Permalink to this definition">¶</a></dt> -<dd><p>Converts a list of arbitrary content into a single string.</p> +<dd><p>Converts a list of arbitrary content into a single string using a given +concatenation character.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> @@ -2665,8 +2664,8 @@ short name of the parameter.</p> <dt id="tools.make_dir"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">make_dir</code><span class="sig-paren">(</span><em class="sig-param">directory</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#make_dir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.make_dir" title="Permalink to this definition">¶</a></dt> <dd><p>Creates a directory.</p> -<p>It gives a warning if the directory already exists and skips process. -The program stops only if there is another problem.</p> +<p>If the directory already exists, an information is printed and the creation +skipped. The program stops only if there is another problem.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>directory</strong> (<em>str</em>) – The path to directory which should be created.</p> @@ -2689,8 +2688,8 @@ before exiting the program.</p> <dl class="function"> <dt id="tools.none_or_int"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">none_or_int</code><span class="sig-paren">(</span><em class="sig-param">value</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#none_or_int"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.none_or_int" title="Permalink to this definition">¶</a></dt> -<dd><p>Converts the input string into pythons None-type if the string -contains string “None”. Otherwise it is converted to an integer value.</p> +<dd><p>Converts the input string into Pythons None-type if it +contains string “None”; otherwise it is converted to an integer value.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>value</strong> (<em>str</em>) – String to be checked for the “None” word.</p> @@ -2709,15 +2708,15 @@ converted into an integer value.</p> <dl class="function"> <dt id="tools.none_or_str"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">none_or_str</code><span class="sig-paren">(</span><em class="sig-param">value</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#none_or_str"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.none_or_str" title="Permalink to this definition">¶</a></dt> -<dd><p>Converts the input string into pythons None-type if the string -contains string “None”.</p> +<dd><p>Converts the input string into Pythons None type if it +contains the string “None”.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>value</strong> (<em>str</em>) – String to be checked for the “None” word.</p> </dd> <dt class="field-even">Returns</dt> <dd class="field-even"><p>Return depends on the content of the input value. If it was “None”, -then the python type None is returned. Otherwise the string itself.</p> +then the Python type None is returned, otherwise the string itself.</p> </dd> <dt class="field-odd">Return type</dt> <dd class="field-odd"><p>None or value</p> @@ -2741,7 +2740,7 @@ then the python type None is returned. Otherwise the string itself.</p> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">product</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwds</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.product" title="Permalink to this definition">¶</a></dt> <dd><p>Creates combinations of all passed arguments.</p> <p>This method combines the single characters of the passed arguments -with each other. So that each character of each argument value +with each other in a way that each character of each argument value will be combined with each character of the other arguments as a tuple.</p> <div class="admonition note"> <p class="admonition-title">Note</p> @@ -2879,7 +2878,7 @@ is done in here.</p> </ul> </dd> <dt class="field-even">Returns</dt> -<dd class="field-even"><p><strong>job_id</strong> – The id number of the job as a reference at the ecmwf server.</p> +<dd class="field-even"><p><strong>job_id</strong> – The id number of the job as a reference at the ECMWF server.</p> </dd> <dt class="field-odd">Return type</dt> <dd class="field-odd"><p>int</p> @@ -2895,9 +2894,8 @@ is done in here.</p> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> <li><p><strong>pars</strong> (<em>str</em>) – Addpar argument from CONTROL file in the format of -parameter names instead of ids. The parameter short -names are sepearted with “/” and they are passed as -one single string.</p></li> +parameter names instead of IDs. The parameter short +names are separated by “/” and passed as one single string.</p></li> <li><p><strong>table</strong> (<em>dict</em>) – Contains the ECMWF grib table 128 information. The key is the parameter number and the value is the short name of the parameter.</p></li> @@ -2916,15 +2914,14 @@ parameter ids in the format of integer.</p> <dl class="function"> <dt id="tools.to_param_id_with_tablenumber"> <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">to_param_id_with_tablenumber</code><span class="sig-paren">(</span><em class="sig-param">pars</em>, <em class="sig-param">table</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#to_param_id_with_tablenumber"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.to_param_id_with_tablenumber" title="Permalink to this definition">¶</a></dt> -<dd><p>Transform parameter names to parameter ids and add table id.</p> +<dd><p>Transform parameter names to parameter IDs and add table ID.</p> <p>Conversion with ECMWF grib table 128.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> <li><p><strong>pars</strong> (<em>str</em>) – Addpar argument from CONTROL file in the format of -parameter names instead of ids. The parameter short -names are sepearted with “/” and they are passed as -one single string.</p></li> +parameter names instead of ID. The parameter short +names are separated by “/” and passed as one single string.</p></li> <li><p><strong>table</strong> (<em>dict</em>) – Contains the ECMWF grib table 128 information. The key is the parameter number and the value is the short name of the parameter.</p></li> @@ -2932,7 +2929,7 @@ short name of the parameter.</p></li> </dd> <dt class="field-even">Returns</dt> <dd class="field-even"><p><strong>spar</strong> – List of addpar parameters from CONTROL file transformed to -parameter ids in the format of integer.</p> +parameter IDs in the format of integer.</p> </dd> <dt class="field-odd">Return type</dt> <dd class="field-odd"><p>str</p> @@ -2947,7 +2944,7 @@ parameter ids in the format of integer.</p> <dl class="function"> <dt id="checks.check_accmaxstep"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_accmaxstep</code><span class="sig-paren">(</span><em class="sig-param">accmaxstep</em>, <em class="sig-param">marsclass</em>, <em class="sig-param">purefc</em>, <em class="sig-param">maxstep</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_accmaxstep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_accmaxstep" title="Permalink to this definition">¶</a></dt> -<dd><p>Guarantees that the accumulation forecast step were set.</p> +<dd><p>Guarantees that the accumulation forecast step was set.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> @@ -2955,7 +2952,7 @@ parameter ids in the format of integer.</p> <li><p><strong>marsclass</strong> (<em>str</em>) – ECMWF data classification identifier.</p></li> <li><p><strong>purefc</strong> (<em>int</em>) – Switch for definition of pure forecast mode or not.</p></li> <li><p><strong>maxstep</strong> (<em>str</em>) – The maximum forecast time step in hours from the forecast base time. -This is the maximum step for non flux (accumulated) forecast data.</p></li> +This is the maximum step for non-flux (accumulated) forecast data.</p></li> </ul> </dd> <dt class="field-even">Returns</dt> @@ -2971,18 +2968,18 @@ This is the maximum step for non flux (accumulated) forecast data.</p></li> <dt id="checks.check_acctime"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_acctime</code><span class="sig-paren">(</span><em class="sig-param">acctime</em>, <em class="sig-param">marsclass</em>, <em class="sig-param">purefc</em>, <em class="sig-param">time</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_acctime"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_acctime" title="Permalink to this definition">¶</a></dt> <dd><p>Guarantees that the accumulation forecast times were set.</p> -<p>If it is not set, it tries to set the value for some of the -most commonly used data sets. Otherwise it raises an error.</p> +<p>If not set, setting the value to some of the most commonly used data sets +is attempted. Otherwise, an eror is raised.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> -<li><p><strong>acctime</strong> (<em>str</em>) – The starting time from the accumulated forecasts.</p></li> +<li><p><strong>acctime</strong> (<em>str</em>) – The starting time for the accumulated forecasts.</p></li> <li><p><strong>marsclass</strong> (<em>str</em>) – ECMWF data classification identifier.</p></li> <li><p><strong>purefc</strong> (<em>int</em>) – Switch for definition of pure forecast mode or not.</p></li> </ul> </dd> <dt class="field-even">Returns</dt> -<dd class="field-even"><p><strong>acctime</strong> – The starting time from the accumulated forecasts.</p> +<dd class="field-even"><p><strong>acctime</strong> – The starting time for the accumulated forecasts.</p> </dd> <dt class="field-odd">Return type</dt> <dd class="field-odd"><p>str</p> @@ -2994,7 +2991,7 @@ most commonly used data sets. Otherwise it raises an error.</p> <dt id="checks.check_acctype"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_acctype</code><span class="sig-paren">(</span><em class="sig-param">acctype</em>, <em class="sig-param">ftype</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_acctype"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_acctype" title="Permalink to this definition">¶</a></dt> <dd><p>Guarantees that the accumulation field type is set.</p> -<p>If not set, it is derivated as in the old method (TYPE[1]).</p> +<p>If not set, it is derived with the old method (TYPE[1]).</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> @@ -3015,8 +3012,8 @@ most commonly used data sets. Otherwise it raises an error.</p> <dt id="checks.check_addpar"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_addpar</code><span class="sig-paren">(</span><em class="sig-param">addpar</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_addpar"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_addpar" title="Permalink to this definition">¶</a></dt> <dd><p>Check that addpar has correct format of additional parameters in -a single string, so that it can be easily appended to the hard coded -parameters that are retrieved in any case.</p> +a single string, so that it can be easily appended to the hard-coded +parameters retrieved in any case.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>addpar</strong> (<em>str</em><em> or </em><em>list of str</em>) – List of additional parameters to be retrieved.</p> @@ -3034,9 +3031,10 @@ parameters that are retrieved in any case.</p> <dt id="checks.check_area"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_area</code><span class="sig-paren">(</span><em class="sig-param">grid</em>, <em class="sig-param">area</em>, <em class="sig-param">upper</em>, <em class="sig-param">lower</em>, <em class="sig-param">left</em>, <em class="sig-param">right</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_area"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_area" title="Permalink to this definition">¶</a></dt> <dd><p>Defines the correct area string.</p> -<p>Checks on the format of the four area components. Wether it is of -the order of 1000 or 1. Also checks wether area was already set by command -line, then the four components are overwritten. +<p>Checks the format of the four area components wether it is on +the order of 1000 or 1. +Also checks wether area was already set on command line, +then the four components are overwritten. Convert to correct format of the order of magnitude “1” and sets the area parameter (North/West/South/East). E.g.: -5./20./10./10.</p> @@ -3045,14 +3043,14 @@ E.g.: -5./20./10./10.</p> <dd class="field-odd"><ul class="simple"> <li><p><strong>grid</strong> (<em>str</em>) – Contains grid information.</p></li> <li><p><strong>area</strong> (<em>str</em>) – Contains area informtion.</p></li> -<li><p><strong>upper</strong> (<em>str</em>) – The northern most latitude.</p></li> -<li><p><strong>lower</strong> (<em>str</em>) – The souther most latitude.</p></li> -<li><p><strong>left</strong> (<em>str</em>) – The western most longitude.</p></li> -<li><p><strong>right</strong> (<em>str</em>) – The eastern most longiude.</p></li> +<li><p><strong>upper</strong> (<em>str</em>) – The northernmost latitude.</p></li> +<li><p><strong>lower</strong> (<em>str</em>) – The southernmost latitude.</p></li> +<li><p><strong>left</strong> (<em>str</em>) – The westernmost longitude.</p></li> +<li><p><strong>right</strong> (<em>str</em>) – The easternmost longitude.</p></li> </ul> </dd> <dt class="field-even">Returns</dt> -<dd class="field-even"><p><strong>grid</strong> – Contains grid in format Lat/lon. E.g. 0.1/0.1</p> +<dd class="field-even"><p><strong>grid</strong> – Contains grid in format lat/lon. E.g. 0.1/0.1</p> </dd> <dt class="field-odd">Return type</dt> <dd class="field-odd"><p>str</p> @@ -3083,7 +3081,7 @@ retrieved.</p> <dl class="function"> <dt id="checks.check_dates"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_dates</code><span class="sig-paren">(</span><em class="sig-param">start</em>, <em class="sig-param">end</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_dates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_dates" title="Permalink to this definition">¶</a></dt> -<dd><p>Checks if there is at least a start date for a one day retrieval.</p> +<dd><p>Checks if there is at least a start date for a one-day retrieval.</p> <p>Checks if end date lies after start date and end date is set.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> @@ -3124,7 +3122,7 @@ Convert to correct grid format and substitute into “Lat/Lon” format string.< <dl class="function"> <dt id="checks.check_job_chunk"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_job_chunk</code><span class="sig-paren">(</span><em class="sig-param">job_chunk</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_job_chunk"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_job_chunk" title="Permalink to this definition">¶</a></dt> -<dd><p>Checks that if job chunk is set, the number is positive and non zero.</p> +<dd><p>Checks that if job chunk is set, the number is positive and nonzero.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>job_chunk</strong> (<em>int</em>) – The number of days for a single job script.</p> @@ -3150,7 +3148,7 @@ Convert to correct grid format and substitute into “Lat/Lon” format string.< <li><p><strong>steps</strong> (<em>str</em>) – Specifies the forecast time step from forecast base time. Valid values are hours (HH) from forecast base time.</p></li> <li><p><strong>maxstep</strong> (<em>int</em>) – The maximum forecast time step in hours from the forecast base time. -This is the maximum step for non flux (accumulated) forecast data.</p></li> +This is the maximum step for non-flux (not accumulated) forecast data.</p></li> <li><p><strong>purefc</strong> (<em>int</em>) – Switch for definition of pure forecast mode or not.</p></li> </ul> </dd> @@ -3185,8 +3183,8 @@ Examples: model level: 1/to/137, pressure levels: 500/to/1000</p></li> correspondence to the selected levtype. Examples: model level: 1/to/137, pressure levels: 500/to/1000</p></li> <li><p><strong>level</strong> (<em>str</em>) – Specifies the maximum level. It has to be one of the -available maximum level number as contained in the variable -MAX_LEVEL_LIST in “_config”. E.g. [16, 19, 31, 40, 50, 60, 62, 91, 137]</p></li> +available maximum level numbers as contained in the variable +MAX_LEVEL_LIST in “_config”: [16, 19, 31, 40, 50, 60, 62, 91, 137]</p></li> </ul> </p> </dd> @@ -3212,7 +3210,7 @@ program.</p></li> <dl class="function"> <dt id="checks.check_mail"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_mail</code><span class="sig-paren">(</span><em class="sig-param">mail</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_mail"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_mail" title="Permalink to this definition">¶</a></dt> -<dd><p>Check the string of mail addresses, seperate them and convert to a list.</p> +<dd><p>Check the string of mail addresses, separate them and convert to list.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><p><strong>mail</strong> (<em>list of str</em><em> or </em><em>str</em>) – Contains email addresses for notifications. @@ -3315,8 +3313,8 @@ of is None otherwise.</p></li> <dl class="function"> <dt id="checks.check_public"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_public</code><span class="sig-paren">(</span><em class="sig-param">public</em>, <em class="sig-param">dataset</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_public"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_public" title="Permalink to this definition">¶</a></dt> -<dd><p>Check wether the dataset parameter is set for a -public data set retrieval.</p> +<dd><p>Check wether the dataset parameter is set to a +public data set.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> @@ -3369,7 +3367,7 @@ transfer through ectrans. E.g. <a class="reference external" href="mailto:name&# <dl class="function"> <dt id="checks.check_request"> <code class="sig-prename descclassname">checks.</code><code class="sig-name descname">check_request</code><span class="sig-paren">(</span><em class="sig-param">request</em>, <em class="sig-param">marsfile</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/checks.html#check_request"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#checks.check_request" title="Permalink to this definition">¶</a></dt> -<dd><p>Check if there is an old mars request file and remove it.</p> +<dd><p>Check if there is an old MARS request file; if so, remove it.</p> <dl class="field-list simple"> <dt class="field-odd">Parameters</dt> <dd class="field-odd"><ul class="simple"> diff --git a/Documentation/html/Ecmwf/access.html b/Documentation/html/Ecmwf/access.html index 80e61ef78cdba06e42fe811091ec7c7ef1e6ee8d..ec3c4bb83cb23394ca9cd2c3f363869e4dddb575 100644 --- a/Documentation/html/Ecmwf/access.html +++ b/Documentation/html/Ecmwf/access.html @@ -180,7 +180,7 @@ <dl class="simple"> <dt><strong>Member state user</strong>:</dt><dd><p>This access mode allows the user to work directly on the ECMWF Linux Member State Servers or via a Web Access Toolkit <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code> through a local Member State Gateway Server. This enables the user to have direct and full access to the Mars archive. There might be some limitations in user rights such as the declined access to the latest forecasts. This has to be discussed with the <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a>. This user group is also able to work from their local facilities without a gateway server in the same way a <strong>public</strong> user would. The only difference is the connection with the Web API. However, this is automatically selected by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p> </dd> -<dt><strong>Public user</strong>:</dt><dd><p>This access mode allows every user to access the ECMWF <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">public datasets</a> from their local facilities. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able (tested for the use with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>) to extract the re-analysis datasets such as ERA-Interim and CERA-20C. The main difference to the <strong>member state user</strong> is the method of access with the Web API and the availability of data. For example, in ERA-Interim there is only a 6-hourly temporal resolution instead of 3 hours. The access method is selected by providing the command line argument “public=1” and providing the MARS keyword “dataset” in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file. Also, the user has to explicitly accept the license of the dataset to be retrieved. This can be done as described in the installation process at section <a class="reference internal" href="../installation.html#ref-licence"><span class="std std-ref">Licence agreement for public datasets</span></a>.</p> +<dt><strong>Public user</strong>:</dt><dd><p>This access mode allows every user to access the ECMWF <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">public datasets</a> from their local facilities. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able (tested for the use with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>) to extract the re-analysis datasets such as ERA-Interim and CERA-20C. The main difference to the <strong>member state user</strong> is the method of access with the Web API and the availability of data. For example, in ERA-Interim there is only a 6-hourly temporal resolution instead of 3 hours. The access method is selected by providing the command line argument “public=1” and providing the MARS keyword “dataset” in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file. Also, the user has to explicitly accept the license of the dataset to be retrieved. This can be done as described in the installation process at section <a class="reference internal" href="../installation.html#ref-licence"><span class="std std-ref">Accept licences for public datasets</span></a>.</p> </dd> </dl> <div class="admonition note"> diff --git a/Documentation/html/Installation/gateway.html b/Documentation/html/Installation/gateway.html index 43725a53b81fc20c34b4315fd7a103b097218caa..7501ad91573c1f2f2a5f9ce820ebd701f94eaf00 100644 --- a/Documentation/html/Installation/gateway.html +++ b/Documentation/html/Installation/gateway.html @@ -91,7 +91,7 @@ <ul class="current"> <li class="toctree-l1 current"><a class="reference internal" href="../installation.html">Installation</a><ul class="current"> <li class="toctree-l2"><a class="reference internal" href="../installation.html#registration-at-ecmwf">Registration at ECMWF</a></li> -<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> +<li class="toctree-l2"><a class="reference internal" href="../installation.html#accept-licences-for-public-datasets">Accept licences for public datasets</a></li> <li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> <li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li> <li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current"> diff --git a/Documentation/html/Installation/local.html b/Documentation/html/Installation/local.html index 71c6bcd6884884b2f3a583db8f279755aa037830..50c6f2b477a4a253e403fce115c445928578814e 100644 --- a/Documentation/html/Installation/local.html +++ b/Documentation/html/Installation/local.html @@ -91,7 +91,7 @@ <ul class="current"> <li class="toctree-l1 current"><a class="reference internal" href="../installation.html">Installation</a><ul class="current"> <li class="toctree-l2"><a class="reference internal" href="../installation.html#registration-at-ecmwf">Registration at ECMWF</a></li> -<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> +<li class="toctree-l2"><a class="reference internal" href="../installation.html#accept-licences-for-public-datasets">Accept licences for public datasets</a></li> <li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> <li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li> <li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current"> diff --git a/Documentation/html/Installation/remote.html b/Documentation/html/Installation/remote.html index 10d265e38743a51953d3970a9debf7b36f83b0f8..80d0898548f0be2cabf6281cb69ac0acfa660c8d 100644 --- a/Documentation/html/Installation/remote.html +++ b/Documentation/html/Installation/remote.html @@ -91,7 +91,7 @@ <ul class="current"> <li class="toctree-l1 current"><a class="reference internal" href="../installation.html">Installation</a><ul class="current"> <li class="toctree-l2"><a class="reference internal" href="../installation.html#registration-at-ecmwf">Registration at ECMWF</a></li> -<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> +<li class="toctree-l2"><a class="reference internal" href="../installation.html#accept-licences-for-public-datasets">Accept licences for public datasets</a></li> <li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> <li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li> <li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current"> diff --git a/Documentation/html/Support/faq.html b/Documentation/html/Support/faq.html index 9d3b481463f39ba041b8b440f34a2ce3b7f1f1a0..0c26d797da2ff3a332cbbea0654b3eb63a39499a 100644 --- a/Documentation/html/Support/faq.html +++ b/Documentation/html/Support/faq.html @@ -98,7 +98,7 @@ <li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li> <li class="toctree-l1"><a class="reference internal" href="../support.html">Support</a></li> <li class="toctree-l1 current"><a class="current reference internal" href="#">FAQ - Frequently asked questions</a><ul> -<li class="toctree-l2"><a class="reference internal" href="#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages">What can I do if I can’t install the third party libraries from distribution packages?</a><ul class="simple"> +<li class="toctree-l2"><a class="reference internal" href="#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages">What can I do if I can’t install the third-party libraries from distribution packages?</a><ul class="simple"> </ul> </li> </ul> @@ -172,25 +172,24 @@ <h1>FAQ - Frequently asked questions<a class="headerlink" href="#faq-frequently-asked-questions" title="Permalink to this headline">¶</a></h1> <div class="contents local topic" id="contents"> <ul class="simple"> -<li><p><a class="reference internal" href="#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages" id="id1">What can I do if I can’t install the third party libraries from distribution packages?</a></p></li> +<li><p><a class="reference internal" href="#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages" id="id1">What can I do if I can’t install the third-party libraries from distribution packages?</a></p></li> </ul> </div> <div class="section" id="what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages"> -<h2><a class="toc-backref" href="#id1">What can I do if I can’t install the third party libraries from distribution packages?</a><a class="headerlink" href="#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages" title="Permalink to this headline">¶</a></h2> -<p>This can be the case if the user does not have admin rights. -It is possible to install the necessary libraries locally from source. -For this case you should follow the following steps:</p> +<h2><a class="toc-backref" href="#id1">What can I do if I can’t install the third-party libraries from distribution packages?</a><a class="headerlink" href="#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages" title="Permalink to this headline">¶</a></h2> +<p>This can be the case if the user does not have admin rights and the sysadmins would not want to provide the libraries. +In this case, a workaround is to install the necessary libraries from source into a user directory, following these steps:</p> <dl class="simple"> -<dt>Installation hints:</dt><dd><ol class="arabic simple"> +<dt>Steps to install libraries from source:</dt><dd><ol class="arabic simple"> <li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">Read Emoslib installation instructions</a></p></li> <li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran">Read ECMWF blog about gfortran</a></p></li> <li><p><a class="reference external" href="http://www.fftw.org">Install FFTW</a></p></li> -<li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">Install EMOSLIB</a> (2 times make! one without any options and one with single precision option)</p></li> +<li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">Install EMOSLIB</a> (execute <code class="docutils literal notranslate"><span class="pre">make</span></code> two times! One time without any options, and another time with the single-precision option.)</p></li> <li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">Install ECCODES</a></p></li> -<li><p>Register at Mars (<a class="reference internal" href="../installation.html#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a>)</p></li> +<li><p>Register for MARS access (<a class="reference internal" href="../installation.html#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a>)</p></li> <li><p>Install Web API’s <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a> and <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API</a></p></li> -<li><p>Check LD_LIBRARY_PATH environment variable if it contains all paths to the libs</p></li> -<li><p>Check available python packages (e.g. import eccodes / import grib_api / import ecmwfapi)</p></li> +<li><p>Check whether LD_LIBRARY_PATH environment variable contains the paths to all the libs</p></li> +<li><p>Check available Python packages (e.g. <code class="docutils literal notranslate"><span class="pre">import</span> <span class="pre">eccodes</span></code> / <code class="docutils literal notranslate"><span class="pre">import</span> <span class="pre">grib_api</span></code> / <code class="docutils literal notranslate"><span class="pre">import</span> <span class="pre">ecmwfapi</span></code>)</p></li> <li><p>Start test retrieval (<a class="reference internal" href="../Installation/local.html#ref-test-local"><span class="std std-ref">Test local environment</span></a>)</p></li> <li><p>Install <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> (<a class="reference internal" href="../installation.html"><span class="doc">Installation</span></a>)</p></li> </ol> diff --git a/Documentation/html/Support/known_bugs_issues.html b/Documentation/html/Support/known_bugs_issues.html index 68a750937a46f4ec522feb43529a639ee40593cc..deae47eb08fae080e0388894d9c883b023a9b9a1 100644 --- a/Documentation/html/Support/known_bugs_issues.html +++ b/Documentation/html/Support/known_bugs_issues.html @@ -174,18 +174,18 @@ <div class="section" id="installation-problems-with-gateway-and-destination-parameters"> <h3>Installation problems with <code class="docutils literal notranslate"><span class="pre">GATEWAY</span></code> and <code class="docutils literal notranslate"><span class="pre">DESTINATION</span></code> parameters<a class="headerlink" href="#installation-problems-with-gateway-and-destination-parameters" title="Permalink to this headline">¶</a></h3> <blockquote> -<div><p>See ticket <a class="reference external" href="https://www.flexpart.eu/ticket/263">#263</a> on flexpart.eu for information.</p> +<div><p>See ticket <a class="reference external" href="https://www.flexpart.eu/ticket/263">#263</a> on flexpart.eu for information. Fixed in v7.1.1.</p> </div></blockquote> </div> <div class="section" id="installation-problems-with-the-fortran-program-calc-etadot"> <h3>Installation problems with the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code><a class="headerlink" href="#installation-problems-with-the-fortran-program-calc-etadot" title="Permalink to this headline">¶</a></h3> <blockquote> -<div><p>See ticket <a class="reference external" href="https://www.flexpart.eu/ticket/264">#264</a> on flexpart.eu for information.</p> +<div><p>See ticket <a class="reference external" href="https://www.flexpart.eu/ticket/264">#264</a> on flexpart.eu for information. Fixed in v7.1.1.</p> </div></blockquote> </div> <div class="section" id="eccodes-error-code-250"> <h3>ECCODES Error Code 250<a class="headerlink" href="#eccodes-error-code-250" title="Permalink to this headline">¶</a></h3> -<p>If you get an error message from ECCODES with code 250, locking like this:</p> +<p>If you get an error message from ECCODES with code 250, looking like this:</p> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ECCODES ERROR : wrong size <span class="o">(</span><span class="m">184</span><span class="o">)</span> <span class="k">for</span> pv it contains <span class="m">276</span> values ECCODES ERROR : get: pv Passed array is too small ... ERROR CODE: <span class="m">250</span> @@ -195,10 +195,12 @@ ECCODES ERROR : get: pv Passed array is too small </pre></div> </div> <p>then you have set a wrong maximum level in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file! -It is important to properly select the maximum level depending on the data set you would like to retrieve. The following model level definitions (number of model levels available) are limited to [16, 19, 31, 40, 50, 60, 62, 91, 137]. The ERA-Interim data set uses 62 model levels and <em>ERA5</em> as well as <em>CERA-20C</em> uses 137. The operational data set uses different model levels depending on the date. For example, on the 25/06/2013 the operational system started to use 137 model levels. Therefore, everytime you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file or define a LEVELLIST=1/to/137. Of course you can stop before the top of the atmosphere, such as 60/to/137, but you have to select the maximum level number as the last one. Table 2 in the <a class="reference external" href="https://www.geosci-model-dev-discuss.net/gmd-2019-358/">scientific model description paper</a> gives an overview of the level lists and the corresponding introducstion date.</p> +It is important to properly select the maximum level depending on the data set you would like to retrieve. Only the following values of the number of model levels available are valid: 16, 19, 31, 40, 50, 60, 62, 91, 137.</p> +<p>The ERA-Interim data set uses 62 model levels and <em>ERA5</em> as well as <em>CERA-20C</em> uses 137.</p> +<p>The operational data sets use different numbers, depending on the date. For example, from 25/06/2013 on, 137 model levels were used in the operational system. Therefore, every time you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file, or you have to define LEVELLIST=1/to/137. Of course, you can stop before the top of the atmosphere, such as 60/to/137, but you have to include the maximum level number (i. e., the lowest level, see note below!) number as the last one. Table 2 in the <a class="reference external" href="https://www.geosci-model-dev-discuss.net/gmd-2019-358/">scientific model description paper</a> gives an overview of the level lists and the corresponding date they were introduced.</p> <div class="admonition note"> <p class="admonition-title">Note</p> -<p>Remember that model level 1 corresponds to the top of the atmosphere and then increases in the direction of the surface.</p> +<p>Be aware that the ECMWF model counts the levels from the top of the atmosphere downward to the surface. Level 1 is the topmost level, and e.g. 137 would be the level closest to the ground.</p> </div> </div> </div> diff --git a/Documentation/html/_modules/checks.html b/Documentation/html/_modules/checks.html index 7faf2c558d2b1664169acfa6da89b2fd9ff3a770..17ab1e555c3eb9164c54fdf8f40b4cdfdeb148ee 100644 --- a/Documentation/html/_modules/checks.html +++ b/Documentation/html/_modules/checks.html @@ -280,9 +280,10 @@ <div class="viewcode-block" id="check_area"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_area">[docs]</a><span class="k">def</span> <span class="nf">check_area</span><span class="p">(</span><span class="n">grid</span><span class="p">,</span> <span class="n">area</span><span class="p">,</span> <span class="n">upper</span><span class="p">,</span> <span class="n">lower</span><span class="p">,</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">):</span> <span class="sd">'''Defines the correct area string.</span> -<span class="sd"> Checks on the format of the four area components. Wether it is of</span> -<span class="sd"> the order of 1000 or 1. Also checks wether area was already set by command</span> -<span class="sd"> line, then the four components are overwritten.</span> +<span class="sd"> Checks the format of the four area components wether it is on</span> +<span class="sd"> the order of 1000 or 1. </span> +<span class="sd"> Also checks wether area was already set on command line, </span> +<span class="sd"> then the four components are overwritten.</span> <span class="sd"> Convert to correct format of the order of magnitude "1" and sets the</span> <span class="sd"> area parameter (North/West/South/East).</span> <span class="sd"> E.g.: -5./20./10./10.</span> @@ -296,21 +297,21 @@ <span class="sd"> Contains area informtion.</span> <span class="sd"> upper : str</span> -<span class="sd"> The northern most latitude.</span> +<span class="sd"> The northernmost latitude.</span> <span class="sd"> lower : str</span> -<span class="sd"> The souther most latitude.</span> +<span class="sd"> The southernmost latitude.</span> <span class="sd"> left : str</span> -<span class="sd"> The western most longitude.</span> +<span class="sd"> The westernmost longitude.</span> <span class="sd"> right : str</span> -<span class="sd"> The eastern most longiude.</span> +<span class="sd"> The easternmost longitude.</span> <span class="sd"> Return</span> <span class="sd"> ------</span> <span class="sd"> grid : str</span> -<span class="sd"> Contains grid in format Lat/lon. E.g. 0.1/0.1</span> +<span class="sd"> Contains grid in format lat/lon. E.g. 0.1/0.1</span> <span class="sd"> '''</span> <span class="k">if</span> <span class="s1">'N'</span> <span class="ow">in</span> <span class="n">grid</span><span class="p">:</span> <span class="c1"># Gaussian output grid</span> <span class="n">area</span> <span class="o">=</span> <span class="s1">'G'</span> @@ -341,7 +342,7 @@ <span class="nb">float</span><span class="p">(</span><span class="n">lower</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">right</span><span class="p">))</span> <span class="k">else</span><span class="p">:</span> - <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'The area components have different '</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Area components have inconsisten or unrecognised '</span> <span class="s1">'formats (upper, lower, left, right): '</span> <span class="s1">'</span><span class="si">{}</span><span class="s1">/</span><span class="si">{}</span><span class="s1">/</span><span class="si">{}</span><span class="s1">/</span><span class="si">{}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">upper</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">lower</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">left</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">right</span><span class="p">)))</span> @@ -370,8 +371,8 @@ <span class="sd"> level : str</span> <span class="sd"> Specifies the maximum level. It has to be one of the</span> -<span class="sd"> available maximum level number as contained in the variable</span> -<span class="sd"> MAX_LEVEL_LIST in "_config". E.g. [16, 19, 31, 40, 50, 60, 62, 91, 137]</span> +<span class="sd"> available maximum level numbers as contained in the variable</span> +<span class="sd"> MAX_LEVEL_LIST in "_config": [16, 19, 31, 40, 50, 60, 62, 91, 137]</span> <span class="sd"> '''</span> <span class="c1"># assure consistency of levelist and level</span> @@ -507,7 +508,7 @@ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ftype</span><span class="p">):</span> <span class="k">if</span> <span class="n">ftype</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'AN'</span> <span class="ow">and</span> <span class="nb">int</span><span class="p">(</span><span class="n">steps</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'Analysis retrievals must have STEP = 0 (now set to 0)'</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'For analysis data, STEP = 0 is needed. Setting to 0 now.)'</span><span class="p">)</span> <span class="n">ftype</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> <span class="k">return</span> <span class="n">ftype</span></div> @@ -547,7 +548,7 @@ <span class="sd"> maxstep : int</span> <span class="sd"> The maximum forecast time step in hours from the forecast base time.</span> -<span class="sd"> This is the maximum step for non flux (accumulated) forecast data.</span> +<span class="sd"> This is the maximum step for non-flux (not accumulated) forecast data.</span> <span class="sd"> purefc : int</span> <span class="sd"> Switch for definition of pure forecast mode or not.</span> @@ -566,7 +567,7 @@ <span class="sd"> '''</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">ftype</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">ftime</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">steps</span><span class="p">):</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: The number of field types, times and steps '</span> - <span class="s1">'are not the same! Please check the setting in the '</span> + <span class="s1">'are not the same! Please check the settings in the '</span> <span class="s1">'CONTROL file!'</span><span class="p">)</span> <span class="c1"># if pure forecast is selected and only one field type/time is set</span> @@ -584,7 +585,7 @@ <span class="k">return</span> <span class="n">ftype</span><span class="p">,</span> <span class="n">ftime</span><span class="p">,</span> <span class="n">steps</span></div> <div class="viewcode-block" id="check_mail"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_mail">[docs]</a><span class="k">def</span> <span class="nf">check_mail</span><span class="p">(</span><span class="n">mail</span><span class="p">):</span> - <span class="sd">'''Check the string of mail addresses, seperate them and convert to a list.</span> + <span class="sd">'''Check the string of mail addresses, separate them and convert to list.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -690,7 +691,7 @@ <span class="k">return</span> <span class="n">odir</span><span class="p">,</span> <span class="n">fpdir</span></div> <div class="viewcode-block" id="check_dates"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_dates">[docs]</a><span class="k">def</span> <span class="nf">check_dates</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">):</span> - <span class="sd">'''Checks if there is at least a start date for a one day retrieval.</span> + <span class="sd">'''Checks if there is at least a start date for a one-day retrieval.</span> <span class="sd"> Checks if end date lies after start date and end date is set.</span> @@ -789,7 +790,7 @@ <span class="k">return</span> <span class="n">basetime</span></div> <div class="viewcode-block" id="check_request"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_request">[docs]</a><span class="k">def</span> <span class="nf">check_request</span><span class="p">(</span><span class="n">request</span><span class="p">,</span> <span class="n">marsfile</span><span class="p">):</span> - <span class="sd">'''Check if there is an old mars request file and remove it.</span> + <span class="sd">'''Check if there is an old MARS request file; if so, remove it.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -812,8 +813,8 @@ <span class="k">return</span></div> <div class="viewcode-block" id="check_public"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_public">[docs]</a><span class="k">def</span> <span class="nf">check_public</span><span class="p">(</span><span class="n">public</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span> - <span class="sd">'''Check wether the dataset parameter is set for a</span> -<span class="sd"> public data set retrieval.</span> + <span class="sd">'''Check wether the dataset parameter is set to a</span> +<span class="sd"> public data set.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -828,14 +829,14 @@ <span class="sd"> '''</span> <span class="k">if</span> <span class="n">public</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">dataset</span><span class="p">:</span> - <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: If public mars data wants to be retrieved, '</span> - <span class="s1">'the "dataset"-parameter has to be set too!'</span><span class="p">)</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: If public MARS data are to be retrieved, '</span> + <span class="s1">'the "dataset"-parameter has to be set, too!'</span><span class="p">)</span> <span class="k">return</span></div> <div class="viewcode-block" id="check_acctype"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_acctype">[docs]</a><span class="k">def</span> <span class="nf">check_acctype</span><span class="p">(</span><span class="n">acctype</span><span class="p">,</span> <span class="n">ftype</span><span class="p">):</span> <span class="sd">'''Guarantees that the accumulation field type is set.</span> -<span class="sd"> If not set, it is derivated as in the old method (TYPE[1]).</span> +<span class="sd"> If not set, it is derived with the old method (TYPE[1]).</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -871,13 +872,13 @@ <div class="viewcode-block" id="check_acctime"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_acctime">[docs]</a><span class="k">def</span> <span class="nf">check_acctime</span><span class="p">(</span><span class="n">acctime</span><span class="p">,</span> <span class="n">marsclass</span><span class="p">,</span> <span class="n">purefc</span><span class="p">,</span> <span class="n">time</span><span class="p">):</span> <span class="sd">'''Guarantees that the accumulation forecast times were set.</span> -<span class="sd"> If it is not set, it tries to set the value for some of the</span> -<span class="sd"> most commonly used data sets. Otherwise it raises an error.</span> +<span class="sd"> If not set, setting the value to some of the most commonly used data sets</span> +<span class="sd"> is attempted. Otherwise, an eror is raised.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> <span class="sd"> acctime : str</span> -<span class="sd"> The starting time from the accumulated forecasts.</span> +<span class="sd"> The starting time for the accumulated forecasts.</span> <span class="sd"> marsclass : str</span> <span class="sd"> ECMWF data classification identifier.</span> @@ -888,11 +889,11 @@ <span class="sd"> Return</span> <span class="sd"> ------</span> <span class="sd"> acctime : str</span> -<span class="sd"> The starting time from the accumulated forecasts.</span> +<span class="sd"> The starting time for the accumulated forecasts.</span> <span class="sd"> '''</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">acctime</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'... Control parameter ACCTIME was not defined.'</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'... Control parameter ACCTIME was not set.'</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'... Value will be set depending on field type:</span><span class="se">\n</span><span class="s1"> '</span> <span class="s1">'</span><span class="se">\t\t</span><span class="s1"> EA=06/18</span><span class="se">\n\t\t</span><span class="s1"> EI/OD=00/12</span><span class="se">\n\t\t</span><span class="s1"> EP=18'</span><span class="p">)</span> <span class="k">if</span> <span class="n">marsclass</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'EA'</span><span class="p">:</span> <span class="c1"># Era 5</span> @@ -906,12 +907,12 @@ <span class="k">elif</span> <span class="n">marsclass</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'OD'</span> <span class="ow">and</span> <span class="n">purefc</span><span class="p">:</span> <span class="c1"># On-demand</span> <span class="n">acctime</span> <span class="o">=</span> <span class="n">time</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span><span class="p">:</span> - <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: Accumulation forecast time can not '</span> - <span class="s1">'automatically be derived!'</span><span class="p">)</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: Accumulation forecast time can not be'</span> + <span class="s1">'derived automatically!'</span><span class="p">)</span> <span class="k">return</span> <span class="n">acctime</span></div> <div class="viewcode-block" id="check_accmaxstep"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_accmaxstep">[docs]</a><span class="k">def</span> <span class="nf">check_accmaxstep</span><span class="p">(</span><span class="n">accmaxstep</span><span class="p">,</span> <span class="n">marsclass</span><span class="p">,</span> <span class="n">purefc</span><span class="p">,</span> <span class="n">maxstep</span><span class="p">):</span> - <span class="sd">'''Guarantees that the accumulation forecast step were set.</span> + <span class="sd">'''Guarantees that the accumulation forecast step was set.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -926,7 +927,7 @@ <span class="sd"> maxstep : str</span> <span class="sd"> The maximum forecast time step in hours from the forecast base time.</span> -<span class="sd"> This is the maximum step for non flux (accumulated) forecast data.</span> +<span class="sd"> This is the maximum step for non-flux (accumulated) forecast data.</span> <span class="sd"> Return</span> <span class="sd"> ------</span> @@ -934,7 +935,7 @@ <span class="sd"> The maximum forecast step for the accumulated forecast fields.</span> <span class="sd"> '''</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">accmaxstep</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'... Control parameter ACCMAXSTEP was not defined.'</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'... Control parameter ACCMAXSTEP was not set.'</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'... Value will be set depending on field type/time: '</span> <span class="s1">'</span><span class="se">\n\t\t</span><span class="s1"> EA/EI/OD=12</span><span class="se">\n\t\t</span><span class="s1"> EP=24'</span><span class="p">)</span> <span class="k">if</span> <span class="n">marsclass</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'EA'</span><span class="p">,</span> <span class="s1">'EI'</span><span class="p">,</span> <span class="s1">'OD'</span><span class="p">]</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">purefc</span><span class="p">:</span> @@ -946,22 +947,22 @@ <span class="n">accmaxstep</span> <span class="o">=</span> <span class="n">maxstep</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'... For pure forecast mode, the accumulated forecast must '</span> <span class="s1">'have the same maxstep as the normal forecast fields!</span><span class="se">\n</span><span class="s1">'</span> - <span class="s1">'</span><span class="se">\t\t</span><span class="s1"> Accmaxstep was set to maxstep!'</span><span class="p">)</span> + <span class="s1">'</span><span class="se">\t\t</span><span class="s1"> ACCMAXSTEP was set to MAXSTEP!'</span><span class="p">)</span> <span class="k">else</span><span class="p">:</span> - <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: Accumulation forecast step can not '</span> - <span class="s1">'automatically be derived!'</span><span class="p">)</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: Accumulation forecast step can not be'</span> + <span class="s1">'derived automatically!'</span><span class="p">)</span> <span class="k">else</span><span class="p">:</span> <span class="k">if</span> <span class="n">purefc</span> <span class="ow">and</span> <span class="nb">int</span><span class="p">(</span><span class="n">accmaxstep</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">maxstep</span><span class="p">):</span> <span class="n">accmaxstep</span> <span class="o">=</span> <span class="n">maxstep</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'... For pure forecast mode, the accumulated forecast must '</span> <span class="s1">'have the same maxstep as the normal forecast fields!</span><span class="se">\n</span><span class="s1">'</span> - <span class="s1">'</span><span class="se">\t\t</span><span class="s1"> Accmaxstep was set to maxstep!'</span><span class="p">)</span> + <span class="s1">'</span><span class="se">\t\t</span><span class="s1"> ACCMAXSTEP was set to MAXSTEP!'</span><span class="p">)</span> <span class="k">return</span> <span class="n">accmaxstep</span></div> <div class="viewcode-block" id="check_addpar"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_addpar">[docs]</a><span class="k">def</span> <span class="nf">check_addpar</span><span class="p">(</span><span class="n">addpar</span><span class="p">):</span> <span class="sd">'''Check that addpar has correct format of additional parameters in</span> -<span class="sd"> a single string, so that it can be easily appended to the hard coded</span> -<span class="sd"> parameters that are retrieved in any case.</span> +<span class="sd"> a single string, so that it can be easily appended to the hard-coded</span> +<span class="sd"> parameters retrieved in any case.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -987,7 +988,7 @@ <div class="viewcode-block" id="check_job_chunk"><a class="viewcode-back" href="../Documentation/Api/api_python.html#checks.check_job_chunk">[docs]</a><span class="k">def</span> <span class="nf">check_job_chunk</span><span class="p">(</span><span class="n">job_chunk</span><span class="p">):</span> - <span class="sd">'''Checks that if job chunk is set, the number is positive and non zero.</span> + <span class="sd">'''Checks that if job chunk is set, the number is positive and nonzero.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -1005,7 +1006,7 @@ <span class="n">job_chunk</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">job_chunk</span><span class="p">)</span> <span class="k">if</span> <span class="n">job_chunk</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span> - <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: The number of job chunk is negative!</span><span class="se">\n</span><span class="s1">'</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'ERROR: The number of job chunks is negative!</span><span class="se">\n</span><span class="s1">'</span> <span class="s1">'It has to be a positive number!'</span><span class="p">)</span> <span class="k">elif</span> <span class="n">job_chunk</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="n">job_chunk</span> <span class="o">=</span> <span class="kc">None</span> diff --git a/Documentation/html/_modules/get_mars_data.html b/Documentation/html/_modules/get_mars_data.html index ac1f2208a4bc39ff2ef42f26d8f4f8b004c6da67..584c5c741d2ec027a06d5f79218d7fdb806498bd 100644 --- a/Documentation/html/_modules/get_mars_data.html +++ b/Documentation/html/_modules/get_mars_data.html @@ -171,9 +171,9 @@ <span class="c1">#</span> <span class="c1"># November 2015 - Leopold Haimberger (University of Vienna):</span> <span class="c1"># - moved the getEIdata program into a function "get_mars_data"</span> -<span class="c1"># - moved the AgurmentParser into a seperate function</span> -<span class="c1"># - adatpted the function for the use in flex_extract</span> -<span class="c1"># - renamed file to get_mars_data</span> +<span class="c1"># - moved the AgurmentParser into a separate function</span> +<span class="c1"># - adapted the function for use in flex_extract</span> +<span class="c1"># - renamed source file to get_mars_data</span> <span class="c1">#</span> <span class="c1"># February 2018 - Anne Philipp (University of Vienna):</span> <span class="c1"># - applied PEP8 style guide</span> @@ -183,7 +183,7 @@ <span class="c1"># (necessary for better documentation with docstrings for later</span> <span class="c1"># online documentation)</span> <span class="c1"># - use of UIFiles class for file selection and deletion</span> -<span class="c1"># - seperated get_mars_data function into several smaller pieces:</span> +<span class="c1"># - separated get_mars_data function into several smaller pieces:</span> <span class="c1"># write_reqheader, mk_server, mk_dates, remove_old, do_retrievment</span> <span class="c1">#</span> <span class="c1"># @License:</span> @@ -197,7 +197,7 @@ <span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span> <span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span> <span class="c1">#*******************************************************************************</span> -<span class="sd">'''This script extracts MARS data from ECMWF servers.</span> +<span class="sd">'''This script extracts MARS data from ECMWF.</span> <span class="sd">At first, the necessary parameters from command line and CONTROL files are</span> <span class="sd">extracted. They define the data set to be extracted from MARS.</span> @@ -205,15 +205,15 @@ <span class="sd">This file can also be imported as a module and contains the following</span> <span class="sd">functions:</span> -<span class="sd"> * main - the main function of the script</span> -<span class="sd"> * get_mars_data - overall control of ECMWF data retrievment</span> +<span class="sd"> * main - the main function of the script</span> +<span class="sd"> * get_mars_data - overall control of ECMWF data retrievment</span> <span class="sd"> * write_reqheader - writes the header into the mars_request file</span> -<span class="sd"> * mk_server - creates the server connection to ECMWF servers</span> -<span class="sd"> * mk_dates - defines the start and end date</span> -<span class="sd"> * remove_old - deletes old retrieved grib files</span> -<span class="sd"> * do_retrievement - creates individual retrievals</span> +<span class="sd"> * mk_server - creates the server connection to ECMWF servers</span> +<span class="sd"> * mk_dates - defines the start and end date</span> +<span class="sd"> * remove_old - deletes old retrieved grib files</span> +<span class="sd"> * do_retrieval - creates individual retrievals</span> -<span class="sd">Type: get_mars_data.py --help</span> +<span class="sd">Type get_mars_data.py --help</span> <span class="sd">to get information about command line parameters.</span> <span class="sd">Read the documentation for usage instructions.</span> <span class="sd">'''</span> @@ -227,8 +227,8 @@ <span class="kn">import</span> <span class="nn">inspect</span> <span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span><span class="p">,</span> <span class="n">timedelta</span> -<span class="c1"># software specific classes and modules from flex_extract</span> -<span class="c1"># add path to local main python path for flex_extract to get full access</span> +<span class="c1"># software-specific classes and modules from flex_extract</span> +<span class="c1"># add path to local main Python path for flex_extract to get full access</span> <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getfile</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">currentframe</span><span class="p">())))</span> <span class="o">+</span> <span class="s1">'/../'</span><span class="p">)</span> <span class="c1"># pylint: disable=wrong-import-position</span> @@ -255,10 +255,10 @@ <span class="c1"># FUNCTION</span> <span class="c1"># ------------------------------------------------------------------------------</span> <div class="viewcode-block" id="main"><a class="viewcode-back" href="../Documentation/Api/api_python.html#get_mars_data.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span> - <span class="sd">'''Controls the program to get data out of mars.</span> + <span class="sd">'''Controls the program to retrieve data from MARS.</span> -<span class="sd"> This is done if it is called directly from command line.</span> -<span class="sd"> Then it also takes program call arguments and control file input.</span> +<span class="sd"> This is done if called directly from command line.</span> +<span class="sd"> Then, arguments and control file are taken as input.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -275,10 +275,10 @@ <span class="k">return</span></div> <div class="viewcode-block" id="get_mars_data"><a class="viewcode-back" href="../Documentation/Api/api_python.html#get_mars_data.get_mars_data">[docs]</a><span class="k">def</span> <span class="nf">get_mars_data</span><span class="p">(</span><span class="n">c</span><span class="p">):</span> - <span class="sd">'''Retrieves the EC data needed for a FLEXPART simulation.</span> + <span class="sd">'''Retrieves the ECMWF data required for a FLEXPART simulation.</span> -<span class="sd"> Start and end dates for retrieval period is set. Retrievals</span> -<span class="sd"> are divided into smaller periods if necessary and datechunk parameter</span> +<span class="sd"> Start and end dates for retrieval period are set. Retrievals</span> +<span class="sd"> are divided into shorter periods if necessary and if datechunk parameter</span> <span class="sd"> is set.</span> <span class="sd"> Parameters</span> @@ -298,12 +298,12 @@ <span class="n">make_dir</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">)</span> <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">request</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s2">"Retrieving EC data!"</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s2">"Retrieving ECMWF data!"</span><span class="p">)</span> <span class="k">else</span><span class="p">:</span> <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">request</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s2">"Printing mars requests!"</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s2">"Printing MARS requests!"</span><span class="p">)</span> <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">request</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s2">"Retrieving EC data and printing mars request!"</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s2">"Retrieving ECMWF data and printing MARS request!"</span><span class="p">)</span> <span class="n">write_reqheader</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="n">_config</span><span class="o">.</span><span class="n">FILE_MARS_REQUESTS</span><span class="p">))</span> <span class="nb">print</span><span class="p">(</span><span class="s2">"start date </span><span class="si">%s</span><span class="s2"> "</span> <span class="o">%</span> <span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">start_date</span><span class="p">))</span> @@ -326,12 +326,12 @@ <span class="k">return</span></div> <div class="viewcode-block" id="write_reqheader"><a class="viewcode-back" href="../Documentation/Api/api_python.html#get_mars_data.write_reqheader">[docs]</a><span class="k">def</span> <span class="nf">write_reqheader</span><span class="p">(</span><span class="n">marsfile</span><span class="p">):</span> - <span class="sd">'''Writes header with column names into mars request file.</span> + <span class="sd">'''Writes header with column names into MARS request file.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> <span class="sd"> marsfile : str</span> -<span class="sd"> Path to the mars request file.</span> +<span class="sd"> Path to the MARS request file.</span> <span class="sd"> Return</span> <span class="sd"> ------</span> @@ -349,11 +349,12 @@ <span class="k">return</span></div> <div class="viewcode-block" id="mk_server"><a class="viewcode-back" href="../Documentation/Api/api_python.html#get_mars_data.mk_server">[docs]</a><span class="k">def</span> <span class="nf">mk_server</span><span class="p">(</span><span class="n">c</span><span class="p">):</span> - <span class="sd">'''Creates a server connection with available python API.</span> + <span class="sd">'''Creates a server connection with available Python API.</span> -<span class="sd"> Which API is used depends on availability and the dataset to be retrieved.</span> -<span class="sd"> The CDS API is used for ERA5 dataset no matter if the user is a member or</span> -<span class="sd"> a public user. ECMWF WebAPI is used for all other available datasets.</span> +<span class="sd"> The API selected depends on availability and the data set to be retrieved.</span> +<span class="sd"> The CDS API is used for ERA5 data, no matter whether the user is a </span> +<span class="sd"> member-state or a public user. </span> +<span class="sd"> ECMWF WebAPI is used for all other available datasets.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -408,14 +409,14 @@ <div class="viewcode-block" id="mk_dates"><a class="viewcode-back" href="../Documentation/Api/api_python.html#get_mars_data.mk_dates">[docs]</a><span class="k">def</span> <span class="nf">mk_dates</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">fluxes</span><span class="p">):</span> - <span class="sd">'''Prepares start and end date depending on flux or non flux data.</span> + <span class="sd">'''Prepares start and end date depending on flux or non-flux type of data.</span> -<span class="sd"> If forecast for maximum one day (upto 24h) are to be retrieved, then</span> +<span class="sd"> If forecasts for a maximum of one day (24 h) are to be retrieved, then</span> <span class="sd"> collect accumulation data (flux data) with additional days in the</span> -<span class="sd"> beginning and at the end (used for complete disaggregation of</span> +<span class="sd"> beginning and at the end (needed for complete disaggregation of</span> <span class="sd"> original period)</span> -<span class="sd"> If forecast data longer than 24h are to be retrieved, then</span> +<span class="sd"> If forecast data for more than +24 h are to be retrieved, then</span> <span class="sd"> collect accumulation data (flux data) with the exact start and end date</span> <span class="sd"> (disaggregation will be done for the exact time period with</span> <span class="sd"> boundary conditions)</span> @@ -475,16 +476,16 @@ <span class="sd"> Parameters</span> <span class="sd"> ----------</span> <span class="sd"> pattern : str</span> -<span class="sd"> The sub string pattern which identifies the files to be deleted.</span> +<span class="sd"> The substring pattern which identifies the files to be deleted.</span> <span class="sd"> inputdir : str, optional</span> -<span class="sd"> Path to the directory where the retrieved data is stored.</span> +<span class="sd"> Path to the directory where the retrieved data are stored.</span> <span class="sd"> Return</span> <span class="sd"> ------</span> <span class="sd"> '''</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'... removing old content of '</span> <span class="o">+</span> <span class="n">inputdir</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'... removing old files in '</span> <span class="o">+</span> <span class="n">inputdir</span><span class="p">)</span> <span class="n">tobecleaned</span> <span class="o">=</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">inputdir</span><span class="p">,</span> <span class="n">pattern</span><span class="p">)</span> <span class="n">tobecleaned</span><span class="o">.</span><span class="n">delete_files</span><span class="p">()</span> @@ -493,7 +494,7 @@ <div class="viewcode-block" id="do_retrievement"><a class="viewcode-back" href="../Documentation/Api/api_python.html#get_mars_data.do_retrievement">[docs]</a><span class="k">def</span> <span class="nf">do_retrievement</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">server</span><span class="p">,</span> <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="n">fluxes</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> - <span class="sd">'''Divides the complete retrieval period in smaller chunks and</span> + <span class="sd">'''Divides the total retrieval period into smaller chunks and</span> <span class="sd"> retrieves the data from MARS.</span> <span class="sd"> Parameters</span> @@ -512,8 +513,7 @@ <span class="sd"> The end date of the retrieval.</span> <span class="sd"> delta_t : datetime</span> -<span class="sd"> Delta_t + 1 is the maximal time period of a single</span> -<span class="sd"> retrieval.</span> +<span class="sd"> Delta_t + 1 is the maximum time period of a single retrieval.</span> <span class="sd"> fluxes : boolean, optional</span> <span class="sd"> Decides if the flux parameters are to be retrieved or</span> @@ -526,8 +526,7 @@ <span class="sd"> '''</span> <span class="c1"># since actual day also counts as one day,</span> - <span class="c1"># we only need to add datechunk - 1 days to retrieval</span> - <span class="c1"># for a period</span> + <span class="c1"># we only need to add datechunk - 1 days to retrieval for a period</span> <span class="n">delta_t_m1</span> <span class="o">=</span> <span class="n">delta_t</span> <span class="o">-</span> <span class="n">timedelta</span><span class="p">(</span><span class="n">days</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="n">day</span> <span class="o">=</span> <span class="n">start</span> diff --git a/Documentation/html/_modules/install.html b/Documentation/html/_modules/install.html index 0431bc32afc585cde9a0e70c82ae91e31d86c8b3..6187f4ff8054811fbfbef9ccd1a1ddc555193f82 100644 --- a/Documentation/html/_modules/install.html +++ b/Documentation/html/_modules/install.html @@ -207,14 +207,14 @@ <span class="sd">'''This script installs the flex_extract program.</span> <span class="sd">Depending on the selected installation environment (locally or on the</span> -<span class="sd">ECMWF server ecgate or cca) the program extracts the commandline</span> +<span class="sd">ECMWF server ecgate or cca) the program extracts the command line</span> <span class="sd">arguments and the CONTROL file parameter and prepares the corresponding</span> <span class="sd">environment.</span> -<span class="sd">The necessary files are collected in a tar-ball and placed</span> -<span class="sd">at the target location. There its untared, the environment variables will</span> -<span class="sd">be set and the Fortran code will be compiled.</span> -<span class="sd">If the ECMWF environment is selected a job script is prepared and submitted</span> -<span class="sd">for the remaining configurations after putting the tar-ball to the</span> +<span class="sd">The necessary files are collected in a tar ball and placed</span> +<span class="sd">at the target location. There, is is untared, the environment variables are</span> +<span class="sd">set, and the Fortran code is compiled.</span> +<span class="sd">If the ECMWF environment is selected, a job script is prepared and submitted</span> +<span class="sd">for the remaining configurations after putting the tar ball on the</span> <span class="sd">target ECMWF server.</span> <span class="sd">Type: install.py --help</span> @@ -268,7 +268,7 @@ <div class="viewcode-block" id="get_install_cmdline_args"><a class="viewcode-back" href="../Documentation/Api/api_python.html#install.get_install_cmdline_args">[docs]</a><span class="k">def</span> <span class="nf">get_install_cmdline_args</span><span class="p">():</span> <span class="sd">'''Decomposes the command line arguments and assigns them to variables.</span> -<span class="sd"> Apply default values for non mentioned arguments.</span> +<span class="sd"> Apply default values for arguments not present.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -288,36 +288,36 @@ <span class="s2"> the latter two are at ECMWF"</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--makefile"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"makefile"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Name of Makefile to use for compiling the '</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Name of makefile for compiling the '</span> <span class="s1">'Fortran program'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--ecuid"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ecuid"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The user id at ECMWF.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'User id at ECMWF'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--ecgid"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ecgid"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The group id at ECMWF.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Group id at ECMWF'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--gateway"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"gateway"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The name of the local gateway server.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Name of the local gateway server'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--destination"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"destination"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The ecaccess association, e.g. '</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'ecaccess association, e.g. '</span> <span class="s1">'myUser@genericSftp'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--installdir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"installdir"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Root directory where '</span> - <span class="s1">'flex_extract will be installed to.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Root directory of the '</span> + <span class="s1">'flex_extract installation'</span><span class="p">)</span> <span class="c1"># arguments for job submission to ECMWF, only needed by submit.py</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--job_template"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">'job_template'</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">"job.template"</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The rudimentary template file to create a batch '</span> - <span class="s1">'job template for submission to ECMWF servers.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Rudimentary template file to create a batch '</span> + <span class="s1">'job template for submission to ECMWF servers'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--controlfile"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"controlfile"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s2">"The file with all CONTROL parameters."</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s2">"A file that contains all CONTROL parameters."</span><span class="p">)</span> <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span> @@ -325,8 +325,8 @@ <div class="viewcode-block" id="install_via_gateway"><a class="viewcode-back" href="../Documentation/Api/api_python.html#install.install_via_gateway">[docs]</a><span class="k">def</span> <span class="nf">install_via_gateway</span><span class="p">(</span><span class="n">c</span><span class="p">):</span> - <span class="sd">'''Prepare data transfer to remote gate and submit a job script which will</span> -<span class="sd"> install everything on the remote gate.</span> + <span class="sd">'''Prepare data transfer to remote gateway and submit a job script which will</span> +<span class="sd"> install everything on the remote gateway.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -420,8 +420,8 @@ <div class="viewcode-block" id="check_install_conditions"><a class="viewcode-back" href="../Documentation/Api/api_python.html#install.check_install_conditions">[docs]</a><span class="k">def</span> <span class="nf">check_install_conditions</span><span class="p">(</span><span class="n">c</span><span class="p">):</span> - <span class="sd">'''Checks a couple of necessary attributes and conditions</span> -<span class="sd"> for the installation such as if they exist and contain values.</span> + <span class="sd">'''Checks necessary attributes and conditions</span> +<span class="sd"> for the installation, e.g. whether they exist and contain values.</span> <span class="sd"> Otherwise set default values.</span> <span class="sd"> Parameters</span> @@ -471,8 +471,8 @@ <div class="viewcode-block" id="mk_tarball"><a class="viewcode-back" href="../Documentation/Api/api_python.html#install.mk_tarball">[docs]</a><span class="k">def</span> <span class="nf">mk_tarball</span><span class="p">(</span><span class="n">tarball_path</span><span class="p">,</span> <span class="n">target</span><span class="p">):</span> <span class="sd">'''Creates a tarball with all necessary files which need to be sent to the</span> <span class="sd"> installation directory.</span> -<span class="sd"> It does not matter if this is local or remote.</span> -<span class="sd"> Collects all python files, the Fortran source and makefiles,</span> +<span class="sd"> It does not matter whether this is local or remote.</span> +<span class="sd"> Collects all Python files, the Fortran source and makefiles,</span> <span class="sd"> the ECMWF_ENV file, the CONTROL files as well as the</span> <span class="sd"> template files.</span> @@ -658,8 +658,8 @@ <span class="sd"> Parameters</span> <span class="sd"> ----------</span> <span class="sd"> makefile : str</span> -<span class="sd"> Name of the makefile which should be used to compile FORTRAN</span> -<span class="sd"> CONVERT2 program.</span> +<span class="sd"> Name of the makefile which should be used to compile the Fortran</span> +<span class="sd"> program.</span> <span class="sd"> ecuid : str</span> <span class="sd"> The user id on ECMWF server.</span> @@ -847,17 +847,17 @@ <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">returncode</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span> <span class="nb">print</span><span class="p">(</span><span class="n">perr</span><span class="o">.</span><span class="n">decode</span><span class="p">())</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'Please edit '</span> <span class="o">+</span> <span class="n">makefile</span> <span class="o">+</span> - <span class="s1">' or try another Makefile in the src directory.'</span><span class="p">)</span> + <span class="s1">' or try another makefile in the src directory.'</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'Most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB '</span> <span class="s1">'and EMOSLIB must be adapted.'</span><span class="p">)</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'Available Makefiles:'</span><span class="p">)</span> - <span class="nb">print</span><span class="p">(</span><span class="n">UioFiles</span><span class="p">(</span><span class="n">src_path</span><span class="p">,</span> <span class="s1">'Makefile*'</span><span class="p">))</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'Available makefiles:'</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="n">UioFiles</span><span class="p">(</span><span class="n">src_path</span><span class="p">,</span> <span class="s1">'makefile*'</span><span class="p">))</span> <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'Compilation failed!'</span><span class="p">)</span> <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'ERROR: Makefile call failed:'</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'ERROR: make of Fortran code failed:'</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> <span class="k">else</span><span class="p">:</span> - <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'ls'</span><span class="p">,</span> <span class="s1">'-l'</span><span class="p">,</span> + <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'ls'</span><span class="p">,</span> <span class="s1">'-l'</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src_path</span><span class="p">,</span> <span class="n">_config</span><span class="o">.</span><span class="n">FORTRAN_EXECUTABLE</span><span class="p">)],</span> <span class="n">error_msg</span><span class="o">=</span><span class="s1">'FORTRAN EXECUTABLE COULD NOT BE FOUND!'</span><span class="p">)</span> diff --git a/Documentation/html/_modules/prepare_flexpart.html b/Documentation/html/_modules/prepare_flexpart.html index 5129ebe57980913eec747a1292eb196208a8677f..1624023ea84871fe3b2fae4c1c9f77bf1982b351 100644 --- a/Documentation/html/_modules/prepare_flexpart.html +++ b/Documentation/html/_modules/prepare_flexpart.html @@ -174,10 +174,10 @@ <span class="c1"># - job submission on ecgate and cca</span> <span class="c1"># - job templates suitable for twice daily operational dissemination</span> <span class="c1"># - dividing retrievals of longer periods into digestable chunks</span> -<span class="c1"># - retrieve also longer term forecasts, not only analyses and</span> -<span class="c1"># short term forecast data</span> +<span class="c1"># - retrieve also longer-term forecasts, not only analyses and</span> +<span class="c1"># short-term forecast data</span> <span class="c1"># - conversion into GRIB2</span> -<span class="c1"># - conversion into .fp format for faster execution of FLEXPART</span> +<span class="c1"># </span> <span class="c1">#</span> <span class="c1"># February 2018 - Anne Philipp (University of Vienna):</span> <span class="c1"># - applied PEP8 style guide</span> @@ -206,9 +206,9 @@ <span class="sd">then used by FLEXPART.</span> <span class="sd">It converts the bunch of grib files extracted via get_mars_data before,</span> -<span class="sd">by doing the necessary conversion to get consistent grids or the</span> +<span class="sd">by doing the necessary conversion to obtain consistent grids or the</span> <span class="sd">disaggregation of flux data. Finally, the data fields are combined</span> -<span class="sd">in files per available hour with the naming convention xxYYMMDDHH,</span> +<span class="sd">in files per hour available with the naming convention xxYYMMDDHH,</span> <span class="sd">where xx should be 2 arbitrary letters (mostly xx is chosen to be "EN").</span> <span class="sd">This file can also be imported as a module which then contains the following</span> @@ -249,10 +249,10 @@ <span class="c1"># FUNCTION</span> <span class="c1"># ------------------------------------------------------------------------------</span> <div class="viewcode-block" id="main"><a class="viewcode-back" href="../Documentation/Api/api_python.html#prepare_flexpart.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span> - <span class="sd">'''Controls the program to prepare flexpart input files from mars data.</span> + <span class="sd">'''Controls the program to prepare FLEXPART input files from MARS data.</span> -<span class="sd"> This is done if it is called directly from command line.</span> -<span class="sd"> Then it also takes program call arguments and control file input.</span> +<span class="sd"> This is done if called directly from the command line.</span> +<span class="sd"> Then, arguments and control file are taken as input.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -269,12 +269,11 @@ <span class="k">return</span></div> <div class="viewcode-block" id="prepare_flexpart"><a class="viewcode-back" href="../Documentation/Api/api_python.html#prepare_flexpart.prepare_flexpart">[docs]</a><span class="k">def</span> <span class="nf">prepare_flexpart</span><span class="p">(</span><span class="n">ppid</span><span class="p">,</span> <span class="n">c</span><span class="p">):</span> - <span class="sd">'''Converts the mars data into flexpart ready input files.</span> + <span class="sd">'''Converts the MARS data into files ready as input for FLEXPART.</span> -<span class="sd"> Specific data fields are converted to a different grid and the flux</span> -<span class="sd"> data are going to be disaggregated. The data fields are collected by</span> -<span class="sd"> hour and stored in a file with a specific FLEXPART relevant naming</span> -<span class="sd"> convention.</span> +<span class="sd"> Certain fields are converted to a different grid and the flux</span> +<span class="sd"> data are disaggregated. Fields are collected by hour and stored in a file </span> +<span class="sd"> with a specific naming convention.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> diff --git a/Documentation/html/_modules/tools.html b/Documentation/html/_modules/tools.html index d2a77b6439c435c6c0dc44e24485c2dd264f72cb..a6eb2c2a0e50b9fc2951e91448db2a7b4e101326 100644 --- a/Documentation/html/_modules/tools.html +++ b/Documentation/html/_modules/tools.html @@ -179,7 +179,7 @@ <span class="c1"># - applied PEP8 style guide</span> <span class="c1"># - added documentation</span> <span class="c1"># - moved all non class methods from former file Flexparttools in here</span> -<span class="c1"># - seperated args and control interpretation</span> +<span class="c1"># - separated args and control interpretation</span> <span class="c1"># - added functions get_list_as_string, read_ecenv, send_mail, make_dir,</span> <span class="c1"># put_file_to_ecserver, submit_job_to_ecserver, get_informations,</span> <span class="c1"># get_dimensions, execute_subprocess, none_or_int, none_or_str</span> @@ -279,8 +279,8 @@ <span class="k">return</span> <span class="n">c</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">ppid</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">queue</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">job_template</span></div> <div class="viewcode-block" id="none_or_str"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.none_or_str">[docs]</a><span class="k">def</span> <span class="nf">none_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span> - <span class="sd">'''Converts the input string into pythons None-type if the string</span> -<span class="sd"> contains string "None".</span> + <span class="sd">'''Converts the input string into Pythons None type if it</span> +<span class="sd"> contains the string "None".</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -291,15 +291,15 @@ <span class="sd"> ------</span> <span class="sd"> None or value:</span> <span class="sd"> Return depends on the content of the input value. If it was "None",</span> -<span class="sd"> then the python type None is returned. Otherwise the string itself.</span> +<span class="sd"> then the Python type None is returned, otherwise the string itself.</span> <span class="sd"> '''</span> <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s1">'None'</span><span class="p">:</span> <span class="k">return</span> <span class="kc">None</span> <span class="k">return</span> <span class="n">value</span></div> <div class="viewcode-block" id="none_or_int"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.none_or_int">[docs]</a><span class="k">def</span> <span class="nf">none_or_int</span><span class="p">(</span><span class="n">value</span><span class="p">):</span> - <span class="sd">'''Converts the input string into pythons None-type if the string</span> -<span class="sd"> contains string "None". Otherwise it is converted to an integer value.</span> + <span class="sd">'''Converts the input string into Pythons None-type if it</span> +<span class="sd"> contains string "None"; otherwise it is converted to an integer value.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -319,7 +319,7 @@ <div class="viewcode-block" id="get_cmdline_args"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.get_cmdline_args">[docs]</a><span class="k">def</span> <span class="nf">get_cmdline_args</span><span class="p">():</span> <span class="sd">'''Decomposes the command line arguments and assigns them to variables.</span> -<span class="sd"> Apply default values for non mentioned arguments.</span> +<span class="sd"> Apply default values for arguments not present.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -327,7 +327,7 @@ <span class="sd"> Return</span> <span class="sd"> ------</span> <span class="sd"> args : Namespace</span> -<span class="sd"> Contains the commandline arguments from script/program call.</span> +<span class="sd"> Contains the command line arguments from the script / program call.</span> <span class="sd"> '''</span> <span class="n">parser</span> <span class="o">=</span> <span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">'Retrieve FLEXPART input from </span><span class="se">\</span> @@ -352,7 +352,7 @@ <span class="n">help</span><span class="o">=</span><span class="s2">"The file with all CONTROL parameters."</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--basetime"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"basetime"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s2">"base such as 0 or 12 (for half day retrievals)"</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s2">"base time such as 0 or 12 (for half day retrievals)"</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--step"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"step"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Forecast steps such as 00/to/48"</span><span class="p">)</span> @@ -361,55 +361,56 @@ <span class="n">help</span><span class="o">=</span><span class="s2">"Vertical levels to be retrieved, e.g. 30/to/60"</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--area"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"area"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s2">"area defined as north/west/south/east"</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s2">"area, defined by north/west/south/east"</span><span class="p">)</span> <span class="c1"># some switches</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--debug"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"debug"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s2">"debug mode - leave temporary files intact"</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s2">"debug mode - temporary files will be conserved"</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--oper"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"oper"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'operational mode - prepares dates with '</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'operational mode - prepares dates from '</span> <span class="s1">'environment variables'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--request"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"request"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s2">"list all mars requests in file mars_requests.dat"</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s2">"list all MARS requests in file mars_requests.dat"</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--public"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"public"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s2">"public mode - retrieves the public datasets"</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s2">"public mode - retrieves public datasets"</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--rrint"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"rrint"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Selection of old or new precipitation '</span> - <span class="s1">'interpolation:</span><span class="se">\n</span><span class="s1">'</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Selection of old or new '</span> + <span class="s1">'interpolation method for precipitation:</span><span class="se">\n</span><span class="s1">'</span> <span class="s1">' 0 - old method</span><span class="se">\n</span><span class="s1">'</span> <span class="s1">' 1 - new method (additional subgrid points)'</span><span class="p">)</span> <span class="c1"># set directories</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--inputdir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"inputdir"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Path to the temporary directory for the '</span> - <span class="s1">'retrieval grib files and other processing files.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Path to temporary directory for '</span> + <span class="s1">'retrieved grib files and other processing files.'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--outputdir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"outputdir"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Path to the final directory where the final '</span> - <span class="s1">'FLEXPART ready input files are stored.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Path to final directory where '</span> + <span class="s1">'FLEXPART input files will be stored.'</span><span class="p">)</span> <span class="c1"># this is only used by prepare_flexpart.py to rerun a postprocessing step</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--ppid"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ppid"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'This is the specify parent process id of a '</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'This is the specify the parent process id of a '</span> <span class="s1">'single flex_extract run to identify the files. '</span> <span class="s1">'It is the second number in the GRIB files.'</span><span class="p">)</span> <span class="c1"># arguments for job submission to ECMWF, only needed by submit.py</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--job_template"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">'job_template'</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">"job.temp"</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The job template file which are adapted to be '</span> - <span class="s1">'submitted to the batch system on ECMWF server.'</span><span class="p">)</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Job template file. Will be used for submission '</span> + <span class="s1">'to the batch system on the ECMWF server after '</span> + <span class="s1">'modification.'</span><span class="p">)</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--queue"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"queue"</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'The ECMWF server name for submission of the '</span> - <span class="s1">'job script to the batch system '</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'The name of the ECMWF server name where the'</span> + <span class="s1">'job script is to be submitted '</span> <span class="s1">'(e.g. ecgate | cca | ccb)'</span><span class="p">)</span> <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span> @@ -450,7 +451,7 @@ <span class="sd">'''Remove files from the intermediate directory (inputdir).</span> <span class="sd"> It keeps the final FLEXPART input files if program runs without</span> -<span class="sd"> ECMWF Api and keywords "ectrans" or "ecstorage" are set to "1".</span> +<span class="sd"> ECMWF API and keywords "ectrans" or "ecstorage" are set to "1".</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -571,7 +572,7 @@ <span class="sd">'''Creates combinations of all passed arguments.</span> <span class="sd"> This method combines the single characters of the passed arguments</span> -<span class="sd"> with each other. So that each character of each argument value</span> +<span class="sd"> with each other in a way that each character of each argument value</span> <span class="sd"> will be combined with each character of the other arguments as a tuple.</span> <span class="sd"> Note</span> @@ -680,9 +681,8 @@ <span class="sd"> ----------</span> <span class="sd"> pars : str</span> <span class="sd"> Addpar argument from CONTROL file in the format of</span> -<span class="sd"> parameter names instead of ids. The parameter short</span> -<span class="sd"> names are sepearted with "/" and they are passed as</span> -<span class="sd"> one single string.</span> +<span class="sd"> parameter names instead of IDs. The parameter short</span> +<span class="sd"> names are separated by "/" and passed as one single string.</span> <span class="sd"> table : dict</span> <span class="sd"> Contains the ECMWF grib table 128 information.</span> @@ -716,7 +716,7 @@ <span class="k">return</span> <span class="n">ipar</span></div> <div class="viewcode-block" id="to_param_id_with_tablenumber"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.to_param_id_with_tablenumber">[docs]</a><span class="k">def</span> <span class="nf">to_param_id_with_tablenumber</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span> <span class="n">table</span><span class="p">):</span> - <span class="sd">'''Transform parameter names to parameter ids and add table id.</span> + <span class="sd">'''Transform parameter names to parameter IDs and add table ID.</span> <span class="sd"> Conversion with ECMWF grib table 128.</span> @@ -724,9 +724,8 @@ <span class="sd"> ----------</span> <span class="sd"> pars : str</span> <span class="sd"> Addpar argument from CONTROL file in the format of</span> -<span class="sd"> parameter names instead of ids. The parameter short</span> -<span class="sd"> names are sepearted with "/" and they are passed as</span> -<span class="sd"> one single string.</span> +<span class="sd"> parameter names instead of ID. The parameter short</span> +<span class="sd"> names are separated by "/" and passed as one single string.</span> <span class="sd"> table : dict</span> <span class="sd"> Contains the ECMWF grib table 128 information.</span> @@ -737,7 +736,7 @@ <span class="sd"> ------</span> <span class="sd"> spar : str</span> <span class="sd"> List of addpar parameters from CONTROL file transformed to</span> -<span class="sd"> parameter ids in the format of integer.</span> +<span class="sd"> parameter IDs in the format of integer.</span> <span class="sd"> '''</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pars</span><span class="p">:</span> <span class="k">return</span> <span class="p">[]</span> @@ -759,7 +758,8 @@ <span class="k">return</span> <span class="s1">'/'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">spar</span><span class="p">)</span></div> <div class="viewcode-block" id="get_list_as_string"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.get_list_as_string">[docs]</a><span class="k">def</span> <span class="nf">get_list_as_string</span><span class="p">(</span><span class="n">list_obj</span><span class="p">,</span> <span class="n">concatenate_sign</span><span class="o">=</span><span class="s1">', '</span><span class="p">):</span> - <span class="sd">'''Converts a list of arbitrary content into a single string.</span> + <span class="sd">'''Converts a list of arbitrary content into a single string using a given</span> +<span class="sd"> concatenation character.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -785,8 +785,8 @@ <div class="viewcode-block" id="make_dir"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.make_dir">[docs]</a><span class="k">def</span> <span class="nf">make_dir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span> <span class="sd">'''Creates a directory.</span> -<span class="sd"> It gives a warning if the directory already exists and skips process.</span> -<span class="sd"> The program stops only if there is another problem.</span> +<span class="sd"> If the directory already exists, an information is printed and the creation </span> +<span class="sd"> skipped. The program stops only if there is another problem.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -802,7 +802,7 @@ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span> <span class="c1"># errno.EEXIST = directory already exists</span> <span class="k">if</span> <span class="n">e</span><span class="o">.</span><span class="n">errno</span> <span class="o">==</span> <span class="n">errno</span><span class="o">.</span><span class="n">EEXIST</span><span class="p">:</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: Directory </span><span class="si">{0}</span><span class="s1"> already exists!'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">directory</span><span class="p">))</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'INFORMATION: Directory </span><span class="si">{0}</span><span class="s1"> already exists!'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">directory</span><span class="p">))</span> <span class="k">else</span><span class="p">:</span> <span class="k">raise</span> <span class="c1"># re-raise exception if a different error occured</span> @@ -881,7 +881,7 @@ <span class="sd"> Return</span> <span class="sd"> ------</span> <span class="sd"> job_id : int</span> -<span class="sd"> The id number of the job as a reference at the ecmwf server.</span> +<span class="sd"> The id number of the job as a reference at the ECMWF server.</span> <span class="sd"> '''</span> <span class="k">try</span><span class="p">:</span> @@ -893,22 +893,22 @@ <span class="nb">print</span><span class="p">(</span><span class="s1">'... ERROR MESSAGE:</span><span class="se">\n</span><span class="s1"> </span><span class="se">\t</span><span class="s1"> '</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">... Do you have a valid ecaccess certification key?'</span><span class="p">)</span> - <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'... ECACCESS-JOB-SUBMIT FAILED!'</span><span class="p">)</span> + <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'... ecaccess-job-submit FAILED!'</span><span class="p">)</span> <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'... ERROR CODE: '</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">errno</span><span class="p">))</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'... ERROR MESSAGE:</span><span class="se">\n</span><span class="s1"> </span><span class="se">\t</span><span class="s1"> '</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">strerror</span><span class="p">))</span> <span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">... Most likely the ECACCESS library is not available!'</span><span class="p">)</span> - <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'... ECACCESS-JOB-SUBMIT FAILED!'</span><span class="p">)</span> + <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'... ecaccess-job-submit FAILED!'</span><span class="p">)</span> <span class="k">return</span> <span class="n">job_id</span><span class="o">.</span><span class="n">decode</span><span class="p">()</span></div> <div class="viewcode-block" id="get_informations"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.get_informations">[docs]</a><span class="k">def</span> <span class="nf">get_informations</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span> - <span class="sd">'''Gets basic information from an example grib file.</span> + <span class="sd">'''Extracts basic information from a sample grib file.</span> -<span class="sd"> These information are important for later use and the</span> -<span class="sd"> initialization of numpy arrays for data storing.</span> +<span class="sd"> This information is needed for later use and the</span> +<span class="sd"> initialization of numpy arrays where data are stored.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -929,7 +929,7 @@ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># --- open file ---</span> - <span class="nb">print</span><span class="p">(</span><span class="s2">"Opening file for getting information data --- </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">filename</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s2">"Opening grib file for extraction of information --- </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">filename</span><span class="p">)</span> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> <span class="c1"># load first message from file</span> <span class="n">gid</span> <span class="o">=</span> <span class="n">codes_grib_new_from_file</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> @@ -946,7 +946,7 @@ <span class="s1">'missingValue'</span><span class="p">,</span> <span class="p">]</span> - <span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Informations are: '</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Information extracted: '</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span> <span class="c1"># Get the value of the key in a grib message.</span> <span class="n">data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">codes_get</span><span class="p">(</span><span class="n">gid</span><span class="p">,</span> <span class="n">key</span><span class="p">)</span> @@ -959,7 +959,7 @@ <div class="viewcode-block" id="get_dimensions"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.get_dimensions">[docs]</a><span class="k">def</span> <span class="nf">get_dimensions</span><span class="p">(</span><span class="n">info</span><span class="p">,</span> <span class="n">purefc</span><span class="p">,</span> <span class="n">dtime</span><span class="p">,</span> <span class="n">index_vals</span><span class="p">,</span> <span class="n">start_date</span><span class="p">,</span> <span class="n">end_date</span><span class="p">):</span> - <span class="sd">'''This function specifies the correct dimensions for x, y and t.</span> + <span class="sd">'''This function specifies the correct dimensions for x, y, and t.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> @@ -978,7 +978,7 @@ <span class="sd"> index_vals : list of list of str</span> <span class="sd"> Contains the values from the keys used for a distinct selection</span> -<span class="sd"> of grib messages in processing the grib files.</span> +<span class="sd"> of GRIB messages in processing the grib files.</span> <span class="sd"> Content looks like e.g.:</span> <span class="sd"> index_vals[0]: ('20171106', '20171107', '20171108') ; date</span> <span class="sd"> index_vals[1]: ('0', '1200', '1800', '600') ; time</span> @@ -1010,23 +1010,22 @@ <div class="viewcode-block" id="execute_subprocess"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.execute_subprocess">[docs]</a><span class="k">def</span> <span class="nf">execute_subprocess</span><span class="p">(</span><span class="n">cmd_list</span><span class="p">,</span> <span class="n">error_msg</span><span class="o">=</span><span class="s1">'SUBPROCESS FAILED!'</span><span class="p">):</span> - <span class="sd">'''Executes a command line instruction via a subprocess.</span> + <span class="sd">'''Executes a command via a subprocess.</span> <span class="sd"> Error handling is done if an error occures.</span> <span class="sd"> Parameters</span> <span class="sd"> ----------</span> <span class="sd"> cmd_list : list of str</span> -<span class="sd"> A list of the components for the command line execution. Each</span> -<span class="sd"> list entry is a single part of the command which is seperated from</span> -<span class="sd"> the rest by a blank space.</span> -<span class="sd"> E.g. ['mv', file1, file2]</span> +<span class="sd"> A list of the components for the command line execution. </span> +<span class="sd"> They will be concatenated with blank space for the command </span> +<span class="sd"> to be submitted, like ['mv', file1, file2] for mv file1 file2.</span> <span class="sd"> Return</span> <span class="sd"> ------</span> <span class="sd"> error_msg : str, optional</span> -<span class="sd"> The possible error message if the subprocess failed.</span> -<span class="sd"> By default it will just tell "SUBPROCESS FAILED!".</span> +<span class="sd"> Error message if the subprocess fails.</span> +<span class="sd"> By default it will just say "SUBPROCESS FAILED!".</span> <span class="sd"> '''</span> <span class="k">try</span><span class="p">:</span> diff --git a/Documentation/html/_sources/Developers/gen_docu.rst.txt b/Documentation/html/_sources/Developers/gen_docu.rst.txt index dd4959cb4ff22c336e2049f41d465054a1bf4d80..bde699516ddf38ad78c8e45e0bb92c3dc651fb98 100644 --- a/Documentation/html/_sources/Developers/gen_docu.rst.txt +++ b/Documentation/html/_sources/Developers/gen_docu.rst.txt @@ -1,13 +1,13 @@ ******************** -Update Documentation +Updating the documentation ******************** UNDER CONSTRUCTION -Additional Software +Additional software =================== -Developers working on ``flex_extract`` should make extensive use of the prepared test cases, unit tests and update the documentation. For this, some additional software is necessary: +Developers working on ``flex_extract`` should make extensive use of the prepared test cases and unit tests, and should also update the documentation. For this, some additional software is necessary: .. code-block:: sh @@ -26,19 +26,19 @@ Developers working on ``flex_extract`` should make extensive use of the prepared -Online-documentation with Sphinx +On-line documentation with Sphinx ================================ -Use the scriot ``gen_docu.sh`` to generate an update of the online documentation of the python component. +Use the script ``gen_docu.sh`` to generate an update of the on-line documentation of the Python component. -It uses ``pyreverse`` to generate a class and a package diagram with graphviz and overwrites the old files in the developers directory. -``pyreverse`` creates ``dot`` files and with the ``dot`` program of the ``graphviz`` software the ``png`` files are created. Everything happens in the Python source directory before moving them finally to the ``For_developers`` directory. The Sphinx source code has a ``_files`` directory which contains links to these ``png`` files and therefore they should not be renamed. +It uses ``pyreverse`` to generate class and package diagrams with ``graphviz`` and overwrites the old files in the developers directory. +``pyreverse`` creates ``dot`` files, and with the ``dot`` program of the ``graphviz`` software, the ``png`` files are created. Everything happens in the Python source directory before moving them finally to the ``For_developers`` directory. The Sphinx source code has a ``_files`` directory which contains links to these ``png`` files and therefore they should not be renamed. Sequence diagramms ------------------ -You might need to adapt the fonts path for the diagrams to a true type font. Currently it is set to: +You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to: .. code-block:: bash @@ -49,7 +49,7 @@ You might need to adapt the fonts path for the diagrams to a true type font. Cur Block diagramms ------------------ -You might need to adapt the fonts path for the diagrams to a true type font. Currently it is set to: +You might need to adapt the fonts path for the diagrams to a true-type font. Currently it is set to: .. code-block:: bash diff --git a/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt b/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt index 1bb81d5baf120630908ebec4a5bac9a6f4c624e2..aa9a468eb0aae1b12921283ceee6db22b14b361c 100644 --- a/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt +++ b/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt @@ -5,14 +5,10 @@ Fortran's Auto Generated Documentation .. contents:: :local: - - -Link to other documentation! - + +`Fortran API <Fortran/index.html>`_ - - -.... f:autoprogram:: preconvert + diff --git a/Documentation/html/_sources/Support/faq.rst.txt b/Documentation/html/_sources/Support/faq.rst.txt index 616850d36a761c822195752b7686d7665de6fc7a..bda2f516462398204a8a1dfccc26a1f813d05806 100644 --- a/Documentation/html/_sources/Support/faq.rst.txt +++ b/Documentation/html/_sources/Support/faq.rst.txt @@ -7,23 +7,22 @@ FAQ - Frequently asked questions -What can I do if I can't install the third party libraries from distribution packages? +What can I do if I can't install the third-party libraries from distribution packages? ====================================================================================== -This can be the case if the user does not have admin rights. -It is possible to install the necessary libraries locally from source. -For this case you should follow the following steps: +This can be the case if the user does not have admin rights and the sysadmins would not want to provide the libraries. +In this case, a workaround is to install the necessary libraries from source into a user directory, following these steps: -Installation hints: +Steps to install libraries from source: 1. `Read Emoslib installation instructions <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ 2. `Read ECMWF blog about gfortran <https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran>`_ 3. `Install FFTW <http://www.fftw.org>`_ - 4. `Install EMOSLIB <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ (2 times make! one without any options and one with single precision option) + 4. `Install EMOSLIB <https://software.ecmwf.int/wiki/display/EMOS/Emoslib>`_ (execute ``make`` two times! One time without any options, and another time with the single-precision option.) 5. `Install ECCODES <https://software.ecmwf.int/wiki/display/ECC>`_ - 6. Register at Mars (:ref:`ref-registration`) + 6. Register for MARS access (:ref:`ref-registration`) 7. Install Web API's `CDS API <https://cds.climate.copernicus.eu/api-how-to>`_ and `ECMWF Web API <https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home>`_ - 8. Check LD_LIBRARY_PATH environment variable if it contains all paths to the libs - 9. Check available python packages (e.g. import eccodes / import grib_api / import ecmwfapi) + 8. Check whether LD_LIBRARY_PATH environment variable contains the paths to all the libs + 9. Check available Python packages (e.g. ``import eccodes`` / ``import grib_api`` / ``import ecmwfapi``) 10. Start test retrieval (:ref:`ref-test-local`) 11. Install ``flex_extract`` (:doc:`../installation`) diff --git a/Documentation/html/_sources/Support/known_bugs_issues.rst.txt b/Documentation/html/_sources/Support/known_bugs_issues.rst.txt index aab5e630aef4729dcff5ad70217ffc8491e8f21a..7e2ba0ba0efa792b3420c94a8f2705ac01465d99 100644 --- a/Documentation/html/_sources/Support/known_bugs_issues.rst.txt +++ b/Documentation/html/_sources/Support/known_bugs_issues.rst.txt @@ -14,18 +14,19 @@ CDS API and ERA5 data Installation problems with ``GATEWAY`` and ``DESTINATION`` parameters --------------------------------------------------------------------- - See ticket `#263 <https://www.flexpart.eu/ticket/263>`_ on flexpart.eu for information. + See ticket `#263 <https://www.flexpart.eu/ticket/263>`_ on flexpart.eu for information. Fixed in v7.1.1. Installation problems with the Fortran program ``calc_etadot`` -------------------------------------------------------------- - See ticket `#264 <https://www.flexpart.eu/ticket/264>`_ on flexpart.eu for information. + See ticket `#264 <https://www.flexpart.eu/ticket/264>`_ on flexpart.eu for information. Fixed in v7.1.1. + ECCODES Error Code 250 ---------------------- -If you get an error message from ECCODES with code 250, locking like this: +If you get an error message from ECCODES with code 250, looking like this: .. code-block:: bash @@ -37,9 +38,13 @@ If you get an error message from ECCODES with code 250, locking like this: ... FORTRAN PROGRAM FAILED! then you have set a wrong maximum level in the :literal:`CONTROL` file! -It is important to properly select the maximum level depending on the data set you would like to retrieve. The following model level definitions (number of model levels available) are limited to [16, 19, 31, 40, 50, 60, 62, 91, 137]. The ERA-Interim data set uses 62 model levels and *ERA5* as well as *CERA-20C* uses 137. The operational data set uses different model levels depending on the date. For example, on the 25/06/2013 the operational system started to use 137 model levels. Therefore, everytime you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the :literal:`CONTROL` file or define a LEVELLIST=1/to/137. Of course you can stop before the top of the atmosphere, such as 60/to/137, but you have to select the maximum level number as the last one. Table 2 in the `scientific model description paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ gives an overview of the level lists and the corresponding introducstion date. +It is important to properly select the maximum level depending on the data set you would like to retrieve. Only the following values of the number of model levels available are valid: 16, 19, 31, 40, 50, 60, 62, 91, 137. + +The ERA-Interim data set uses 62 model levels and *ERA5* as well as *CERA-20C* uses 137. + +The operational data sets use different numbers, depending on the date. For example, from 25/06/2013 on, 137 model levels were used in the operational system. Therefore, every time you extract data from a date later than 25/06/2013 you have to select LEVEL=137 in the :literal:`CONTROL` file, or you have to define LEVELLIST=1/to/137. Of course, you can stop before the top of the atmosphere, such as 60/to/137, but you have to include the maximum level number (i. e., the lowest level, see note below!) number as the last one. Table 2 in the `scientific model description paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ gives an overview of the level lists and the corresponding date they were introduced. .. note:: - Remember that model level 1 corresponds to the top of the atmosphere and then increases in the direction of the surface. + Be aware that the ECMWF model counts the levels from the top of the atmosphere downward to the surface. Level 1 is the topmost level, and e.g. 137 would be the level closest to the ground. diff --git a/Documentation/html/_sources/changelog.rst.txt b/Documentation/html/_sources/changelog.rst.txt index dc8b3d387e8d4a76c4b17b95360041b0cd18d3c4..b3f98e0544b60c1c70d0fc0804f71c9a1c80e60b 100644 --- a/Documentation/html/_sources/changelog.rst.txt +++ b/Documentation/html/_sources/changelog.rst.txt @@ -19,7 +19,7 @@ Bug fixes ######### * corrected naming of makefiles and Fortran program executable in online documentation * adapted checking for ``GATEWAY`` and ``DESTINATION`` parameter - * fixed makefiles to use f90 Fortran files for ECMWF server + * fixed Fortran makefiles to use the .f90 files on ECMWF servers .. _ref-v71: @@ -41,9 +41,9 @@ Changes * upgraded to Python3 * applied PEP8 style guide * use of genshi templates - * modularization of python source code + * modularization of Python source code * upgrade from grib_api to ecCodes - * completely revised/refactored python section + * completely revised/refactored Python section * restructured program directories * Fortran program name changed from ``CONVERT2`` to ``calc_etadot`` @@ -59,8 +59,8 @@ New Features Bug fixes ######### - * diverse problems with ERA 5 retrieval - * diverse problems with CERA-20C retrieval + * various problems with ERA 5 retrieval + * various problems with CERA-20C retrieval * BASETIME retrieval option * `CONVERT2` FORTRAN program: initialise fields to 0. (introduced initialization of :literal:`field` variable in the Fortran program @@ -73,7 +73,7 @@ Release v7.0.3 New Features ############ - * output of mars requests to an extra file (debugging and documentation) + * output of MARS requests to an extra file (debugging and documentation) * CERA-20C download * ERA 5 download * public user interface with `ECMWF Web API`_ @@ -86,16 +86,16 @@ Release v7.0.2 New Features ############ - * Python based version + * Python-based version Changes ####### - * korn shell scripts were substituted by python scripts + * korn shell scripts substituted by Python scripts .. _ref-v60: Release v0.1 - v6.0 ------------------- - * old version which should no longer be used anymore + * old version which should no longer be used diff --git a/Documentation/html/_sources/index.rst.txt b/Documentation/html/_sources/index.rst.txt index 9835e975aa60a61927233136b935645fea4d0126..04def90b123a55441c469874a3a57785d6643b23 100644 --- a/Documentation/html/_sources/index.rst.txt +++ b/Documentation/html/_sources/index.rst.txt @@ -7,7 +7,7 @@ Welcome to ``flex_extract``'s user documentation! ================================================= -``Flex_extract`` is an open-source software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to serve as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system. +``Flex_extract`` is an open-source software to retrieve meteorological fields from the MARS archive of the European Centre for Medium-Range Weather Forecasts (ECMWF) to serve as input for the FLEXTRA/FLEXPART atmospheric transport modelling system. .. raw:: html @@ -31,8 +31,8 @@ Welcome to ``flex_extract``'s user documentation! <h2><a href="ecmwf_data.html">ECMWF data</a></h2> <ul> <li><a href="ecmwf_data.html">Overview</a></li> - <li><a href="Ecmwf/access.html">Access Modes</a></li> - <li><a href="Ecmwf/ec-links.html">Link Collection</a></li> + <li><a href="Ecmwf/access.html">Access modes</a></li> + <li><a href="Ecmwf/ec-links.html">Link collection</a></li> </ul> </td> <td style="width:30%;height:150px;"> @@ -42,8 +42,8 @@ Welcome to ``flex_extract``'s user documentation! <h2><a href="documentation.html">Documentation</a></h2> <ul> <li><a href="Documentation/overview.html">Overview</a></li> - <li><a href="Documentation/input.html">Control & Input Data</a></li> - <li><a href="Documentation/output.html">Output Data</a></li> + <li><a href="Documentation/input.html">Control & input data</a></li> + <li><a href="Documentation/output.html">Output data</a></li> </ul> </td> </tr> @@ -76,9 +76,9 @@ Welcome to ``flex_extract``'s user documentation! </div> <h2><a href="dev_guide.html">Developer</a></h2> <ul> - <li><a href="Developers/gen_docu.html">Update Documentation</a></li> - <li><a href=""></a><Placeholder></li> - <li><a href=""></a><Placeholder></li> + <li><a href="Developers/gen_docu.html">Updateing the documentation</a></li> +<!-- <li><a href=""></a><Placeholder></li> + <li><a href=""></a><Placeholder></li>--> </ul> </td> </tr> diff --git a/Documentation/html/_sources/installation.rst.txt b/Documentation/html/_sources/installation.rst.txt index 7e7bbe2c8e0f50082df056671b9e55e7014fa65c..c78d3665b54cdd0571497d338f882ac445365075 100644 --- a/Documentation/html/_sources/installation.rst.txt +++ b/Documentation/html/_sources/installation.rst.txt @@ -39,22 +39,22 @@ Installation The ``flex_extract`` software package contains python and shell scripts as well as a Fortran program. These components rely on several libraries which need to be available before starting the installation process. Currently, the software is only tested for a GNU/Linux environment. Feel free to try it out on other platforms. -At first, go to the `user group <Ecmwf/access.html>`_ section and decide which group you belong to and follow the instructions at :ref:`ref-registration` to obtain an account at ECMWF (if you don't have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible :doc:`Documentation/Overview/app_modes`: +At first, find out to which `user group <Ecmwf/access.html>`_ you belong and follow the instructions at :ref:`ref-registration` to obtain an account at ECMWF (if you don't have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible :doc:`Documentation/Overview/app_modes`: - Remote (member-state users only) :ref:`[installation]<ref-remote-mode>` - Gateway (member-state users only) :ref:`[installation]<ref-gateway-mode>` - Local, member-state user :ref:`[installation]<ref-local-mode>` - Local, public user :ref:`[installation]<ref-local-mode>` -Please follow the link :doc:`Documentation/Overview/app_modes` to get a description of the modes. +More information can be found in :doc:`Documentation/Overview/app_modes`. .. note:: If you encounter any problems in the installation process, you can ask for :doc:`support`. - - - - + + + + .. _ref-registration: @@ -91,10 +91,10 @@ Registration options: .. _ref-licence: -Licence agreement for public datasets +Accept licences for public datasets ===================================== -Each ECMWF public dataset has its own licence which has to be accepted, regardless of the user group. +Each ECMWF :underline:`public` dataset has its own licence whose acceptance requires user activity, regardless of the user group. For the *ERA-Interim* and *CERA-20C* datasets this can be done at the ECMWF website `Available ECMWF Public Datasets <https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets>`_. Log in and follow the licence links on the right side for each dataset and accept it. diff --git a/Documentation/html/_sources/quick_start.rst.txt b/Documentation/html/_sources/quick_start.rst.txt index ee94135c001d64b31b2280f53aade09a3f938a85..97d70b4d88a68ab5cac9c1dde5094e6a51dcbaa3 100644 --- a/Documentation/html/_sources/quick_start.rst.txt +++ b/Documentation/html/_sources/quick_start.rst.txt @@ -2,15 +2,15 @@ Quick Start *********** -``Flex_extract`` by itself is a command-line tool. With version 7.1 an upstream shell script was implemented which calls ``flex_extract`` with the command-line parameters. +``flex_extract`` is a command-line tool. In the first versions, it was started via a korn shell script and since version 6, the entry point was a python script. From version 7.1, a bash shell script was implemented to call ``flex_extract`` with the command-line parameters. -To submit a job with ``flex_extract`` change the working directory to the ``Run`` directory which is placed directly under the ``flex_extract_vX.X`` root directory (``X.X`` is the version number): +To submit an extraction job, change the working directory to the subdirectory ``Run`` (directly under the ``flex_extract_vX.X`` root directory, where ``X.X`` is the version number): .. code-block:: bash cd <path-to-flex_extract_vX.X>/Run -Within this directory you can find everything you need to modify and run ``flex_extract``. The following tree shows a shortened list of directories and important files. The ``*`` serves as a wildcard. The brackets ``[]`` means that the file appearance depends on the mode of application and night not be present. +Within this directory you can find everything you need to modify and run ``flex_extract``. The following tree shows a shortened list of directories and important files. The ``*`` serves as a wildcard. The brackets ``[]`` indicate that the file is present only in certain modes of application. .. code-block:: bash @@ -28,30 +28,30 @@ Within this directory you can find everything you need to modify and run ``flex_ ├── run_local.sh └── run.sh -The ``Jobscripts`` directory is used to store the Korn shell job scripts generated by a ``flex_extract`` run in the **Remote** or **Gateway** mode. They are used to submit the setup information to the ECMWF server and start the jobs in ECMWF's batch mode. The typical user must not touch these files. They will be generated from template files which are stored in the ``Templates`` directory under ``flex_extract_vX.X``. Usually there will be a ``compilejob.ksh`` and a ``job.ksh`` script which are explained in the section :doc:`Documentation/input`. In the rare case of operational data extraction there will be a ``joboper.ksh`` which is designed to get the time parameters from environment variables at the ECMWF servers. +The ``Jobscripts`` directory is used to store the Korn shell job scripts generated by a ``flex_extract`` run in the **Remote** or **Gateway** mode. They are used to submit the setup information to the ECMWF server and start the jobs in ECMWF's batch mode. The typical user must not touch these files. They are generated from template files which are stored in the ``Templates`` directory under ``flex_extract_vX.X``. Usually there will be a ``compilejob.ksh`` and a ``job.ksh`` script which are explained in the section :doc:`Documentation/input`. In the rare case of operational data extraction there will be a ``joboper.ksh`` which reads time information from environment variables at the ECMWF servers. -The ``Controls`` directory contains a number of example ``CONTROL`` files. These ``CONTROL`` files represent the current range of possible dataset retrievals with ``flex_extract``. Some parameters in the ``CONTROL`` files can be adapted and some others should not be changed. In this :doc:`quick_start` guide we explain how an extraction with ``flex_extract`` can be started in the different :doc:`Documentation/Overview/app_modes` and point out some specifics of each dataset and ``CONTROL`` file. +The ``Controls`` directory contains a number of sample ``CONTROL`` files. They cover the current range of possible kinds of extractions. Some parameters in the ``CONTROL`` files can be adapted and some others should not be changed. In this :doc:`quick_start` guide we explain how an extraction with ``flex_extract`` can be started in the different :doc:`Documentation/Overview/app_modes` and point out some specifics of each dataset and ``CONTROL`` file. Directly under ``Run`` you find the files ``run.sh`` and ``run_local.sh`` and according to your selected :doc:`Documentation/Overview/app_modes` there might also be a file named ``ECMWF_ENV`` for the user credentials to quickly and automatically access ECMWF servers. -From version 7.1 on, the ``run.sh`` (or ``run_local.sh``) script is the main access point to ``flex_extract``. +From version 7.1 on, the ``run.sh`` (or ``run_local.sh``) script is the main entry point to ``flex_extract``. .. note:: - Note that, for experienced users (or users of older versions), it is still possible to access ``flex_extract`` directly via the ``submit.py`` script which can be found in the directory ``flex_extract_vX.X/Source/Python``. + Note that for experienced users (or users of older versions), it is still possible to start ``flex_extract`` directly via the ``submit.py`` script in directory ``flex_extract_vX.X/Source/Python``. Job preparation =============== -To actually start a job with ``flex_extract`` it is only necessary to submit the ``run.sh`` or ``run_local.sh`` script on the command-line. For the specification of dataset and the selection of the access mode it is necessary to select and modify a ``CONTROL`` file and change the parameters in the user section of the ``run`` scripts. The following sections describes the differences in the application modes and where the results will be stored. +To actually start a job with ``flex_extract`` it is sufficient to start either ``run.sh`` or ``run_local.sh``. Data sets and access modes are selected in ``CONTROL`` files and within the user section of the ``run`` scripts. One should select one of the sample ``CONTROL`` files. The following sections describes the differences in the application modes and where the results will be stored. Remote and gateway modes ------------------------ -For member state users it is recommended to use the *remote* or *gateway* mode, especially for more demanding tasks, to retrieve and convert data on ECMWF machines and to transfer only the final output files to the local host. +For member-state users it is recommended to use the *remote* or *gateway* mode, especially for more demanding tasks, which retrieve and convert the data on ECMWF machines; only the final output files are transferrred to the local host. Remote mode The only difference between both modes is the users working location. In the *remote* mode you have to login to the ECMWF server and then go to the ``Run`` directory as shown above. At ECMWF servers ``flex_extract`` is installed in the ``$HOME`` directory. However, to be able to start the program you have to load the ``Python3`` environment with the module system first. diff --git a/Documentation/html/_sources/support.rst.txt b/Documentation/html/_sources/support.rst.txt index 1bfcc5e5b6e1482401bcbe267a86a96d54ed74b5..1a11e5f8dac4d26b76dbacf0ce85c63c29475887 100644 --- a/Documentation/html/_sources/support.rst.txt +++ b/Documentation/html/_sources/support.rst.txt @@ -15,10 +15,10 @@ Ticket system ------------- .. _ticket system: https://www.flexpart.eu/report/1 -The community website http://flexpart.eu contains a -`ticket system`_ which can be used to report any issue or a proposition for a new feature. +The community website https://flexpart.eu/ contains a +`ticket system`_ which can be used to report any issue or to propose new features. -The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the ``flexpart.eu[at]zamg.ac.at`` and you will receive your credentials (with some delay). +The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the ``flexpart.eu[at]zamg.ac.at`` and you will receive your credentials (possibly with some delay). Event though a category "Support" is available, in most cases asking questions in the mailing list (see next paragraph below) will be more appropriate. .. _ref-mailing-list: @@ -26,11 +26,10 @@ The tickets can be viewed by anyone, to create a ticket a registration is necess Mailing list ------------ -The mailing list is mainly for the ``FLEXPART`` users to ask questions or share experiences regarding the whole ``FLEXPART`` process with the community. This can be a lot faster than asking only the developers for help. Since ``flex_extract`` is a preprocessor to ``FLEXPART`` this is the right place to ask for help. +A mailing list exists for the ``FLEXPART`` users to ask questions or share experiences with the community, regarding the whole ``FLEXPART`` process. This may be faster than asking only the developers for help through tickets. Since ``flex_extract`` is a preprocessor to ``FLEXPART`` this is the right place to ask for help. -Additionally, from time to time, there will be announcements for all FLEXPART users, such as new release versions of ``FLEXPART`` or ``flex_extract``. - -Just write a mail to: ``flexpart[at]lists.univie.ac.at`` +New release versions of ``FLEXPART`` or ``flex_extract`` or other important annoucements will also be made through this mailling list. +The subscription process is explained at the bottom of https://www.flexpart.eu/wiki/RegisteredUser. Once subscribed, write e-mail to ``flexpart[at]lists.univie.ac.at`` to post to the list. .. _ref-reporting: @@ -40,12 +39,11 @@ Reporting an issue To properly report a problem or bug, please provide as much information as possible. This includes: - -* the flex_extract version -* a flex_extract log file (output of submit.py script) -* the CONTROL file -* the commandline arguments or run(_local).sh settings and -* a description of the environment you used (Unix/Linux version, library version, application mode, etc.). +* the ``flex_extract`` version +* a ``flex_extract log`` file (output of ``submit.py`` script) +* the ``CONTROL`` file +* the command-line arguments or ``run(_local).sh`` settings and +* a description of your environment (Unix/Linux version, library version, application mode, etc.). .. _ref-known-issues: diff --git a/Documentation/html/changelog.html b/Documentation/html/changelog.html index 9f06cd876f3220cb586100c6178aa2d01f2a34b9..d22da68576d4d8646ed1814883a3b4c3431926e4 100644 --- a/Documentation/html/changelog.html +++ b/Documentation/html/changelog.html @@ -39,7 +39,7 @@ <link rel="index" title="Index" href="genindex.html" /> <link rel="search" title="Search" href="search.html" /> <link rel="next" title="Support" href="support.html" /> - <link rel="prev" title="Update Documentation" href="Developers/gen_docu.html" /> + <link rel="prev" title="Updating the documentation" href="Developers/gen_docu.html" /> </head> <body class="wy-body-for-nav"> @@ -201,7 +201,7 @@ <div><ul class="simple"> <li><p>corrected naming of makefiles and Fortran program executable in online documentation</p></li> <li><p>adapted checking for <code class="docutils literal notranslate"><span class="pre">GATEWAY</span></code> and <code class="docutils literal notranslate"><span class="pre">DESTINATION</span></code> parameter</p></li> -<li><p>fixed makefiles to use f90 Fortran files for ECMWF server</p></li> +<li><p>fixed Fortran makefiles to use the .f90 files on ECMWF servers</p></li> </ul> </div></blockquote> </div> @@ -228,9 +228,9 @@ <li><p>upgraded to Python3</p></li> <li><p>applied PEP8 style guide</p></li> <li><p>use of genshi templates</p></li> -<li><p>modularization of python source code</p></li> +<li><p>modularization of Python source code</p></li> <li><p>upgrade from grib_api to ecCodes</p></li> -<li><p>completely revised/refactored python section</p></li> +<li><p>completely revised/refactored Python section</p></li> <li><p>restructured program directories</p></li> <li><p>Fortran program name changed from <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> to <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></p></li> </ul> @@ -251,8 +251,8 @@ <h3>Bug fixes<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3> <blockquote> <div><ul class="simple"> -<li><p>diverse problems with ERA 5 retrieval</p></li> -<li><p>diverse problems with CERA-20C retrieval</p></li> +<li><p>various problems with ERA 5 retrieval</p></li> +<li><p>various problems with CERA-20C retrieval</p></li> <li><p>BASETIME retrieval option</p></li> <li><p><cite>CONVERT2</cite> FORTRAN program: initialise fields to 0. (introduced initialization of <code class="docutils literal notranslate"><span class="pre">field</span></code> variable in the Fortran program @@ -267,7 +267,7 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span <h3>New Features<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3> <blockquote> <div><ul class="simple"> -<li><p>output of mars requests to an extra file (debugging and documentation)</p></li> +<li><p>output of MARS requests to an extra file (debugging and documentation)</p></li> <li><p>CERA-20C download</p></li> <li><p>ERA 5 download</p></li> <li><p>public user interface with <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API</a></p></li> @@ -282,7 +282,7 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span <h3>New Features<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3> <blockquote> <div><ul class="simple"> -<li><p>Python based version</p></li> +<li><p>Python-based version</p></li> </ul> </div></blockquote> </div> @@ -290,7 +290,7 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span <h3>Changes<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3> <blockquote> <div><ul class="simple"> -<li><p>korn shell scripts were substituted by python scripts</p></li> +<li><p>korn shell scripts substituted by Python scripts</p></li> </ul> </div></blockquote> </div> @@ -299,7 +299,7 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span <span id="ref-v60"></span><h2>Release v0.1 - v6.0<a class="headerlink" href="#release-v0-1-v6-0" title="Permalink to this headline">¶</a></h2> <blockquote> <div><ul class="simple"> -<li><p>old version which should no longer be used anymore</p></li> +<li><p>old version which should no longer be used</p></li> </ul> </div></blockquote> </div> @@ -316,7 +316,7 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span <a href="support.html" class="btn btn-neutral float-right" title="Support" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a> - <a href="Developers/gen_docu.html" class="btn btn-neutral float-left" title="Update Documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a> + <a href="Developers/gen_docu.html" class="btn btn-neutral float-left" title="Updating the documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a> </div> diff --git a/Documentation/html/dev_guide.html b/Documentation/html/dev_guide.html index 03085d3ee5436e5b83b8ac8142f021f752ef5c0d..074d324ab28895a603a9fbfe46892cfaa02074b0 100644 --- a/Documentation/html/dev_guide.html +++ b/Documentation/html/dev_guide.html @@ -38,7 +38,7 @@ <link rel="stylesheet" href="_static/css/theme_overrides.css" type="text/css" /> <link rel="index" title="Index" href="genindex.html" /> <link rel="search" title="Search" href="search.html" /> - <link rel="next" title="Update Documentation" href="Developers/gen_docu.html" /> + <link rel="next" title="Updating the documentation" href="Developers/gen_docu.html" /> <link rel="prev" title="Metrics" href="Evaluation/metrics.html" /> </head> @@ -95,7 +95,7 @@ <li class="toctree-l1"><a class="reference internal" href="documentation.html">Documentation</a></li> <li class="toctree-l1"><a class="reference internal" href="evaluation.html">Evaluation</a></li> <li class="toctree-l1 current"><a class="current reference internal" href="#">Developer Guide</a><ul> -<li class="toctree-l2"><a class="reference internal" href="Developers/gen_docu.html">Update Documentation</a></li> +<li class="toctree-l2"><a class="reference internal" href="Developers/gen_docu.html">Updating the documentation</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li> @@ -187,7 +187,7 @@ <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation"> - <a href="Developers/gen_docu.html" class="btn btn-neutral float-right" title="Update Documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a> + <a href="Developers/gen_docu.html" class="btn btn-neutral float-right" title="Updating the documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a> <a href="Evaluation/metrics.html" class="btn btn-neutral float-left" title="Metrics" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a> diff --git a/Documentation/html/index.html b/Documentation/html/index.html index 9802a9e1b867600d0ed2931fc7a3a0f68c229f23..ba412cf65cfeb339f46e3b240bb1440f87b800b9 100644 --- a/Documentation/html/index.html +++ b/Documentation/html/index.html @@ -164,7 +164,7 @@ <div class="section" id="welcome-to-flex-extract-s-user-documentation"> <h1>Welcome to <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>’s user documentation!<a class="headerlink" href="#welcome-to-flex-extract-s-user-documentation" title="Permalink to this headline">¶</a></h1> -<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is an open-source software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to serve as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system.</p> +<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is an open-source software to retrieve meteorological fields from the MARS archive of the European Centre for Medium-Range Weather Forecasts (ECMWF) to serve as input for the FLEXTRA/FLEXPART atmospheric transport modelling system.</p> <table style="width:100%;"> <tr> <td style="width:30%;height:150px;"> @@ -185,8 +185,8 @@ <h2><a href="ecmwf_data.html">ECMWF data</a></h2> <ul> <li><a href="ecmwf_data.html">Overview</a></li> - <li><a href="Ecmwf/access.html">Access Modes</a></li> - <li><a href="Ecmwf/ec-links.html">Link Collection</a></li> + <li><a href="Ecmwf/access.html">Access modes</a></li> + <li><a href="Ecmwf/ec-links.html">Link collection</a></li> </ul> </td> <td style="width:30%;height:150px;"> @@ -196,8 +196,8 @@ <h2><a href="documentation.html">Documentation</a></h2> <ul> <li><a href="Documentation/overview.html">Overview</a></li> - <li><a href="Documentation/input.html">Control & Input Data</a></li> - <li><a href="Documentation/output.html">Output Data</a></li> + <li><a href="Documentation/input.html">Control & input data</a></li> + <li><a href="Documentation/output.html">Output data</a></li> </ul> </td> </tr> @@ -230,46 +230,68 @@ </div> <h2><a href="dev_guide.html">Developer</a></h2> <ul> - <li><a href="Developers/gen_docu.html">Update Documentation</a></li> - <li><a href=""></a><Placeholder></li> - <li><a href=""></a><Placeholder></li> - </ul> - </td> - </tr> - </table> - <table style="width:100%;"> - <tr> - <td style="width:15%"> - </td> - <td style="width:30%;height:150px;"> - <div style="width:100%;height:60px;margin-left:10%;position:relative;"> - <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/change_icon.png"> - </div> - <h2><a href="changelog.html">Changelog</a></h2> - <ul> - <li><a href="changelog.html#ref-v711">v7.1.1</a></li> - <li><a href="changelog.html#ref-v71">v7.1</a></li> - <li><a href="changelog.html#ref-v704">v7.0.4</a></li> - <li><a href="changelog.html#ref-v703">v7.0.3</a></li> - </ul> - </td> - <td style="width:30%;height:150px;"> - <div style="width:100%;height:60px;margin-left:10%;position:relative;"> - <img style="position:absolute;height:100%;vertical-align:bottom;" src="_static/help_icon.png"> - </div> - <h2><a href="support.html">Support</a></h2> - <ul> - <li><a href="support.html#ref-ticket-system">Ticket system</a></li> - <li><a href="support.html#ref-mailing-list">Mailing list</a></li> - <li><a href="Support/known_bugs_issues.html">Known bugs or issues</a></li> - <li><a href="Support/faq.html">FAQ</a></li> - </ul> - </td> - <td style="width:10%"> - </td> - </tr> -</table> -<p></p><div class="admonition note"> + <li><a href="Developers/gen_docu.html">Updateing the documentation</a></li><dl> +<dt><!– <li><a href=””></a><Placeholder></li></dt><dd><blockquote> +<div><blockquote> +<div><blockquote> +<div><blockquote> +<div><p><li><a href=””></a><Placeholder></li>–></p> +</div></blockquote> +<p></ul></p> +</div></blockquote> +<p></td></p> +</div></blockquote> +<p></tr> +</table> +<table style=”width:100%;”> +<tr></p> +<blockquote> +<div><p><td style=”width:15%”> +</td> +<td style=”width:30%;height:150px;”></p> +<blockquote> +<div><dl class="simple"> +<dt><div style=”width:100%;height:60px;margin-left:10%;position:relative;”></dt><dd><p><img style=”position:absolute;height:90%;vertical-align:bottom;” src=”_static/change_icon.png”></p> +</dd> +</dl> +<p></div> +<h2><a href=”changelog.html”>Changelog</a></h2> +<ul></p> +<blockquote> +<div><p><li><a href=”changelog.html#ref-v711”>v7.1.1</a></li> +<li><a href=”changelog.html#ref-v71”>v7.1</a></li> +<li><a href=”changelog.html#ref-v704”>v7.0.4</a></li> +<li><a href=”changelog.html#ref-v703”>v7.0.3</a></li></p> +</div></blockquote> +<p></ul></p> +</div></blockquote> +<p></td> +<td style=”width:30%;height:150px;”></p> +<blockquote> +<div><p><div style=”width:100%;height:60px;margin-left:10%;position:relative;”> +<img style=”position:absolute;height:100%;vertical-align:bottom;” src=”_static/help_icon.png”> +</div> +<h2><a href=”support.html”>Support</a></h2> +<ul></p> +<blockquote> +<div><p><li><a href=”support.html#ref-ticket-system”>Ticket system</a></li> +<li><a href=”support.html#ref-mailing-list”>Mailing list</a></li> +<li><a href=”Support/known_bugs_issues.html”>Known bugs or issues</a></li> +<li><a href=”Support/faq.html”>FAQ</a></li></p> +</div></blockquote> +<p></ul></p> +</div></blockquote> +<p></td> +<td style=”width:10%”> +</td></p> +</div></blockquote> +<p></tr></p> +</div></blockquote> +<p></table> +<p></p></p> +</dd> +</dl> +<div class="admonition note"> <p class="admonition-title">Note</p> <div class="figure align-default"> <a class="reference internal image-reference" href="_images/cc-by-40.png"><img alt="_images/cc-by-40.png" src="_images/cc-by-40.png" style="width: 100px;" /></a> @@ -284,7 +306,7 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p> <ul> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul> <li class="toctree-l2"><a class="reference internal" href="installation.html#registration-at-ecmwf">Registration at ECMWF</a></li> -<li class="toctree-l2"><a class="reference internal" href="installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> +<li class="toctree-l2"><a class="reference internal" href="installation.html#accept-licences-for-public-datasets">Accept licences for public datasets</a></li> <li class="toctree-l2"><a class="reference internal" href="installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> <li class="toctree-l2"><a class="reference internal" href="installation.html#dependencies">Dependencies</a></li> <li class="toctree-l2"><a class="reference internal" href="installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> @@ -354,7 +376,7 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Support/faq.html">FAQ - Frequently asked questions</a><ul> -<li class="toctree-l2"><a class="reference internal" href="Support/faq.html#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages">What can I do if I can’t install the third party libraries from distribution packages?</a></li> +<li class="toctree-l2"><a class="reference internal" href="Support/faq.html#what-can-i-do-if-i-can-t-install-the-third-party-libraries-from-distribution-packages">What can I do if I can’t install the third-party libraries from distribution packages?</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="authors.html">Developer Team</a></li> diff --git a/Documentation/html/installation.html b/Documentation/html/installation.html index 98aaec065a57693a8c5fa9e228a23d291d40176b..ab3c73a93fae265a73471a076a3e77b5e7bdcd36 100644 --- a/Documentation/html/installation.html +++ b/Documentation/html/installation.html @@ -91,7 +91,7 @@ <ul class="current"> <li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul> <li class="toctree-l2"><a class="reference internal" href="#registration-at-ecmwf">Registration at ECMWF</a></li> -<li class="toctree-l2"><a class="reference internal" href="#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> +<li class="toctree-l2"><a class="reference internal" href="#accept-licences-for-public-datasets">Accept licences for public datasets</a></li> <li class="toctree-l2"><a class="reference internal" href="#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> <li class="toctree-l2"><a class="reference internal" href="#dependencies">Dependencies</a></li> <li class="toctree-l2"><a class="reference internal" href="#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul> @@ -186,14 +186,14 @@ <div class="toctree-wrapper compound"> </div> <p>The <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> software package contains python and shell scripts as well as a Fortran program. These components rely on several libraries which need to be available before starting the installation process. Currently, the software is only tested for a GNU/Linux environment. Feel free to try it out on other platforms.</p> -<p>At first, go to the <a class="reference external" href="Ecmwf/access.html">user group</a> section and decide which group you belong to and follow the instructions at <a class="reference internal" href="#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a> to obtain an account at ECMWF (if you don’t have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a>:</p> +<p>At first, find out to which <a class="reference external" href="Ecmwf/access.html">user group</a> you belong and follow the instructions at <a class="reference internal" href="#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a> to obtain an account at ECMWF (if you don’t have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a>:</p> <ul class="simple"> <li><p>Remote (member-state users only) <a class="reference internal" href="Installation/remote.html#ref-remote-mode"><span class="std std-ref">[installation]</span></a></p></li> <li><p>Gateway (member-state users only) <a class="reference internal" href="Installation/gateway.html#ref-gateway-mode"><span class="std std-ref">[installation]</span></a></p></li> <li><p>Local, member-state user <a class="reference internal" href="Installation/local.html#ref-local-mode"><span class="std std-ref">[installation]</span></a></p></li> <li><p>Local, public user <a class="reference internal" href="Installation/local.html#ref-local-mode"><span class="std std-ref">[installation]</span></a></p></li> </ul> -<p>Please follow the link <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> to get a description of the modes.</p> +<p>More information can be found in <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a>.</p> <div class="admonition note"> <p class="admonition-title">Note</p> <p>If you encounter any problems in the installation process, you can ask for <a class="reference internal" href="support.html"><span class="doc">Support</span></a>.</p> @@ -258,9 +258,9 @@ <p>3.) Access through the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a>. Extra registration for member-state users is required at <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">Copernicus Climate Data Store</a> including the configurations of the CDS key as described. This mode is currently not available for public users. See the note at <a class="reference external" href="Ecmwf/access.html">user group</a> for information.</p> </div></blockquote> </div> -<div class="section" id="licence-agreement-for-public-datasets"> -<span id="ref-licence"></span><h2>Licence agreement for public datasets<a class="headerlink" href="#licence-agreement-for-public-datasets" title="Permalink to this headline">¶</a></h2> -<p>Each ECMWF public dataset has its own licence which has to be accepted, regardless of the user group.</p> +<div class="section" id="accept-licences-for-public-datasets"> +<span id="ref-licence"></span><h2>Accept licences for public datasets<a class="headerlink" href="#accept-licences-for-public-datasets" title="Permalink to this headline">¶</a></h2> +<p>Each ECMWF <span class="underline">public</span> dataset has its own licence whose acceptance requires user activity, regardless of the user group.</p> <p>For the <em>ERA-Interim</em> and <em>CERA-20C</em> datasets this can be done at the ECMWF website <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">Available ECMWF Public Datasets</a>. Log in and follow the licence links on the right side for each dataset and accept it.</p> <p>For the <em>ERA5</em> dataset this has to be done at the <a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset">Climate Data Store (CDS) website</a>. Log in and select, on the left panel, product type “Reanalysis” for finding <em>ERA5</em> datasets. Then follow any link with <em>ERA5</em> to the full dataset record, click on tab “Download data” and scroll down. There is a section “Terms of use” where you have to click the <span class="underline">Accept terms</span> button.</p> </div> diff --git a/Documentation/html/objects.inv b/Documentation/html/objects.inv index 1e625b249615126d33701c9a23b6b3fc0b8f5acb..5691032e411866d090f5821d86d31f0688fe040e 100644 Binary files a/Documentation/html/objects.inv and b/Documentation/html/objects.inv differ diff --git a/Documentation/html/quick_start.html b/Documentation/html/quick_start.html index 971a7148cfacacc390771d54d5ae2a9627dd77f7..c5c011ac754b19a480235b3ab73ac8e04dc2890b 100644 --- a/Documentation/html/quick_start.html +++ b/Documentation/html/quick_start.html @@ -184,12 +184,12 @@ <div class="section" id="quick-start"> <h1>Quick Start<a class="headerlink" href="#quick-start" title="Permalink to this headline">¶</a></h1> -<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> by itself is a command-line tool. With version 7.1 an upstream shell script was implemented which calls <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command-line parameters.</p> -<p>To submit a job with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> change the working directory to the <code class="docutils literal notranslate"><span class="pre">Run</span></code> directory which is placed directly under the <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code> root directory (<code class="docutils literal notranslate"><span class="pre">X.X</span></code> is the version number):</p> +<p><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is a command-line tool. In the first versions, it was started via a korn shell script and since version 6, the entry point was a python script. From version 7.1, a bash shell script was implemented to call <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command-line parameters.</p> +<p>To submit an extraction job, change the working directory to the subdirectory <code class="docutils literal notranslate"><span class="pre">Run</span></code> (directly under the <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code> root directory, where <code class="docutils literal notranslate"><span class="pre">X.X</span></code> is the version number):</p> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> <path-to-flex_extract_vX.X>/Run </pre></div> </div> -<p>Within this directory you can find everything you need to modify and run <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. The following tree shows a shortened list of directories and important files. The <code class="docutils literal notranslate"><span class="pre">*</span></code> serves as a wildcard. The brackets <code class="docutils literal notranslate"><span class="pre">[]</span></code> means that the file appearance depends on the mode of application and night not be present.</p> +<p>Within this directory you can find everything you need to modify and run <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. The following tree shows a shortened list of directories and important files. The <code class="docutils literal notranslate"><span class="pre">*</span></code> serves as a wildcard. The brackets <code class="docutils literal notranslate"><span class="pre">[]</span></code> indicate that the file is present only in certain modes of application.</p> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>Run ├── Control │ ├── CONTROL_* @@ -205,20 +205,20 @@ └── run.sh </pre></div> </div> -<p>The <code class="docutils literal notranslate"><span class="pre">Jobscripts</span></code> directory is used to store the Korn shell job scripts generated by a <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> run in the <strong>Remote</strong> or <strong>Gateway</strong> mode. They are used to submit the setup information to the ECMWF server and start the jobs in ECMWF’s batch mode. The typical user must not touch these files. They will be generated from template files which are stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory under <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code>. Usually there will be a <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code> and a <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code> script which are explained in the section <a class="reference internal" href="Documentation/input.html"><span class="doc">Control & Input Data</span></a>. In the rare case of operational data extraction there will be a <code class="docutils literal notranslate"><span class="pre">joboper.ksh</span></code> which is designed to get the time parameters from environment variables at the ECMWF servers.</p> -<p>The <code class="docutils literal notranslate"><span class="pre">Controls</span></code> directory contains a number of example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files. These <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files represent the current range of possible dataset retrievals with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. Some parameters in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files can be adapted and some others should not be changed. In this <a class="reference internal" href="#"><span class="doc">Quick Start</span></a> guide we explain how an extraction with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> can be started in the different <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and point out some specifics of each dataset and <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p> +<p>The <code class="docutils literal notranslate"><span class="pre">Jobscripts</span></code> directory is used to store the Korn shell job scripts generated by a <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> run in the <strong>Remote</strong> or <strong>Gateway</strong> mode. They are used to submit the setup information to the ECMWF server and start the jobs in ECMWF’s batch mode. The typical user must not touch these files. They are generated from template files which are stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory under <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code>. Usually there will be a <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code> and a <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code> script which are explained in the section <a class="reference internal" href="Documentation/input.html"><span class="doc">Control & Input Data</span></a>. In the rare case of operational data extraction there will be a <code class="docutils literal notranslate"><span class="pre">joboper.ksh</span></code> which reads time information from environment variables at the ECMWF servers.</p> +<p>The <code class="docutils literal notranslate"><span class="pre">Controls</span></code> directory contains a number of sample <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files. They cover the current range of possible kinds of extractions. Some parameters in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files can be adapted and some others should not be changed. In this <a class="reference internal" href="#"><span class="doc">Quick Start</span></a> guide we explain how an extraction with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> can be started in the different <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and point out some specifics of each dataset and <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p> <p>Directly under <code class="docutils literal notranslate"><span class="pre">Run</span></code> you find the files <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> and <code class="docutils literal notranslate"><span class="pre">run_local.sh</span></code> and according to your selected <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> there might also be a file named <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> for the user credentials to quickly and automatically access ECMWF servers.</p> -<p>From version 7.1 on, the <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> (or <code class="docutils literal notranslate"><span class="pre">run_local.sh</span></code>) script is the main access point to <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p> +<p>From version 7.1 on, the <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> (or <code class="docutils literal notranslate"><span class="pre">run_local.sh</span></code>) script is the main entry point to <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p> <div class="admonition note"> <p class="admonition-title">Note</p> -<p>Note that, for experienced users (or users of older versions), it is still possible to access <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly via the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script which can be found in the directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Python</span></code>.</p> +<p>Note that for experienced users (or users of older versions), it is still possible to start <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly via the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script in directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Python</span></code>.</p> </div> <div class="section" id="job-preparation"> <h2>Job preparation<a class="headerlink" href="#job-preparation" title="Permalink to this headline">¶</a></h2> -<p>To actually start a job with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> it is only necessary to submit the <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> or <code class="docutils literal notranslate"><span class="pre">run_local.sh</span></code> script on the command-line. For the specification of dataset and the selection of the access mode it is necessary to select and modify a <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file and change the parameters in the user section of the <code class="docutils literal notranslate"><span class="pre">run</span></code> scripts. The following sections describes the differences in the application modes and where the results will be stored.</p> +<p>To actually start a job with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> it is sufficient to start either <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> or <code class="docutils literal notranslate"><span class="pre">run_local.sh</span></code>. Data sets and access modes are selected in <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files and within the user section of the <code class="docutils literal notranslate"><span class="pre">run</span></code> scripts. One should select one of the sample <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files. The following sections describes the differences in the application modes and where the results will be stored.</p> <div class="section" id="remote-and-gateway-modes"> <h3>Remote and gateway modes<a class="headerlink" href="#remote-and-gateway-modes" title="Permalink to this headline">¶</a></h3> -<p>For member state users it is recommended to use the <em>remote</em> or <em>gateway</em> mode, especially for more demanding tasks, to retrieve and convert data on ECMWF machines and to transfer only the final output files to the local host.</p> +<p>For member-state users it is recommended to use the <em>remote</em> or <em>gateway</em> mode, especially for more demanding tasks, which retrieve and convert the data on ECMWF machines; only the final output files are transferrred to the local host.</p> <dl> <dt>Remote mode</dt><dd><p>The only difference between both modes is the users working location. In the <em>remote</em> mode you have to login to the ECMWF server and then go to the <code class="docutils literal notranslate"><span class="pre">Run</span></code> directory as shown above. At ECMWF servers <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. However, to be able to start the program you have to load the <code class="docutils literal notranslate"><span class="pre">Python3</span></code> environment with the module system first.</p> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Remote mode</span> diff --git a/Documentation/html/searchindex.js b/Documentation/html/searchindex.js index aa859fce5489e0a6903ac805637ab796f6104a35..1692dac23ceb6a3ae16b855c347bed7f377f562f 100644 --- a/Documentation/html/searchindex.js +++ b/Documentation/html/searchindex.js @@ -1 +1 @@ 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Data","Control & Input Data","Output Data","Overview","Vertical Coordinate","Access Modes","Link Collection for Quick finder","Hints to specify dataset retrieval","Available Datasets for Member State users","Available Datasets for Public users","Metrics","Static Code Analysis","Testcases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Documentation","ECMWF Data","Evaluation","Welcome to <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code>\u2019s user documentation!","Installation","Quick 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\ No newline at end of file diff --git a/Documentation/html/support.html b/Documentation/html/support.html index d95f9fe4fbf79e47c66a4680cae5179d126db3b4..f2c31207f8d75a1163a113b692ce1655a65f1f34 100644 --- a/Documentation/html/support.html +++ b/Documentation/html/support.html @@ -185,27 +185,25 @@ </div> <div class="section" id="ticket-system"> <span id="ref-ticket-system"></span><h2><a class="toc-backref" href="#id2">Ticket system</a><a class="headerlink" href="#ticket-system" title="Permalink to this headline">¶</a></h2> -<p>The community website <a class="reference external" href="http://flexpart.eu">http://flexpart.eu</a> contains a -<a class="reference external" href="https://www.flexpart.eu/report/1">ticket system</a> which can be used to report any issue or a proposition for a new feature.</p> -<p>The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the <code class="docutils literal notranslate"><span class="pre">flexpart.eu[at]zamg.ac.at</span></code> and you will receive your credentials (with some delay).</p> +<p>The community website <a class="reference external" href="https://flexpart.eu/">https://flexpart.eu/</a> contains a +<a class="reference external" href="https://www.flexpart.eu/report/1">ticket system</a> which can be used to report any issue or to propose new features.</p> +<p>The tickets can be viewed by anyone, to create a ticket a registration is necessary. Since the automatic registration is unavailable, please send an email to the <code class="docutils literal notranslate"><span class="pre">flexpart.eu[at]zamg.ac.at</span></code> and you will receive your credentials (possibly with some delay). Event though a category “Support” is available, in most cases asking questions in the mailing list (see next paragraph below) will be more appropriate.</p> </div> <div class="section" id="mailing-list"> <span id="ref-mailing-list"></span><h2><a class="toc-backref" href="#id3">Mailing list</a><a class="headerlink" href="#mailing-list" title="Permalink to this headline">¶</a></h2> -<p>The mailing list is mainly for the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> users to ask questions or share experiences regarding the whole <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> process with the community. This can be a lot faster than asking only the developers for help. Since <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is a preprocessor to <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> this is the right place to ask for help.</p> -<p>Additionally, from time to time, there will be announcements for all FLEXPART users, such as new release versions of <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> or <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p> -<p>Just write a mail to: <code class="docutils literal notranslate"><span class="pre">flexpart[at]lists.univie.ac.at</span></code></p> +<p>A mailing list exists for the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> users to ask questions or share experiences with the community, regarding the whole <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> process. This may be faster than asking only the developers for help through tickets. Since <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is a preprocessor to <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> this is the right place to ask for help.</p> +<p>New release versions of <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> or <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> or other important annoucements will also be made through this mailling list. +The subscription process is explained at the bottom of <a class="reference external" href="https://www.flexpart.eu/wiki/RegisteredUser">https://www.flexpart.eu/wiki/RegisteredUser</a>. Once subscribed, write e-mail to <code class="docutils literal notranslate"><span class="pre">flexpart[at]lists.univie.ac.at</span></code> to post to the list.</p> </div> <div class="section" id="reporting-an-issue"> <span id="ref-reporting"></span><h2><a class="toc-backref" href="#id4">Reporting an issue</a><a class="headerlink" href="#reporting-an-issue" title="Permalink to this headline">¶</a></h2> <p>To properly report a problem or bug, please provide as much information as possible. -This includes:</p> -<ul class="simple"> -<li><p>the flex_extract version</p></li> -<li><p>a flex_extract log file (output of submit.py script)</p></li> -<li><p>the CONTROL file</p></li> -<li><p>the commandline arguments or run(_local).sh settings and</p></li> -<li><p>a description of the environment you used (Unix/Linux version, library version, application mode, etc.).</p></li> -</ul> +This includes: +* the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version +* a <code class="docutils literal notranslate"><span class="pre">flex_extract</span> <span class="pre">log</span></code> file (output of <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script) +* the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file +* the command-line arguments or <code class="docutils literal notranslate"><span class="pre">run(_local).sh</span></code> settings and +* a description of your environment (Unix/Linux version, library version, application mode, etc.).</p> </div> <div class="section" id="known-bugs-and-issues"> <span id="ref-known-issues"></span><h2><a class="toc-backref" href="#id5">Known bugs and issues</a><a class="headerlink" href="#known-bugs-and-issues" title="Permalink to this headline">¶</a></h2> diff --git a/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst b/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst index 1bb81d5baf120630908ebec4a5bac9a6f4c624e2..aa9a468eb0aae1b12921283ceee6db22b14b361c 100644 --- a/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst +++ b/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst @@ -5,14 +5,10 @@ Fortran's Auto Generated Documentation .. contents:: :local: - - -Link to other documentation! - + +`Fortran API <Fortran/index.html>`_ - - -.... f:autoprogram:: preconvert +