diff --git a/Documentation/html/Documentation/Api/api_fortran.html b/Documentation/html/Documentation/Api/api_fortran.html
index 1ed5ca1d74329ff5c4048805a10703f317425798..baeb75acea9adbbb98829ea6d8084b6b4d3453fd 100644
--- a/Documentation/html/Documentation/Api/api_fortran.html
+++ b/Documentation/html/Documentation/Api/api_fortran.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Fortran’s Auto Generated Documentation — flex_extract 7.1 alpha documentation</title>
+ <title>Auto-generated documentation for the Fortran programme — flex_extract 7.1 alpha documentation</title>
@@ -39,7 +39,7 @@
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="next" title="Evaluation" href="../../evaluation.html" />
- <link rel="prev" title="Python’s Auto Generated Documentation" href="api_python.html" />
+ <link rel="prev" title="Auto-generated documentation for the Python scripts" href="api_python.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,13 +94,13 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../api.html">Auto Generated Documentation</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="api_python.html">Python’s Auto Generated Documentation</a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Fortran’s Auto Generated Documentation</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../api.html">Auto-generated documentation</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="api_python.html">Auto-generated documentation for the Python scripts</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Auto-generated documentation for the Fortran programme</a><ul class="simple">
</ul>
</li>
</ul>
@@ -160,9 +160,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../api.html">Auto Generated Documentation</a> »</li>
+ <li><a href="../api.html">Auto-generated documentation</a> »</li>
- <li>Fortran’s Auto Generated Documentation</li>
+ <li>Auto-generated documentation for the Fortran programme</li>
<li class="wy-breadcrumbs-aside">
@@ -181,8 +181,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <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>
+ <div class="section" id="auto-generated-documentation-for-the-fortran-programme">
+<h1>Auto-generated documentation for the Fortran programme<a class="headerlink" href="#auto-generated-documentation-for-the-fortran-programme" title="Permalink to this headline">¶</a></h1>
<p><a class="reference external" href="Fortran/index.html">Fortran API</a></p>
<div class="toctree-wrapper compound">
</div>
@@ -199,7 +199,7 @@
<a href="../../evaluation.html" class="btn btn-neutral float-right" title="Evaluation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="api_python.html" class="btn btn-neutral float-left" title="Python’s Auto Generated Documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="api_python.html" class="btn btn-neutral float-left" title="Auto-generated documentation for the Python scripts" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Api/api_python.html b/Documentation/html/Documentation/Api/api_python.html
index 51fcfcc162c61aa2436fb1b282509f57a80c8617..c13b3d66be2984c9f05b0586b882bf2d2f87c0cb 100644
--- a/Documentation/html/Documentation/Api/api_python.html
+++ b/Documentation/html/Documentation/Api/api_python.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Python’s Auto Generated Documentation — flex_extract 7.1 alpha documentation</title>
+ <title>Auto-generated documentation for the Python scripts — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Fortran’s Auto Generated Documentation" href="api_fortran.html" />
- <link rel="prev" title="Auto Generated Documentation" href="../api.html" />
+ <link rel="next" title="Auto-generated documentation for the Fortran programme" href="api_fortran.html" />
+ <link rel="prev" title="Auto-generated documentation" href="../api.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,18 +94,18 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../api.html">Auto Generated Documentation</a><ul class="current">
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Python’s Auto Generated Documentation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../api.html">Auto-generated documentation</a><ul class="current">
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Auto-generated documentation for the Python scripts</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#programs">Programs</a></li>
<li class="toctree-l4"><a class="reference internal" href="#classes">Classes</a></li>
<li class="toctree-l4"><a class="reference internal" href="#modules">Modules</a></li>
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="api_fortran.html">Fortran’s Auto Generated Documentation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="api_fortran.html">Auto-generated documentation for the Fortran programme</a></li>
</ul>
</li>
</ul>
@@ -163,9 +163,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../api.html">Auto Generated Documentation</a> »</li>
+ <li><a href="../api.html">Auto-generated documentation</a> »</li>
- <li>Python’s Auto Generated Documentation</li>
+ <li>Auto-generated documentation for the Python scripts</li>
<li class="wy-breadcrumbs-aside">
@@ -184,8 +184,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="python-s-auto-generated-documentation">
-<h1>Python’s Auto Generated Documentation<a class="headerlink" href="#python-s-auto-generated-documentation" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="auto-generated-documentation-for-the-python-scripts">
+<h1>Auto-generated documentation for the Python scripts<a class="headerlink" href="#auto-generated-documentation-for-the-python-scripts" title="Permalink to this headline">¶</a></h1>
<div class="contents local topic" id="contents">
<ul class="simple">
<li><p><a class="reference internal" href="#programs" id="id3">Programs</a></p>
@@ -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">
@@ -3588,10 +3586,10 @@ E.g. [[array_t1], [array_t2], [array_t3], [array_t4]]</p>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="api_fortran.html" class="btn btn-neutral float-right" title="Fortran’s Auto Generated Documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="api_fortran.html" class="btn btn-neutral float-right" title="Auto-generated documentation for the Fortran programme" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="../api.html" class="btn btn-neutral float-left" title="Auto Generated Documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="../api.html" class="btn btn-neutral float-left" title="Auto-generated documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/changes.html b/Documentation/html/Documentation/Input/changes.html
index 364053201b2a0133d8442dba142790f024883fde..8c180eeea23cc98d6c988e0b18b7e0f8bceffbef 100644
--- a/Documentation/html/Documentation/Input/changes.html
+++ b/Documentation/html/Documentation/Input/changes.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="ECMWF User Credential file ECMWF_ENV" href="ecmwf_env.html" />
+ <link rel="next" title="ECMWF user credential file ECMWF_ENV" href="ecmwf_env.html" />
<link rel="prev" title="CONTROL file examples" href="examples.html" />
</head>
@@ -94,26 +94,26 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">CONTROL file changes</a><ul class="simple">
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -169,7 +169,7 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
<li>CONTROL file changes</li>
@@ -198,8 +198,8 @@
<li><p>grid resolution not in 1/1000 degress anymore (but is still available for downward compatibility)</p></li>
<li><p>comments available with <code class="docutils literal notranslate"><span class="pre">#</span></code></p></li>
<li><p>only parameters which are needed to override the default values are necessary</p></li>
-<li><p>number of type/step/time elements do not have to be 24 any more. Just select the interval you need.</p></li>
-<li><p>the <code class="docutils literal notranslate"><span class="pre">dtime</span></code> parameter needs to be consistent with <code class="docutils literal notranslate"><span class="pre">type/step/time</span></code>. For example <code class="docutils literal notranslate"><span class="pre">dtime</span></code> can be coarser as <code class="docutils literal notranslate"><span class="pre">time</span></code> intervals are available, but not finer.</p></li>
+<li><p>number of type/step/time elements does not have to be 24 anymore. Just provide what you need.</p></li>
+<li><p>the <code class="docutils literal notranslate"><span class="pre">dtime</span></code> parameter needs to be consistent with <code class="docutils literal notranslate"><span class="pre">type/step/time</span></code>, for example, <code class="docutils literal notranslate"><span class="pre">dtime</span></code> can be coarser than the <code class="docutils literal notranslate"><span class="pre">time</span></code> intervals available, but not finer.</p></li>
</ul>
</dd>
</dl>
@@ -215,7 +215,7 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="ecmwf_env.html" class="btn btn-neutral float-right" title="ECMWF User Credential file ECMWF_ENV" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="ecmwf_env.html" class="btn btn-neutral float-right" title="ECMWF user credential file ECMWF_ENV" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="examples.html" class="btn btn-neutral float-left" title="CONTROL file examples" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/Documentation/Input/compilejob.html b/Documentation/html/Documentation/Input/compilejob.html
index 9b7056bd11a817ee968f29c1d7c9e248a56636a3..2f34ede875f1563b2cbbce72b88534c474e08e9d 100644
--- a/Documentation/html/Documentation/Input/compilejob.html
+++ b/Documentation/html/Documentation/Input/compilejob.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The Compilation Jobscript compilejob.ksh — flex_extract 7.1 alpha documentation</title>
+ <title>The compilation job script compilejob.ksh — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="The Fortran Makefile - calc_etadot" href="fortran_makefile.html" />
- <link rel="prev" title="The Installation Script - setup.sh" href="setup.html" />
+ <link rel="next" title="The Fortran makefile for calc_etadot" href="fortran_makefile.html" />
+ <link rel="prev" title="The installation script - setup.sh" href="setup.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,28 +94,28 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a><ul>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="#what-does-the-compilation-script-do">What does the compilation script do?</a></li>
<li class="toctree-l4"><a class="reference internal" href="#example-compilejob-ksh">Example <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -171,9 +171,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
- <li>The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></li>
+ <li>The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></li>
<li class="wy-breadcrumbs-aside">
@@ -192,26 +192,26 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="the-compilation-jobscript-compilejob-ksh">
-<h1>The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code><a class="headerlink" href="#the-compilation-jobscript-compilejob-ksh" title="Permalink to this headline">¶</a></h1>
-<p>The compilejob is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">compilejob.template</span></code> in the template directory.</p>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
+ <div class="section" id="the-compilation-job-script-compilejob-ksh">
+<h1>The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code><a class="headerlink" href="#the-compilation-job-script-compilejob-ksh" title="Permalink to this headline">¶</a></h1>
+<p>The compile job is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">compilejob.template</span></code> in the template directory.</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
the Korn-shell script from the template files by substituting the individual parameters.
These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
-<p>The jobscript has a number of settings for the batch system which are fixed and differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
+<p>The job script has a number of settings for the batch system which are fixed, and it differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
server system to load the necessary modules for the environment when submitted to the batch queue.</p>
<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
<div class="section" id="what-does-the-compilation-script-do">
<h2>What does the compilation script do?<a class="headerlink" href="#what-does-the-compilation-script-do" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><ol class="arabic simple">
-<li><p>It sets necessary batch system parameters</p></li>
+<li><p>It sets the necessary batch-system parameters</p></li>
<li><p>It prepares the job environment at the ECMWF servers by loading the necessary library modules</p></li>
-<li><p>It sets some environment variabels for the single session</p></li>
+<li><p>It sets some environment variables for the single session</p></li>
<li><p>It creates the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> path of the user</p></li>
-<li><p>It untars the tar-ball into the root directory.</p></li>
-<li><p>It compiles the Fortran programs’s <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>.</p></li>
-<li><p>At the end it checks if the script returned an error or not and send the log file via email to the user.</p></li>
+<li><p>It untars the tarball into the root directory.</p></li>
+<li><p>It compiles the Fortran program using <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>.</p></li>
+<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
</ol>
</div></blockquote>
</div>
@@ -303,10 +303,10 @@ ls -l calc_etadot >>flexcompile
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="fortran_makefile.html" class="btn btn-neutral float-right" title="The Fortran Makefile - calc_etadot" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="fortran_makefile.html" class="btn btn-neutral float-right" title="The Fortran makefile for calc_etadot" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="setup.html" class="btn btn-neutral float-left" title="The Installation Script - setup.sh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="setup.html" class="btn btn-neutral float-left" title="The installation script - setup.sh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/control.html b/Documentation/html/Documentation/Input/control.html
index 60306d7f4e0b815fc224a57a0c8fd9c1c4f035ba..9433ec13f7fad081d40389279f2f86a94a51487a 100644
--- a/Documentation/html/Documentation/Input/control.html
+++ b/Documentation/html/Documentation/Input/control.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="The CONTROL parameters" href="control_params.html" />
- <link rel="prev" title="The Jobscript job.ksh" href="jobscript.html" />
+ <link rel="prev" title="The job script job.ksh" href="jobscript.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,12 +94,12 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">The CONTROL file</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#format-of-control-files">Format of CONTROL files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#example-control-files">Example CONTROL files</a></li>
@@ -109,14 +109,14 @@
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -172,7 +172,7 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
<li>The CONTROL file</li>
@@ -196,36 +196,37 @@
<div class="section" id="the-control-file">
<h1>The CONTROL file<a class="headerlink" href="#the-control-file" title="Permalink to this headline">¶</a></h1>
<p>This file is an input file for <code class="docutils literal notranslate"><span class="pre">flex_extract's</span></code> main script <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>.
-It contains the controlling parameters <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> needs to decide on dataset specifications,
-handling of the retrieved data and general bahaviour. The naming convention is usually (but not necessary):</p>
+It contains the controlling parameters which <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> needs to decide on data set specifications,
+handling of the data retrieved, and general behaviour. The naming convention is usually (but not necessarily):</p>
<blockquote>
<div><p><code class="docutils literal notranslate"><span class="pre">CONTROL_<Dataset>[.optionalIndications]</span></code></p>
</div></blockquote>
-<p>The tested datasets are the operational dataset and the re-analysis datasets CERA-20C, ERA5 and ERA-Interim.
-The optional extra indications for the re-analysis datasets mark the files for <em>public users</em>
-and <em>global</em> domain. For the operational datasets (<em>OD</em>) the file names contain also information of
-the stream, the field type for forecasts, the method for extracting the vertical coordinate and other things like time or horizontal resolution.</p>
+<p>There are a number of data sets for which the procedures have been tested, the operational data and the re-analysis datasets CERA-20C, ERA5, and ERA-Interim.
+The optional indications for the re-analysis data sets mark the files for <em>public users</em>
+and <em>global</em> domain. For the operational data sets (<em>OD</em>), the file names contain also information of
+the stream, the field type for forecasts, the method for extracting the vertical wind, and other information such as temporal or horizontal resolution.</p>
<div class="section" id="format-of-control-files">
<h2>Format of CONTROL files<a class="headerlink" href="#format-of-control-files" title="Permalink to this headline">¶</a></h2>
<p>The first string of each line is the parameter name, the following string(s) (separated by spaces) is (are) the parameter values.
-The parameters can be sorted in any order with one parameter per line.
+The parameters can be listed in any order with one parameter per line.
Comments are started with a ‘#’ - sign. Some of these parameters can be overruled by the command line
parameters given to the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script.
-All parameters have default values. Only those parameters which have to be changed
-must be listed in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
+All parameters have default values; only those parameters which deviate from default
+have be listed in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
</div>
<div class="section" id="example-control-files">
<h2>Example CONTROL files<a class="headerlink" href="#example-control-files" title="Permalink to this headline">¶</a></h2>
<p>A number of example files can be found in the directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Run/Control/</span></code>.
-They can be used as a template for adaptations and understand what’s possible to
-retrieve from ECMWF’s archive.
-For each main dataset there is an example and additionally some variances in resolution, type of field or type of retrieving the vertical coordinate.</p>
+They can be used as a template for adaptation, and to understand what can be
+retrievee from ECMWF’s archives.
+There is an example for each main data set, and in addition, some more varied with respect to resolution, type of field, or way of retrieving the vertical wind.</p>
</div>
<div class="section" id="control-file">
<h2>CONTROL file<a class="headerlink" href="#control-file" title="Permalink to this headline">¶</a></h2>
<p>The file <code class="docutils literal notranslate"><span class="pre">CONTROL.documentation</span></code> documents the available parameters
-in grouped sections with their default values. In <a class="reference internal" href="control_params.html"><span class="doc">The CONTROL parameters</span></a> you can find a more
-detailed description with additional hints, possible values and some useful information about
+in grouped sections together with their default values.
+In <a class="reference internal" href="control_params.html"><span class="doc">The CONTROL parameters</span></a>, you can find a more
+detailed description with additional hints, possible values, and further information about
the setting of these parameters.</p>
<div class="literal-block-wrapper docutils container" id="id1">
<div class="code-block-caption"><span class="caption-text">CONTROL.documentation</span><a class="headerlink" href="#id1" title="Permalink to this code">¶</a></div>
@@ -363,7 +364,7 @@ ADDPAR None
<a href="control_params.html" class="btn btn-neutral float-right" title="The CONTROL parameters" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="jobscript.html" class="btn btn-neutral float-left" title="The Jobscript job.ksh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="jobscript.html" class="btn btn-neutral float-left" title="The job script job.ksh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/control_params.html b/Documentation/html/Documentation/Input/control_params.html
index d4d45d98601d97bac8622091ee0ffeede1762cff..93b27d55a5885ce3269fa00d56c31e806e4f032f 100644
--- a/Documentation/html/Documentation/Input/control_params.html
+++ b/Documentation/html/Documentation/Input/control_params.html
@@ -94,12 +94,12 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">The CONTROL parameters</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#user-section">User Section</a></li>
@@ -115,14 +115,14 @@
</li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -178,7 +178,7 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
<li>The CONTROL parameters</li>
@@ -204,7 +204,7 @@
<div class="section" id="user-section">
<span id="ref-control-user"></span><h2>User Section<a class="headerlink" href="#user-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id1">
-<caption><span class="caption-text">User parameter in CONTROL file</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">User parameters in CONTROL file</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 18%" />
<col style="width: 10%" />
@@ -257,7 +257,7 @@
<div class="section" id="general-section">
<span id="ref-control-general"></span><h2>General Section<a class="headerlink" href="#general-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id2">
-<caption><span class="caption-text">General parameter in CONTROL file</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">General parameters in CONTROL file</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 13%" />
<col style="width: 7%" />
@@ -349,7 +349,7 @@ Possible selections are:
<div class="section" id="time-section">
<span id="ref-control-time"></span><h2>Time Section<a class="headerlink" href="#time-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id3">
-<caption><span class="caption-text">Time parameter in CONTROL file</span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Time parameters in CONTROL file</span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 15%" />
<col style="width: 8%" />
@@ -409,7 +409,7 @@ Possible selections are:
<div class="section" id="data-section">
<span id="ref-control-data"></span><h2>Data Section<a class="headerlink" href="#data-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id4">
-<caption><span class="caption-text">Data parameter in CONTROL file</span><a class="headerlink" href="#id4" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Data parameters in CONTROL file</span><a class="headerlink" href="#id4" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 13%" />
<col style="width: 7%" />
@@ -479,7 +479,7 @@ only when using FLEXPART versions >9.2 or FLEXPART hast to be adapted for rea
<div class="section" id="data-field-section">
<span id="ref-control-datafield"></span><h2>Data field Section<a class="headerlink" href="#data-field-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id5">
-<caption><span class="caption-text">Data field parameter in CONTROL file</span><a class="headerlink" href="#id5" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Data field parameters in CONTROL file</span><a class="headerlink" href="#id5" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 15%" />
<col style="width: 8%" />
@@ -533,7 +533,7 @@ With MAXSTEP > 24 the forecasts from different days overlap, the naming schem
<div class="section" id="flux-data-section">
<span id="ref-control-fluxdata"></span><h2>Flux data Section<a class="headerlink" href="#flux-data-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id6">
-<caption><span class="caption-text">Flux data parameter in CONTROL file</span><a class="headerlink" href="#id6" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Flux data parameters in CONTROL file</span><a class="headerlink" href="#id6" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 15%" />
<col style="width: 8%" />
@@ -587,7 +587,7 @@ Hittmeir, S.; Philipp, A.; Seibert, P. (2017): A conservative interpolation sche
<div class="section" id="domain-section">
<span id="ref-control-domain"></span><h2>Domain Section<a class="headerlink" href="#domain-section" title="Permalink to this headline">¶</a></h2>
<table class="colwidths-given docutils align-default" id="id7">
-<caption><span class="caption-text">Domain parameter in CONTROL file</span><a class="headerlink" href="#id7" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Domain parameters in CONTROL file</span><a class="headerlink" href="#id7" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 13%" />
<col style="width: 13%" />
@@ -765,7 +765,7 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<div class="section" id="additional-data-section">
<span id="ref-control-adddata"></span><h2>Additional data Section<a class="headerlink" href="#additional-data-section" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id9">
-<caption><span class="caption-text">Additional data parameter in CONTROL file</span><a class="headerlink" href="#id9" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Additional data parameters in CONTROL file</span><a class="headerlink" href="#id9" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 17%" />
<col style="width: 9%" />
diff --git a/Documentation/html/Documentation/Input/ecmwf_env.html b/Documentation/html/Documentation/Input/ecmwf_env.html
index dba07cf730de153b4ce1cc0761103dd75d5c39be..1dbd81a97b149282d358a6141a4f64d4b3560fa7 100644
--- a/Documentation/html/Documentation/Input/ecmwf_env.html
+++ b/Documentation/html/Documentation/Input/ecmwf_env.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ECMWF User Credential file ECMWF_ENV — flex_extract 7.1 alpha documentation</title>
+ <title>ECMWF user credential file ECMWF_ENV — flex_extract 7.1 alpha documentation</title>
@@ -94,27 +94,27 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a><ul>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="#content-of-ecmwf-env">Content of <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -170,9 +170,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
- <li>ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></li>
+ <li>ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></li>
<li class="wy-breadcrumbs-aside">
@@ -192,7 +192,7 @@
<div itemprop="articleBody">
<div class="section" id="ecmwf-user-credential-file-ecmwf-env">
-<h1>ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code><a class="headerlink" href="#ecmwf-user-credential-file-ecmwf-env" title="Permalink to this headline">¶</a></h1>
+<h1>ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code><a class="headerlink" href="#ecmwf-user-credential-file-ecmwf-env" title="Permalink to this headline">¶</a></h1>
<p>This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Run</span></code> directory and will be created in the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
<p>This file is based on the template <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV.template</span></code> which is located in the <code class="docutils literal notranslate"><span class="pre">templates</span></code> directory.</p>
<div class="admonition note">
@@ -201,7 +201,7 @@
</div>
<div class="section" id="content-of-ecmwf-env">
<h2>Content of <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code><a class="headerlink" href="#content-of-ecmwf-env" title="Permalink to this headline">¶</a></h2>
-<p>The following shows an example of the content of an <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> file:</p>
+<p>An example of the content of an <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> file is shown below:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ECUID user_name
ECGID user_group
GATEWAY gateway_name
diff --git a/Documentation/html/Documentation/Input/examples.html b/Documentation/html/Documentation/Input/examples.html
index f2fc4f4c9125b2803c3e6d0dd8ad7f701ae162af..262c55049ed3fe15c1647f9f99cacd7032b6bc88 100644
--- a/Documentation/html/Documentation/Input/examples.html
+++ b/Documentation/html/Documentation/Input/examples.html
@@ -94,26 +94,26 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">CONTROL file examples</a><ul class="simple">
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -169,7 +169,7 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
<li>CONTROL file examples</li>
@@ -192,10 +192,10 @@
<div class="section" id="control-file-examples">
<h1>CONTROL file examples<a class="headerlink" href="#control-file-examples" title="Permalink to this headline">¶</a></h1>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a couple of example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files for a number of different data set constellations in the directory path <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Run/Control</span></code>.</p>
-<p>Here is a list of the example files and a description of the data set:</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> comes with a number of example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files for a number of different data set constellations in the directory path <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Run/Control</span></code>.</p>
+<p>Here is a list of the example files:</p>
<dl class="simple">
-<dt>CONTROL.documentation</dt><dd><p>This file is not intended to be used with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. It has a list of all possible parameters and their default values for a quick overview.</p>
+<dt>CONTROL.documentation</dt><dd><p>This file is not intended to be used with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. It just contains a list of all possible parameters and their default values for a quick overview.</p>
</dd>
</dl>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_CERA
@@ -219,10 +219,14 @@ CONTROL_OD.OPER.FC.eta.global
CONTROL_OD.OPER.FC.eta.highres
CONTROL_OD.OPER.FC.gauss.highres
CONTROL_OD.OPER.FC.operational
-CONTROL_OD.OPER.FC.twiceaday.1hourly
-CONTROL_OD.OPER.FC.twiceaday.3hourly
+CONTROL_OD.OPER.FC.twicedaily.1hourly
+CONTROL_OD.OPER.FC.twicedaily.3hourly
</pre></div>
</div>
+<div class="admonition-todo admonition" id="id1">
+<p class="admonition-title">Todo</p>
+<p>#PS some information to be added.</p>
+</div>
<div class="toctree-wrapper compound">
</div>
</div>
diff --git a/Documentation/html/Documentation/Input/fortran_makefile.html b/Documentation/html/Documentation/Input/fortran_makefile.html
index 3772226a9a17b15284ca7823b3bff4c720d0d49a..a7061a64079f36fc5f5a7d6ec9b1a61a55237dbb 100644
--- a/Documentation/html/Documentation/Input/fortran_makefile.html
+++ b/Documentation/html/Documentation/Input/fortran_makefile.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The Fortran Makefile - calc_etadot — flex_extract 7.1 alpha documentation</title>
+ <title>The Fortran makefile for calc_etadot — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="The executable Script - run.sh" href="run.html" />
- <link rel="prev" title="The Compilation Jobscript compilejob.ksh" href="compilejob.html" />
+ <link rel="next" title="The executable script - run.sh" href="run.html" />
+ <link rel="prev" title="The compilation job script compilejob.ksh" href="compilejob.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,26 +94,26 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a><ul class="simple">
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a><ul class="simple">
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -169,9 +169,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
- <li>The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></li>
+ <li>The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></li>
<li class="wy-breadcrumbs-aside">
@@ -190,42 +190,36 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="the-fortran-makefile-calc-etadot">
-<h1>The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code><a class="headerlink" href="#the-fortran-makefile-calc-etadot" title="Permalink to this headline">¶</a></h1>
-<p id="ref-convert"><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code>’s Fortran program will be compiled during
-the installation process to get the executable named <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a couple of <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> prepared which can be found in the directory
-<code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.
-A list of these <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> are shown below:</p>
+ <div class="section" id="the-fortran-makefile-for-calc-etadot">
+<h1>The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code><a class="headerlink" href="#the-fortran-makefile-for-calc-etadot" title="Permalink to this headline">¶</a></h1>
+<p id="ref-convert">The Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during
+the installation process to produce the executable called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> includes several <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> which can be found in the directory
+<code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted by the current flex_extract version number.
+A list of these <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> is shown below:</p>
<div class="line-block">
<div class="line"><strong>Remote/Gateway mode</strong>:</div>
<div class="line">Files to be used as they are!</div>
</div>
<blockquote>
<div><div class="line-block">
-<div class="line"><strong>makefile_ecgate</strong></div>
-<div class="line">For the use on ECMWF’s server <strong>ecgate</strong>.</div>
-</div>
-<div class="line-block">
-<div class="line"><strong>makefile_cray</strong></div>
-<div class="line">For the use on ECMWF’s server <strong>cca/ccb</strong>.</div>
+<div class="line"><strong>makefile_ecgate</strong>: For use on ECMWF’s server <strong>ecgate</strong>.</div>
+<div class="line"><strong>makefile_cray</strong>: For use on ECMWF’s server <strong>cca/ccb</strong>.</div>
</div>
</div></blockquote>
<div class="line-block">
<div class="line"><strong>Local mode</strong></div>
-<div class="line">It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong></div>
+<div class="line">It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> if they don’t correspond to the standard paths pre-set in the makefiles.</div>
</div>
<blockquote>
<div><div class="line-block">
-<div class="line"><strong>makefile_fast</strong></div>
-<div class="line">For the use with gfortran compiler and optimization mode.</div>
-</div>
-<div class="line-block">
-<div class="line"><strong>makefile_debug</strong></div>
-<div class="line">For the use with gfortran compiler in debugging mode.</div>
+<div class="line"><strong>makefile_fast</strong>: For use with the gfortran compiler and optimisation mode.</div>
+<div class="line"><strong>makefile_debug</strong>: For use with the gfortran compiler and debugging mode. Primarily for developers.</div>
</div>
</div></blockquote>
-<p>For instructions on how to adapt the <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> for the local application mode
+<p>If you want to use another compiler than gfortran locally, you can still take <code class="docutils literal notranslate"><span class="pre">makefile_fast</span></code>,
+and adapt everything that is compiler-specific in this file.</p>
+<p>For instructions on how to adapt the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> (local application mode only),
please see <a class="reference internal" href="../../Installation/local.html#ref-install-local"><span class="std std-ref">Local installation</span></a>.</p>
<div class="toctree-wrapper compound">
</div>
@@ -239,10 +233,10 @@ please see <a class="reference internal" href="../../Installation/local.html#ref
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="run.html" class="btn btn-neutral float-right" title="The executable Script - run.sh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="run.html" class="btn btn-neutral float-right" title="The executable script - run.sh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="compilejob.html" class="btn btn-neutral float-left" title="The Compilation Jobscript compilejob.ksh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="compilejob.html" class="btn btn-neutral float-left" title="The compilation job script compilejob.ksh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/jobscript.html b/Documentation/html/Documentation/Input/jobscript.html
index 9c54826b14dc655d77a74912a1553cdfbf447681..b213e304f91a9b7d100acd28ac4f8e2a933d980a 100644
--- a/Documentation/html/Documentation/Input/jobscript.html
+++ b/Documentation/html/Documentation/Input/jobscript.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The Jobscript job.ksh — flex_extract 7.1 alpha documentation</title>
+ <title>The job script job.ksh — flex_extract 7.1 alpha documentation</title>
@@ -39,7 +39,7 @@
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="next" title="The CONTROL file" href="control.html" />
- <link rel="prev" title="The executable Script - run.sh" href="run.html" />
+ <link rel="prev" title="The executable script - run.sh" href="run.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,13 +94,13 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#what-does-the-jobscript-do">What does the jobscript do?</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#what-does-the-job-script-do">What does the job script do?</a></li>
<li class="toctree-l4"><a class="reference internal" href="#example-jobscript-ksh">Example <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code></a></li>
</ul>
</li>
@@ -108,14 +108,14 @@
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -171,9 +171,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
- <li>The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></li>
+ <li>The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></li>
<li class="wy-breadcrumbs-aside">
@@ -192,28 +192,28 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="the-jobscript-job-ksh">
-<h1>The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code><a class="headerlink" href="#the-jobscript-job-ksh" title="Permalink to this headline">¶</a></h1>
-<p>The jobscript is a Korn-shell script which will be created at runtime for each <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> execution in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
-<p>It is based on the <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> template file which is stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory.
-This template is by itself generated in the installation process from a <code class="docutils literal notranslate"><span class="pre">job.template</span></code> template file.</p>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
+ <div class="section" id="the-job-script-job-ksh">
+<h1>The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code><a class="headerlink" href="#the-job-script-job-ksh" title="Permalink to this headline">¶</a></h1>
+<p>The job script is a Korn-shell script which will be created at runtime for each <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> execution in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
+<p>It is based on the <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> template file stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory.
+This template is generated in the installation process from a <code class="docutils literal notranslate"><span class="pre">job.template</span></code> template file.</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
-<p>The jobscript has a number of settings for the batch system which are fixed and differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
+These individual parameters are marked by <code class="docutils literal notranslate"><span class="pre">$$</span></code> in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
+<p>The job script has a number of settings for the batch system which are fixed, and differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
server system to load the necessary modules for the environment when submitted to the batch queue.</p>
<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
-<div class="section" id="what-does-the-jobscript-do">
-<h2>What does the jobscript do?<a class="headerlink" href="#what-does-the-jobscript-do" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="what-does-the-job-script-do">
+<h2>What does the job script do?<a class="headerlink" href="#what-does-the-job-script-do" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><ol class="arabic simple">
-<li><p>It sets necessary batch system parameters</p></li>
-<li><p>It prepares the job environment at the ECMWF servers by loading the necessary library modules</p></li>
-<li><p>It sets some environment variabels for the single session</p></li>
-<li><p>It creates the directory structure in the users <code class="docutils literal notranslate"><span class="pre">$SCRATCH</span></code> file system</p></li>
-<li><p>It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code>. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a set of parameters which are given to the jobscript with its default or the user defined values. It also sets the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> as an environment variable.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is started from within the <code class="docutils literal notranslate"><span class="pre">work</span></code> directory of the new directory structure by calling the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script. It sets new pathes for input and output directory and the recently generated <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p></li>
-<li><p>At the end it checks if the script returned an error or not and send the log file via email to the user.</p></li>
+<li><p>It sets necessary batch system parameters.</p></li>
+<li><p>It prepares the job environment at the ECMWF servers by loading the necessary library modules.</p></li>
+<li><p>It sets some environment variables for the single session.</p></li>
+<li><p>It creates the directory structure in the user’s <code class="docutils literal notranslate"><span class="pre">$SCRATCH</span></code> file system.</p></li>
+<li><p>It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code>. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> as an environment variable.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is started from within the <code class="docutils literal notranslate"><span class="pre">work</span></code> directory of the new directory structure by calling the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script. It sets new paths for input and output directories and the recently generated <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p></li>
+<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
</ol>
</div></blockquote>
</div>
@@ -385,7 +385,7 @@ submit.py --controlfile<span class="o">=</span><span class="si">${</span><span c
<a href="control.html" class="btn btn-neutral float-right" title="The CONTROL file" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="run.html" class="btn btn-neutral float-left" title="The executable Script - run.sh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="run.html" class="btn btn-neutral float-left" title="The executable script - run.sh" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/run.html b/Documentation/html/Documentation/Input/run.html
index 3fac39c824cf62da860519963c5ee588cb84a525..787e6b69045670e6f9760f237a6cceecbb372ea6 100644
--- a/Documentation/html/Documentation/Input/run.html
+++ b/Documentation/html/Documentation/Input/run.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The executable Script - run.sh — flex_extract 7.1 alpha documentation</title>
+ <title>The executable script - run.sh — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="The Jobscript job.ksh" href="jobscript.html" />
- <link rel="prev" title="The Fortran Makefile - calc_etadot" href="fortran_makefile.html" />
+ <link rel="next" title="The job script job.ksh" href="jobscript.html" />
+ <link rel="prev" title="The Fortran makefile for calc_etadot" href="fortran_makefile.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,29 +94,29 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#submission-parameter">Submission Parameter</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#submission-parameters">Submission parameters</a></li>
<li class="toctree-l4"><a class="reference internal" href="#content-of-run-sh">Content of <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#usage-of-submit-py-optional">Usage of <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> (optional)</a></li>
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -172,9 +172,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
- <li>The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></li>
+ <li>The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></li>
<li class="wy-breadcrumbs-aside">
@@ -194,16 +194,16 @@
<div itemprop="articleBody">
<div class="section" id="the-executable-script-run-sh">
-<h1>The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code><a class="headerlink" href="#the-executable-script-run-sh" title="Permalink to this headline">¶</a></h1>
-<p>The execution of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by the <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> Shell script, which is a wrapping script for the top-level Python script <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>.
+<h1>The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code><a class="headerlink" href="#the-executable-script-run-sh" title="Permalink to this headline">¶</a></h1>
+<p>The execution of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by the <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> shell script, which is a wrapper script for the top-level Python script <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>.
The Python script constitutes the entry point to ECMWF data retrievals with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> and controls the program flow.</p>
-<p><code class="docutils literal notranslate"><span class="pre">submit.py</span></code> has two (three) sources for input parameters with information about program flow and ECMWF data selection, the so-called <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file,
-the command line parameters and the so-called <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> file. Whereby, the command line parameters will override the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file parameters.</p>
-<p>Based on these input information <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> applies one of the application modes to either retrieve the ECMWF data via a Web API on a local maschine or submit a jobscript to ECMWF servers and retrieve the data there with sending the files to the local system eventually.</p>
-<div class="section" id="submission-parameter">
-<h2>Submission Parameter<a class="headerlink" href="#submission-parameter" title="Permalink to this headline">¶</a></h2>
+<p><code class="docutils literal notranslate"><span class="pre">submit.py</span></code> has two (or three) sources for input parameters with information about program flow and ECMWF data selection, the so-called <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file,
+the command line parameters, and the so-called <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> file. Command line parameters will override parameters specified in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p>
+<p>Based on this input information, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> applies one of the application modes to either retrieve the ECMWF data via a web API on a local maschine, or submit a job script to an ECMWF server and retrieve the data there, and at the end sends the files to the local system.</p>
+<div class="section" id="submission-parameters">
+<h2>Submission parameters<a class="headerlink" href="#submission-parameters" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id1">
-<caption><span class="caption-text">Parameter for Submission</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Parameters for submission</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 12%" />
<col style="width: 9%" />
@@ -483,10 +483,10 @@ the command line parameters and the so-called <code class="docutils literal notr
</div>
</div>
<div class="section" id="usage-of-submit-py-optional">
-<span id="ref-install-script"></span><h2>Usage of <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> (optional)<a class="headerlink" href="#usage-of-submit-py-optional" title="Permalink to this headline">¶</a></h2>
-<p>It is also possible to start <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly from command line by using the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script instead of the wrapping Shell script <code class="docutils literal notranslate"><span class="pre">run.sh</span></code>. This top-level script is located in
-<code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Python</span></code> and is executable. With the <code class="docutils literal notranslate"><span class="pre">help</span></code> parameter we see again all possible
-command line parameter.</p>
+<h2>Usage of <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> (optional)<a class="headerlink" href="#usage-of-submit-py-optional" title="Permalink to this headline">¶</a></h2>
+<p>It is also possible to start <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly from command line by using the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script instead of the wrapper shell script <code class="docutils literal notranslate"><span class="pre">run.sh</span></code>. This top-level script is located in
+<code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Python</span></code> and is executable. With the <code class="docutils literal notranslate"><span class="pre">--help</span></code> parameter
+we see again all possible command line parameters.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>submit.py --help
usage: submit.py <span class="o">[</span>-h<span class="o">]</span> <span class="o">[</span>--start_date START_DATE<span class="o">]</span> <span class="o">[</span>--end_date END_DATE<span class="o">]</span>
@@ -560,10 +560,10 @@ usage: submit.py <span class="o">[</span>-h<span class="o">]</span> <span class=
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="jobscript.html" class="btn btn-neutral float-right" title="The Jobscript job.ksh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="jobscript.html" class="btn btn-neutral float-right" title="The job script job.ksh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="fortran_makefile.html" class="btn btn-neutral float-left" title="The Fortran Makefile - calc_etadot" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="fortran_makefile.html" class="btn btn-neutral float-left" title="The Fortran makefile for calc_etadot" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/setup.html b/Documentation/html/Documentation/Input/setup.html
index 3c60d5f283ab3c506e1bd587bebc70785c4fe41d..b84014e9a29ec5a327c699c1090e1e73bfa2d5ae 100644
--- a/Documentation/html/Documentation/Input/setup.html
+++ b/Documentation/html/Documentation/Input/setup.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The Installation Script - setup.sh — flex_extract 7.1 alpha documentation</title>
+ <title>The installation script - setup.sh — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="The Compilation Jobscript compilejob.ksh" href="compilejob.html" />
- <link rel="prev" title="Control & Input Data" href="../input.html" />
+ <link rel="next" title="The compilation job script compilejob.ksh" href="compilejob.html" />
+ <link rel="prev" title="Control & input data" href="../input.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,29 +94,29 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3 current"><a class="current reference internal" href="#">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#installation-parameter">Installation Parameter</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3 current"><a class="current reference internal" href="#">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#installation-parameters">Installation parameters</a></li>
<li class="toctree-l4"><a class="reference internal" href="#content-of-setup-sh">Content of <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#usage-of-install-py-optional">Usage of <code class="docutils literal notranslate"><span class="pre">install.py</span></code> (optional)</a></li>
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -172,9 +172,9 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
- <li>The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></li>
+ <li>The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></li>
<li class="wy-breadcrumbs-aside">
@@ -194,39 +194,39 @@
<div itemprop="articleBody">
<div class="section" id="the-installation-script-setup-sh">
-<h1>The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code><a class="headerlink" href="#the-installation-script-setup-sh" title="Permalink to this headline">¶</a></h1>
-<p>The installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by the Shell script <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> which is located in the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.
-It calls the top-level Python script <code class="docutils literal notranslate"><span class="pre">install.py</span></code> which does all necessary operations to prepare the selected application environment. This includes:</p>
+<h1>The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code><a class="headerlink" href="#the-installation-script-setup-sh" title="Permalink to this headline">¶</a></h1>
+<p>The installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by the shell script <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> located in the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.
+It calls the top-level Python script <code class="docutils literal notranslate"><span class="pre">install.py</span></code> which does all the necessary operations to prepare the application environment selected. This includes:</p>
<ul class="simple">
-<li><p>preparing the file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> with the user credentials for member state access to ECMWF servers (in <strong>remote</strong> and <strong>gateway</strong> mode)</p></li>
+<li><p>preparing the file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> with the user credentials for member-state access to ECMWF servers (in <strong>remote</strong> and <strong>gateway</strong> mode)</p></li>
<li><p>preparation of a compilation Korn-shell script (in <strong>remote</strong> and <strong>gateway</strong> mode)</p></li>
<li><p>preparation of a job template with user credentials (in <strong>remote</strong> and <strong>gateway</strong> mode)</p></li>
-<li><p>create a tar-ball of all necessary files</p></li>
-<li><p>copying tar-ball to target location (depending on application mode and installation path)</p></li>
-<li><p>submit compilation script to batch queue at ECMWF servers (in <strong>remote</strong> and <strong>gateway</strong> mode) or just untar tar-ball at target location (<strong>local mode</strong>)</p></li>
-<li><p>compilation of the FORTRAN90 program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></p></li>
+<li><p>create a tarball of all necessary files</p></li>
+<li><p>copying the tarball to the target location (depending on application mode and installation path)</p></li>
+<li><p>submit the compilation script to the batch queue at ECMWF servers (in <strong>remote</strong> and <strong>gateway</strong> mode) or just untar the tarball at target location (<strong>local mode</strong>)</p></li>
+<li><p>compilation of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></p></li>
</ul>
-<p>The Python installation script <code class="docutils literal notranslate"><span class="pre">install.py</span></code> has a couple of command line arguments which are defined in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> in the section labelled with “<em>AVAILABLE COMMANDLINE ARGUMENTS TO SET</em>”. The user has to adapt these parameters for his personal use. The parameters are listed and described in <a class="reference internal" href="#ref-instparams"><span class="std std-ref">Installation Parameter</span></a>. The script also does some checks to guarantee necessary parameters were set.</p>
+<p>The Python installation script <code class="docutils literal notranslate"><span class="pre">install.py</span></code> has several command line arguments defined in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>, in the section labelled “<em>AVAILABLE COMMANDLINE ARGUMENTS TO SET</em>”. The user has to adapt these parameters according to his/her personal needs. The parameters are listed and described in <a class="reference internal" href="#ref-instparams"><span class="std std-ref">Installation parameters</span></a>. The script also does some checks to guarantee that the necessary parameters were set.</p>
<p>After the installation process, some tests can be conducted. They are described in section <a class="reference internal" href="../../installation.html#ref-testinstallfe"><span class="std std-ref">Test installation</span></a>.</p>
-<p>The following diagram sketches the involved files and scripts in the installation process:</p>
+<p>The following diagram sketches the files and scripts involved in the installation process:</p>
<div><img height="440" id="ref-install-blockdiag" src="../../_images/blockdiag-f0a58657deb31f0c134ffed39d9be96f0d278617.png" width="1600" /></div><div class="figure align-default" id="id1">
-<div><img height="120" src="../../_images/blockdiag-c5183a0da960384d172e76fcbb0cc6765f0b1945.png" width="832" /></div><p class="caption"><span class="caption-text">Diagram of data flow during the installation process. The trapezoids are input files with the light blue area being the template files. The edge-rounded, orange boxes are the executable files which start the installation process and reads the input files. The rectangular, green boxes are the output files. The light green files are files which are only needed in the remota and gateway mode.</span><a class="headerlink" href="#id1" title="Permalink to this image">¶</a></p>
+<div><img height="120" src="../../_images/blockdiag-c5183a0da960384d172e76fcbb0cc6765f0b1945.png" width="832" /></div><p class="caption"><span class="caption-text">Diagram of data flow during the installation process. Trapezoids are input files with the light blue area being the template files. Round-edge orange boxes are executable files which start the installation process and read the input files. Rectangular green boxes are output files. Light green files are needed only in the remota and gateway mode.</span><a class="headerlink" href="#id1" title="Permalink to this image">¶</a></p>
</div>
-<div class="section" id="installation-parameter">
-<span id="ref-instparams"></span><h2>Installation Parameter<a class="headerlink" href="#installation-parameter" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="installation-parameters">
+<span id="ref-instparams"></span><h2>Installation parameters<a class="headerlink" href="#installation-parameters" title="Permalink to this headline">¶</a></h2>
<table class="docutils align-default" id="id2">
<caption><span class="caption-text">Parameter for Installation</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
<colgroup>
-<col style="width: 10%" />
-<col style="width: 5%" />
+<col style="width: 9%" />
+<col style="width: 7%" />
<col style="width: 15%" />
<col style="width: 11%" />
-<col style="width: 58%" />
+<col style="width: 57%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Parameter</p></th>
<th class="head"><p>Format</p></th>
-<th class="head"><p>Possible value range</p></th>
+<th class="head"><p>Possible values</p></th>
<th class="head"><p>Default</p></th>
<th class="head"><p>Description</p></th>
</tr>
@@ -236,25 +236,25 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<td><p>String</p></td>
<td><p>local, ecgate, cca</p></td>
<td><p>None</p></td>
-<td><p>Defines which flex_extract application mode will be used. Local = local mode; egate = Remote or Gateway mode, cca = Remote or Gateway mode. Wether the local mode is for public or member state users doesn’t matter during the installation process.</p></td>
+<td><p>Defines the flex_extract application mode to be used. Local = local mode; egate = Remote or Gateway mode, cca = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
</tr>
<tr class="row-odd"><td><p>MAKEFILE</p></td>
<td><p>String</p></td>
-<td><p>any Makefile present, according to environment</p></td>
-<td><p>Makefile.gfortran</p></td>
-<td><p>Name of the makefile in source/fortran directory to be used for compiling the Fortran program. “Makefile.gfortran” has the configuration for the ecgate environment. For local server versions there are templates “Makefile.local.gfortran” and “Makefile.local.ifort” which have to be adapted (pathes to the eccodes library) by the user.</p></td>
+<td><p>any makefile present in the Fortran source directory</p></td>
+<td><p>None</p></td>
+<td><p>Name of the makefile in source/fortran directory to be used for compiling the Fortran program. </p></td>
</tr>
<tr class="row-even"><td><p>ECUID</p></td>
<td><p>String</p></td>
-<td><p>e.g. “ecname”</p></td>
+<td><p>e.g. “myecname”</p></td>
<td><p>None</p></td>
-<td><p>The user id at ECMWF. Necessary for access to ECMWF server. (Remote and Gateway mode) </p></td>
+<td><p>The user name (not Linux uid!) at ECMWF. Necessary for access to ECMWF server. (Remote and Gateway mode) </p></td>
</tr>
<tr class="row-odd"><td><p>ECGID</p></td>
<td><p>String</p></td>
-<td><p>e.g. “groupname”</p></td>
+<td><p>e.g. “mygroupname”</p></td>
<td><p>None</p></td>
-<td><p>The group id at ECMWF. Necessary for access to ECMWF server. (Remote and Gateway mode)</p></td>
+<td><p>The group name (not Linux gid!) at ECMWF. Necessary for access to ECMWF server. (Remote and Gateway mode)</p></td>
</tr>
<tr class="row-even"><td><p>GATEWAY</p></td>
<td><p>String</p></td>
@@ -271,20 +271,20 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<tr class="row-even"><td><p>INSTALLDIR</p></td>
<td><p>String</p></td>
<td><p>a full path </p></td>
-<td><p>$HOME on ECMWF server and current flex_extract root path on local server</p></td>
-<td><p>Root path where flex_extract should be installed. If it is not set it will be set to $HOME on ECMWF server and set to the current flex_extract root path on local servers. </p></td>
+<td><p>$HOME on ECMWF server and current flex_extract root path on local machine</p></td>
+<td><p>Root path where flex_extract should be installed. If it is not set, it will be $HOME on ECMWF servers and to the current flex_extract root path on local servers. </p></td>
</tr>
<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
<td><p>job.template</p></td>
<td><p>job.template</p></td>
-<td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed since it is optimized for ECMWF server. (Remote and Gateway mode)</p></td>
+<td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed because it is already optimised for ECMWF servers. (Remote and Gateway mode)</p></td>
</tr>
<tr class="row-even"><td><p>CONTROLFILE</p></td>
<td><p>String</p></td>
<td><p>any CONTROL file</p></td>
<td><p>CONTROL_EA5</p></td>
-<td><p>The file with all CONTROL parameters. It does not matter which CONTROL file is used. Due to interval process it is just necessary that there is a CONTROL file in place which can be opend. </p></td>
+<td><p>File containing all CONTROL parameters. Any CONTROL file may be used. Due to interval process it is just necessary that there is a CONTROL file in place which can be opend. </p></td>
</tr>
</tbody>
</table>
@@ -387,9 +387,9 @@ It calls the top-level Python script <code class="docutils literal notranslate">
</div>
<div class="section" id="usage-of-install-py-optional">
<span id="ref-install-script"></span><h2>Usage of <code class="docutils literal notranslate"><span class="pre">install.py</span></code> (optional)<a class="headerlink" href="#usage-of-install-py-optional" title="Permalink to this headline">¶</a></h2>
-<p>It is also possible to start the installation process of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly from command line by using the <code class="docutils literal notranslate"><span class="pre">install.py</span></code> script instead of the wrapping Shell script <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>. This top-level script is located in
-<code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Python</span></code> and is executable. With the <code class="docutils literal notranslate"><span class="pre">help</span></code> parameter we see again all possible
-command line parameter.</p>
+<p>It is also possible to start the installation process of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly from the command line by using the <code class="docutils literal notranslate"><span class="pre">install.py</span></code> script instead of the wrapper shell script <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>. This top-level script is located in
+<code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Python</span></code> and is executable. With the <code class="docutils literal notranslate"><span class="pre">--help</span></code> parameter,
+we see again all possible command line parameters.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>install.py --help
usage: install.py <span class="o">[</span>-h<span class="o">]</span> <span class="o">[</span>--target INSTALL_TARGET<span class="o">]</span> <span class="o">[</span>--makefile MAKEFILE<span class="o">]</span>
@@ -408,7 +408,7 @@ optional arguments:
program <span class="o">(</span>default: None<span class="o">)</span>
--ecuid ECUID The user id at ECMWF. <span class="o">(</span>default: None<span class="o">)</span>
--ecgid ECGID The group id at ECMWF. <span class="o">(</span>default: None<span class="o">)</span>
- --gateway GATEWAY The name of the <span class="nb">local</span> gateway server. <span class="o">(</span>default: None<span class="o">)</span>
+ --gateway GATEWAY The IP name <span class="o">(</span>or IP address<span class="o">)</span> of the <span class="nb">local</span> gateway server. <span class="o">(</span>default: None<span class="o">)</span>
--destination DESTINATION
The ecaccess association, e.g. myUser@genericSftp
<span class="o">(</span>default: None<span class="o">)</span>
@@ -437,10 +437,10 @@ optional arguments:
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="compilejob.html" class="btn btn-neutral float-right" title="The Compilation Jobscript compilejob.ksh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="compilejob.html" class="btn btn-neutral float-right" title="The compilation job script compilejob.ksh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="../input.html" class="btn btn-neutral float-left" title="Control & Input Data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="../input.html" class="btn btn-neutral float-left" title="Control & input data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Input/templates.html b/Documentation/html/Documentation/Input/templates.html
index cdd8aefbc464dd27f6a1e4ede8f263f664e0b168..0dfedfbad0b9ff7ff5da4fd6226c9845a49ae659 100644
--- a/Documentation/html/Documentation/Input/templates.html
+++ b/Documentation/html/Documentation/Input/templates.html
@@ -38,8 +38,8 @@
<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="Output Data" href="../output.html" />
- <link rel="prev" title="ECMWF User Credential file ECMWF_ENV" href="ecmwf_env.html" />
+ <link rel="next" title="Output data" href="../output.html" />
+ <link rel="prev" title="ECMWF user credential file ECMWF_ENV" href="ecmwf_env.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,17 +94,17 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & Input Data</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control & input data</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">Templates</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#convert-nl">convert.nl</a></li>
<li class="toctree-l4"><a class="reference internal" href="#ecmwf-env-template">ecmwf_env.template</a></li>
@@ -115,10 +115,10 @@
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -174,7 +174,7 @@
<li><a href="../../documentation.html">Documentation</a> »</li>
- <li><a href="../input.html">Control & Input Data</a> »</li>
+ <li><a href="../input.html">Control & input data</a> »</li>
<li>Templates</li>
@@ -197,17 +197,17 @@
<div class="section" id="templates">
<h1>Templates<a class="headerlink" href="#templates" title="Permalink to this headline">¶</a></h1>
-<p>In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> we use the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to create specific files from templates. It is the most efficient way to be able to quickly adapt e.g. the job scripts send to the ECMWF batch queue system or the namelist file für the Fortran program without the need to change the program code.</p>
+<p>In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> is used to create specific files from templates. It is the most efficient way to be able to quickly adapt, e. g., the job scripts sent to the ECMWF batch queue system, or the namelist file für the Fortran program, without the need to change the program code.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>Usually it is not recommended to change anything in these files without being able to understand the effects.</p>
+<p>Do not change anything in these files unless you understand the effects!</p>
</div>
-<p>Each template file has its content framework and keeps so-called placeholder variables in the positions where the values needs to be substituted at run time. These placeholders are marked by a leading <code class="docutils literal notranslate"><span class="pre">$</span></code> sign. In case of the Kornshell job scripts, where (environment) variables are used the <code class="docutils literal notranslate"><span class="pre">$</span></code> sign needs to be doubled to <cite>escape</cite> and keep a single <code class="docutils literal notranslate"><span class="pre">$</span></code> sign as it is.</p>
-<p>The following templates are used and can be found in directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Templates</span></code>:</p>
+<p>Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading <code class="docutils literal notranslate"><span class="pre">$</span></code> sign. In case of the Kornshell job scripts, where (environment) variables are used, the <code class="docutils literal notranslate"><span class="pre">$</span></code> sign needs to be doubled for <cite>escaping</cite>.</p>
+<p>The following templates are used; they can be found in the directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Templates</span></code>:</p>
<div class="section" id="convert-nl">
<h2>convert.nl<a class="headerlink" href="#convert-nl" title="Permalink to this headline">¶</a></h2>
<blockquote>
-<div><p>This is the template for a Fortran namelist file called <code class="docutils literal notranslate"><span class="pre">fort.4</span></code> which will be read by <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>.
+<div><p>This is the template for a Fortran namelist file called <code class="docutils literal notranslate"><span class="pre">fort.4</span></code> read by <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>.
It contains all the parameters <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> needs.</p>
<div class="highlight-fortran notranslate"><div class="highlight"><pre><span></span>&NAMGEN
maxl = $maxl,
@@ -248,11 +248,11 @@ DESTINATION <span class="nv">$destination_name</span>
<h2>compilejob.template<a class="headerlink" href="#compilejob-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the job script file called <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code> during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
-<p>At the beginning some directives for the batch system are set.
-On the <strong>ecgate</strong> server the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>.
-For the high performance computers <strong>cca</strong> and <strong>ccb</strong> the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary and can be view at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p>
-<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
-<p>Afterwards the installation steps as such are done. Including the generation of the root directory, putting files in place, compiling the Fortran program and sending a log file via email.</p>
+<p>At the beginning, some directives for the batch system are set.
+On the <strong>ecgate</strong> server, the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>.
+For the high-performance computers <strong>cca</strong> and <strong>ccb</strong>, the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary; for details see <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p>
+<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending on the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
+<p>Afterwards, the installation steps as such are done. They included the generation of the root directory, putting files in place, compiling the Fortran program, and sending a log file by email.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -332,11 +332,12 @@ ls -l <span class="nv">$fortran_program</span> >>flexcompile
<h2>job.temp<a class="headerlink" href="#job-temp" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the actual job script file called <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code> for the execution of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
-<p>At the beginning some directives for the batch system are set.
-On the <strong>ecgate</strong> server the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>.
-For the high performance computers <strong>cca</strong> and <strong>ccb</strong> the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary and can be view at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p>
-<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
-<p>Afterwards the run directory and the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file are created and <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is executed. In the end a log file is send via email.</p>
+<p>At the beginning, some directives for the batch system are set.
+On the <strong>ecgate</strong> server, the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>.
+For the high performance computers <strong>cca</strong> and <strong>ccb</strong>, the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary;
+for details see <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p>
+<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending on the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
+<p>Afterwards, the run directory and the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file are created and <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is executed. In the end, a log file is send by email.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -423,7 +424,7 @@ submit.py --controlfile<span class="o">=</span><span class="nv">$$</span><span c
<div class="section" id="job-template">
<h2>job.template<a class="headerlink" href="#job-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
-<div><p>This template is used to create the template for the execution job script <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the installation process. A description of the file can be found under <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>. A couple of parameters are set in this process, such as the user credentials and the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version number.</p>
+<div><p>This template is used to create the template for the execution job script <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the installation process. A description of the file can be found under <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>. Several parameters are set in this process, such as the user credentials and the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version number.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -519,10 +520,10 @@ submit.py --controlfile<span class="o">=</span><span class="nv">$$$$</span><span
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="../output.html" class="btn btn-neutral float-right" title="Output Data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="../output.html" class="btn btn-neutral float-right" title="Output data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="ecmwf_env.html" class="btn btn-neutral float-left" title="ECMWF User Credential file ECMWF_ENV" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="ecmwf_env.html" class="btn btn-neutral float-left" title="ECMWF user credential file ECMWF_ENV" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/Overview/app_modes.html b/Documentation/html/Documentation/Overview/app_modes.html
index 7ee380c6851513179932ea2785328f5d4a5518f2..1e436e6c5a91f654d04e1c978eeb77f0d47bf7e2 100644
--- a/Documentation/html/Documentation/Overview/app_modes.html
+++ b/Documentation/html/Documentation/Overview/app_modes.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Application Modes — flex_extract 7.1 alpha documentation</title>
+ <title>Application modes — flex_extract 7.1 alpha documentation</title>
@@ -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="Program Flow" href="prog_flow.html" />
+ <link rel="next" title="Program flow" href="prog_flow.html" />
<link rel="prev" title="Overview" href="../overview.html" />
</head>
@@ -94,17 +94,17 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="../overview.html">Overview</a><ul class="current">
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Application Modes</a><ul class="simple">
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Application modes</a><ul class="simple">
</ul>
</li>
-<li class="toctree-l3"><a class="reference internal" href="prog_flow.html">Program Flow</a></li>
+<li class="toctree-l3"><a class="reference internal" href="prog_flow.html">Program flow</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -162,7 +162,7 @@
<li><a href="../overview.html">Overview</a> »</li>
- <li>Application Modes</li>
+ <li>Application modes</li>
<li class="wy-breadcrumbs-aside">
@@ -182,12 +182,12 @@
<div itemprop="articleBody">
<div class="section" id="application-modes">
-<h1>Application Modes<a class="headerlink" href="#application-modes" title="Permalink to this headline">¶</a></h1>
-<p id="ref-app-modes">Arising from the two user groups described in <a class="reference internal" href="../../Ecmwf/access.html"><span class="doc">Access Modes</span></a>, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> has 4 different <span class="underline">user application modes</span>:</p>
+<h1>Application modes<a class="headerlink" href="#application-modes" title="Permalink to this headline">¶</a></h1>
+<p id="ref-app-modes">Arising from the two user groups described in <a class="reference internal" href="../../Ecmwf/access.html"><span class="doc">Access modes</span></a>, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> has four different <span class="underline">user application modes</span>:</p>
<blockquote id="ref-remote-desc">
<div><ol class="arabic simple">
<li><dl class="simple">
-<dt>Remote (member)</dt><dd><p>In the <strong>Remote mode</strong> the user works directly on ECMWF Linux member state server, such as <code class="docutils literal notranslate"><span class="pre">ecgate</span></code> or <code class="docutils literal notranslate"><span class="pre">cca/ccb</span></code>. The software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. The user does not need to install any of the additional third-party libraries mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> as ECMWF provides everything with environment modules. The module selection will be done automatically in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
+<dt>Remote (member)</dt><dd><p>In the <strong>Remote mode</strong> the user works directly on a ECMWF member-state Linux server, such as <code class="docutils literal notranslate"><span class="pre">ecgate</span></code> or <code class="docutils literal notranslate"><span class="pre">cca/ccb</span></code>. The software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. The user does not need to install any of the third-party libraries mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a>, as ECMWF provides everything with environment modules. The module selection will be done automatically by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
</dd>
</dl>
</li>
@@ -196,7 +196,7 @@
<blockquote id="ref-gateway-desc">
<div><ol class="arabic simple" start="2">
<li><dl class="simple">
-<dt>Gateway (member)</dt><dd><p>The <strong>Gateway mode</strong> can be used if a local member state gateway server is in place. Then the job scripts can be submitted to the ECMWF Linux member state server via the ECMWF web access tool <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code>. The installation script of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> must be executed at the local gateway server such that the software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory at the ECMWF server and some extra setup is done in the local <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory at the local gateway server. For more information about establishing a gateway server please see <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/ECaccess+Home">ECMWF’s instructions on gateway server</a>. For the <strong>Gateway mode</strong> the necessary environment has to be established which is described in <a class="reference internal" href="../../Installation/gateway.html#ref-prep-gateway"><span class="std std-ref">Prepare gateway environment</span></a>.</p>
+<dt>Gateway (member)</dt><dd><p>The <strong>Gateway mode</strong> can be used if a local member-state gateway server is in place. Then, the job scripts can be submitted to the ECMWF member-state Linux server via the ECMWF web access tool <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code>. The installation script of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> must be executed on the local gateway server such that the software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory at the ECMWF server and that some extra setup is done in the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory on the local gateway server. For more information about establishing a gateway server, please refer to <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/ECaccess+Home">ECMWF’s instructions on gateway server</a>. For the <strong>Gateway mode</strong> the necessary environment has to be established which is described in <a class="reference internal" href="../../Installation/gateway.html#ref-prep-gateway"><span class="std std-ref">Prepare gateway environment</span></a>.</p>
</dd>
</dl>
</li>
@@ -205,12 +205,12 @@
<blockquote id="ref-local-desc">
<div><ol class="arabic simple" start="3">
<li><dl class="simple">
-<dt>Local member</dt><dd><p>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>.</p>
+<dt>Local member</dt><dd><p>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario, a software environment similar to that at ECMWF is required. Additionally, web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
-<dt>Local public</dt><dd><p>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>. In this case a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.</p>
+<dt>Local public</dt><dd><p>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario, a software environment similar to that at ECMWF is required. Additionally, web API’s have to be installed to access ECMWF servers. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>. In this case, a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.</p>
</dd>
</dl>
</li>
@@ -233,7 +233,7 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="prog_flow.html" class="btn btn-neutral float-right" title="Program Flow" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="prog_flow.html" class="btn btn-neutral float-right" title="Program flow" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="../overview.html" class="btn btn-neutral float-left" title="Overview" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/Documentation/Overview/prog_flow.html b/Documentation/html/Documentation/Overview/prog_flow.html
index 95407efb895fd1a7d882e6658bafaf9cb9d7d9ac..279c36d5b140613f9d34fe314a05839d7e255187 100644
--- a/Documentation/html/Documentation/Overview/prog_flow.html
+++ b/Documentation/html/Documentation/Overview/prog_flow.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Program Flow — flex_extract 7.1 alpha documentation</title>
+ <title>Program flow — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Control & Input Data" href="../input.html" />
- <link rel="prev" title="Application Modes" href="app_modes.html" />
+ <link rel="next" title="Control & input data" href="../input.html" />
+ <link rel="prev" title="Application modes" href="app_modes.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,8 +94,8 @@
<li class="toctree-l1"><a class="reference internal" href="../../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="../overview.html">Overview</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="app_modes.html">Application Modes</a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Program Flow</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="app_modes.html">Application modes</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Program flow</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#general-program-flow">General program flow</a></li>
<li class="toctree-l4"><a class="reference internal" href="#workflows-of-different-application-modes">Workflows of different application modes</a></li>
<li class="toctree-l4"><a class="reference internal" href="#example-application-setting-for-a-local-member-user">Example application setting for a local member user</a></li>
@@ -103,11 +103,11 @@
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../evaluation.html">Evaluation</a></li>
@@ -165,7 +165,7 @@
<li><a href="../overview.html">Overview</a> »</li>
- <li>Program Flow</li>
+ <li>Program flow</li>
<li class="wy-breadcrumbs-aside">
@@ -185,29 +185,29 @@
<div itemprop="articleBody">
<div class="section" id="program-flow">
-<h1>Program Flow<a class="headerlink" href="#program-flow" title="Permalink to this headline">¶</a></h1>
+<h1>Program flow<a class="headerlink" href="#program-flow" title="Permalink to this headline">¶</a></h1>
<div class="section" id="general-program-flow">
<h2>General program flow<a class="headerlink" href="#general-program-flow" title="Permalink to this headline">¶</a></h2>
<p>The following flow diagram shows the general steps performed by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
<div class="figure align-default" id="id2">
<span id="ref-fig-submit"></span><img alt="../../_images/submit.png" src="../../_images/submit.png" />
-<p class="caption"><span class="caption-text">Overview of the call of python’s <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script and raw sequence of working steps done in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</span><a class="headerlink" href="#id2" title="Permalink to this image">¶</a></p>
+<p class="caption"><span class="caption-text">Overview of the call of the``submit.py`` Python script and raw sequence of work steps in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</span><a class="headerlink" href="#id2" title="Permalink to this image">¶</a></p>
</div>
-<p>The <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> Python program is called by the Shell script <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> and accomplish the following steps:</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> Python script is called by the shell script <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> and accomplishes the following steps:</p>
<blockquote>
<div><ol class="arabic simple">
<li><dl class="simple">
-<dt>Setup the control data:</dt><dd><p>It gets all command-line and <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file parameters as well as optionally the ECMWF user credentials. Depending the <a class="reference internal" href="app_modes.html"><span class="doc">Application Modes</span></a>, it might also prepare a job script which is then send to the ECMWF queue.</p>
+<dt>Setup of control data:</dt><dd><p>Command-line and <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code>-file parameters are read, as well as (optionally) the ECMWF user credentials. Depending the <a class="reference internal" href="app_modes.html"><span class="doc">Application modes</span></a>, a job script might be prepared which is then sent to the ECMWF queue.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
-<dt>Retrieves data from MARS:</dt><dd><p>It creates and sends MARS-requests either on the local machine or on ECMWF server, that receives the data and stores them in a specific format in GRIB files. If the parameter <code class="docutils literal notranslate"><span class="pre">REQUEST</span></code> was set <code class="docutils literal notranslate"><span class="pre">1</span></code> the data are not received but a file <code class="docutils literal notranslate"><span class="pre">mars_requests.csv</span></code> is created with a list of MARS requests and their settings. If it is set to <code class="docutils literal notranslate"><span class="pre">2</span></code> the file is created in addition to retrieving the data. The requests are created in an optimised way by splitting in time, jobs and parameters.</p>
+<dt>Retrieval of data from MARS:</dt><dd><p>MARS requests are created either on the local machine or on the ECMWF server and then submitted which retrieve the data and store them in GRIB files. If the parameter <code class="docutils literal notranslate"><span class="pre">REQUEST</span></code> was set <code class="docutils literal notranslate"><span class="pre">1</span></code>, the data are not retrieved and instead a file <code class="docutils literal notranslate"><span class="pre">mars_requests.csv</span></code> is created, which contains a list of the MARS requests and their settings. If <code class="docutils literal notranslate"><span class="pre">REQEST</span></code> is set to <code class="docutils literal notranslate"><span class="pre">2</span></code>, the csv file is created in addition to retrieving the data. The requests are created in an optimised way by splitting with respect to time, jobs and parameters.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
-<dt>Post-process data to create final <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files:</dt><dd><p>After all data is retrieved, the disaggregation of flux fields (<a class="reference external" href="../disagg.html">see here</a> ) is done as well as the calculation of vertical velocity (<a class="reference external" href="../vertco.html">see here</a>) by the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>. Eventually, the GRIB fields are merged together such that a single grib file per time step is available with all fields for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>. Since model level fields are typically in <em>GRIB2</em> format whereas surface level fields are still in <em>GRIB1</em> format, they can be converted into GRIB2 if parameter <code class="docutils literal notranslate"><span class="pre">FORMAT</span></code> is set to <em>GRIB2</em>. Please note, however, that older versions of FLEXPART may have difficulties reading pure <em>GRIB2</em> files since some parameter IDs change in <em>GRIB2</em>. If the retrieval is executed remotely at ECMWF, the resulting files can be communicated to the local gateway server via the <code class="docutils literal notranslate"><span class="pre">ECtrans</span></code> utility if the parameter <code class="docutils literal notranslate"><span class="pre">ECTRANS</span></code> is set to <code class="docutils literal notranslate"><span class="pre">1</span></code> and the parameters <code class="docutils literal notranslate"><span class="pre">GATEWAY</span></code>, <code class="docutils literal notranslate"><span class="pre">DESTINATION</span></code> have been set properly during installation. The status of the transfer can be checked with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-ectrans-list</span></code> (on the local gateway server). If the script is executed locally the progress of the script can be followed with the usual Linux tools.</p>
+<dt>Post-processing of data to create final <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files:</dt><dd><p>After all data have been retrieved, flux fields are disaggregated (<a class="reference external" href="../disagg.html">see here</a> ) and the vertical velocity is calculated (<a class="reference external" href="../vertco.html">see here</a>) by the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>. Finally, the GRIB fields are merged into a single grib file per time step containing all the fields for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>. Since model-level fields are typically in <em>GRIB2</em> format, whereas surface-level fields are still in <em>GRIB1</em> format, they will be converted into GRIB2 if parameter <code class="docutils literal notranslate"><span class="pre">FORMAT</span></code> is set to <em>GRIB2</em>. Please note, however, that older versions of FLEXPART may have difficulties to read these <em>GRIB2</em> files since some parameter IDs have been change in <em>GRIB2</em>. If the retrieval is executed remotely at ECMWF, the resulting files will be sent to the local gateway server via the <code class="docutils literal notranslate"><span class="pre">ECtrans</span></code> utility if the parameter <code class="docutils literal notranslate"><span class="pre">ECTRANS</span></code> is set to <code class="docutils literal notranslate"><span class="pre">1</span></code> and the parameters <code class="docutils literal notranslate"><span class="pre">GATEWAY</span></code>, <code class="docutils literal notranslate"><span class="pre">DESTINATION</span></code> have been set properly during installation. The status of the transfer can be checked with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-ectrans-list</span></code> (on the local gateway server). If the script is executed locally, the progress of the script can be followed with the usual Linux tools.</p>
</dd>
</dl>
</li>
@@ -216,7 +216,7 @@
</div>
<div class="section" id="workflows-of-different-application-modes">
<h2>Workflows of different application modes<a class="headerlink" href="#workflows-of-different-application-modes" title="Permalink to this headline">¶</a></h2>
-<p>More details on how different the program flow is for the different <a class="reference internal" href="app_modes.html"><span class="doc">Application Modes</span></a> is sketched in the following diagrams:</p>
+<p>The following diagrams show how different the program flow is for the different <a class="reference internal" href="app_modes.html"><span class="doc">Application modes</span></a>:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 51%" />
@@ -270,10 +270,10 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="../input.html" class="btn btn-neutral float-right" title="Control & Input Data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="../input.html" class="btn btn-neutral float-right" title="Control & input data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="app_modes.html" class="btn btn-neutral float-left" title="Application Modes" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="app_modes.html" class="btn btn-neutral float-left" title="Application modes" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/api.html b/Documentation/html/Documentation/api.html
index 19ec211c03fec503a464af0edf09deace2fcda83..c87c3b7a97a525c1b8d19629837c7926939e5198 100644
--- a/Documentation/html/Documentation/api.html
+++ b/Documentation/html/Documentation/api.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto Generated Documentation — flex_extract 7.1 alpha documentation</title>
+ <title>Auto-generated documentation — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Python’s Auto Generated Documentation" href="Api/api_python.html" />
- <link rel="prev" title="Vertical Coordinate" href="vertco.html" />
+ <link rel="next" title="Auto-generated documentation for the Python scripts" href="Api/api_python.html" />
+ <link rel="prev" title="Vertical wind" href="vertco.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,13 +94,13 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Auto Generated Documentation</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="Api/api_python.html">Python’s Auto Generated Documentation</a></li>
-<li class="toctree-l3"><a class="reference internal" href="Api/api_fortran.html">Fortran’s Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical wind</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Auto-generated documentation</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="Api/api_python.html">Auto-generated documentation for the Python scripts</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Api/api_fortran.html">Auto-generated documentation for the Fortran programme</a></li>
</ul>
</li>
</ul>
@@ -158,7 +158,7 @@
<li><a href="../documentation.html">Documentation</a> »</li>
- <li>Auto Generated Documentation</li>
+ <li>Auto-generated documentation</li>
<li class="wy-breadcrumbs-aside">
@@ -178,9 +178,9 @@
<div itemprop="articleBody">
<div class="section" id="auto-generated-documentation">
-<h1>Auto Generated Documentation<a class="headerlink" href="#auto-generated-documentation" title="Permalink to this headline">¶</a></h1>
-<p><a class="reference internal" href="Api/api_python.html"><span class="doc">Python’s Auto Generated Documentation</span></a></p>
-<p><a class="reference internal" href="Api/api_fortran.html"><span class="doc">Fortran’s Auto Generated Documentation</span></a></p>
+<h1>Auto-generated documentation<a class="headerlink" href="#auto-generated-documentation" title="Permalink to this headline">¶</a></h1>
+<p><a class="reference internal" href="Api/api_python.html"><span class="doc">Auto-generated documentation for the Python scripts</span></a></p>
+<p><a class="reference internal" href="Api/api_fortran.html"><span class="doc">Auto-generated documentation for the Fortran programme</span></a></p>
<div class="toctree-wrapper compound">
</div>
</div>
@@ -193,10 +193,10 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="Api/api_python.html" class="btn btn-neutral float-right" title="Python’s Auto Generated Documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="Api/api_python.html" class="btn btn-neutral float-right" title="Auto-generated documentation for the Python scripts" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="vertco.html" class="btn btn-neutral float-left" title="Vertical Coordinate" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="vertco.html" class="btn btn-neutral float-left" title="Vertical wind" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/disagg.html b/Documentation/html/Documentation/disagg.html
index 6e98c3f0f03be2a5899509eecbe45268549525b9..7f0cb74bdce4e60d10863d9b0de94837320c4b29 100644
--- a/Documentation/html/Documentation/disagg.html
+++ b/Documentation/html/Documentation/disagg.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Disaggregation of Flux Data — flex_extract 7.1 alpha documentation</title>
+ <title>Disaggregation of flux data — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Vertical Coordinate" href="vertco.html" />
- <link rel="prev" title="Output Data" href="output.html" />
+ <link rel="next" title="Vertical wind" href="vertco.html" />
+ <link rel="prev" title="Output data" href="output.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,18 +94,18 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="output.html">Output Data</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Disaggregation of Flux Data</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html">Output data</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Disaggregation of flux data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#disaggregation-for-precipitation-in-older-versions">Disaggregation for precipitation in older versions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#disaggregation-for-precipitation-in-version-7-1">Disaggregation for precipitation in version 7.1</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#disaggregation-for-the-rest-of-the-flux-fields">Disaggregation for the rest of the flux fields</a><ul class="simple">
+<li class="toctree-l3"><a class="reference internal" href="#disaggregation-for-the-other-flux-fields">Disaggregation for the other flux fields</a><ul class="simple">
</ul>
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
@@ -161,7 +161,7 @@
<li><a href="../documentation.html">Documentation</a> »</li>
- <li>Disaggregation of Flux Data</li>
+ <li>Disaggregation of flux data</li>
<li class="wy-breadcrumbs-aside">
@@ -181,10 +181,15 @@
<div itemprop="articleBody">
<div class="section" id="disaggregation-of-flux-data">
-<h1>Disaggregation of Flux Data<a class="headerlink" href="#disaggregation-of-flux-data" title="Permalink to this headline">¶</a></h1>
-<p><code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> interpolates meteorological input data linearly to the position of computational particles in time and space. This method requires point values in the discrete input fields. However, flux data (as listed in table <a class="reference internal" href="#ref-table-fluxpar"><span class="std std-ref">flux fields</span></a>) from the ECMWF represent cell averages or integrals and are accumulated over a specific time interval, depending on the dataset. Hence, to conserve the integral quantity with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>’s linear interpolation a pre-processing scheme has to be applied.</p>
+<h1>Disaggregation of flux data<a class="headerlink" href="#disaggregation-of-flux-data" title="Permalink to this headline">¶</a></h1>
+<p><code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> interpolates meteorological input data linearly to the position of computational
+particles in time and space. This method requires point values in the discrete input fields.
+However, flux data (as listed in table <a class="reference internal" href="#ref-table-fluxpar"><span class="std std-ref">Flux fields</span></a> below) from the ECMWF represent cell
+averages or integrals and are accumulated over a specific time interval, depending on the data
+set. Hence, to conserve the integral quantity with the linear interpolation used in <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>,
+pre-processing has to be applied.</p>
<span id="ref-table-fluxpar"></span><table class="colwidths-given docutils align-center" id="id1">
-<caption><span class="caption-text">flux fields</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
+<caption><span class="caption-text">Flux fields</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 14%" />
<col style="width: 43%" />
@@ -231,19 +236,20 @@
</tr>
</tbody>
</table>
-<p>The first step is to <em>de-accumulate</em> the fields in time so that each value represents an integral in x, y, t space.
-Afterwards, a <em>disaggregation</em> scheme is applied which means to break down the integral value into point values.
-In order to be able to carry out the disaggregation procedure proposed by Paul James, additional flux data is retrieved automatically for one day at the beginning and one day at the end of the period specified. Thus, data for flux computation will be requested for the period START_DATE-1 to END_DATE+1. Note that these (additional) dates are used only for interpolation within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> and are not communicated to the final <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files.</p>
-<p>The flux disaggregation produces files named <code class="docutils literal notranslate"><span class="pre">fluxYYYYMMDDHH</span></code>, where <code class="docutils literal notranslate"><span class="pre">YYYYMMDDHH</span></code> is the date format. Note, that the first two and last two flux files do not contain any data.</p>
+<p>The first step is to <em>de-accumulate</em> the fields in time so that each value represents non-overlapping integrals in x-, y-, and t-space.
+Afterwards, a <em>disaggregation</em> scheme is applied which means to convert the integral value to corresponding point values to be used late for the interpolation.
+The disaggregation procedure as proposed by Paul James (currently, the standard) requires additional flux data for one day at the beginning and one day at the end of the period specified.
+They are retrieved automatically. Thus, data for flux computation will be requested for the period START_DATE-1 to END_DATE+1. Note that these (additional) dates are used only for interpolation within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> and are not contained in the final <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files.</p>
+<p>The flux disaggregation produces files named <code class="docutils literal notranslate"><span class="pre">fluxYYYYMMDDHH</span></code>, where <code class="docutils literal notranslate"><span class="pre">YYYYMMDDHH</span></code> is the date format. Note that the first two and last two flux files do not contain any data.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>Note also that for operational retrievals (<code class="docutils literal notranslate"><span class="pre">BASETIME</span></code> set to 00 or 12) forecast fluxes are only available until <code class="docutils literal notranslate"><span class="pre">BASETIME</span></code>, so that no polynomial interpolation is possible in the last two time intervals. This is the reason why setting <code class="docutils literal notranslate"><span class="pre">BASETIME</span></code> is not recommended for on demand scripts.</p>
+<p>Note also that for operational retrievals (<code class="docutils literal notranslate"><span class="pre">BASETIME</span></code> set to 00 or 12), forecast fluxes are only available until <code class="docutils literal notranslate"><span class="pre">BASETIME</span></code>, so that no polynomial interpolation is possible in the last two time intervals. This is the reason why setting <code class="docutils literal notranslate"><span class="pre">BASETIME</span></code> is not recommended for on-demand scripts.</p>
</div>
<div class="section" id="disaggregation-for-precipitation-in-older-versions">
<h2>Disaggregation for precipitation in older versions<a class="headerlink" href="#disaggregation-for-precipitation-in-older-versions" title="Permalink to this headline">¶</a></h2>
-<p>In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> up to version 5 the disaggregation was done with a Fortran program (FLXACC2). In version 6 this part was converted to Python.</p>
-<p>In the old versions (below 7.1) a relatively simple method processes the precipitation fields in a way that is consistent with the scheme applied in <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> for all variables: linear interpolation between times where input fields are available.
-At first the accumulated values are divided by the number of hours (i.e., 3 or 6).
+<p>In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.</p>
+<p>In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> for all variables.
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -253,9 +259,9 @@ Horizontally, the precipitation values are averages for a grid cell around the g
However, the supporting points in space are not shifted between precipitation and other variables as is the case for the temporal dimension.</p>
<div class="align-center figure align-default" id="id2">
<span id="ref-fig-olddisagg"></span><img alt="../_images/old_disagg.png" src="../_images/old_disagg.png" />
-<p class="caption"><span class="caption-text">Fig. 1: Example of disaggregation scheme as implemented in older versions for an isolated precipitation event lasting one time interval (thick blue line). The amount of original precipitation after de-accumulation is given by the blue-shaded area. The green circles represent the discrete grid points after disaggregation and linearly interpolate in between them as indicated by the green line and the green-shaded area. Note that supporting points for the interpolation are shifted by a half-time interval compared to the times when other meteorological fields are available (Hittmeir et al. 2018).</span><a class="headerlink" href="#id2" title="Permalink to this image">¶</a></p>
+<p class="caption"><span class="caption-text">Fig. 1: Example of disaggregation scheme as implemented in older versions for an isolated precipitation event lasting one time interval (thick blue line). The amount of original precipitation after de-accumulation is given by the blue-shaded area. The green circles represent the discrete grid points after disaggregation and linearly interpolate in between them as indicated by the green line and the green-shaded area. Note that supporting points for the interpolation are shifted by half a time interval compared to the times when other meteorological fields are available (Hittmeir et al. 2018).</span><a class="headerlink" href="#id2" title="Permalink to this image">¶</a></p>
</div>
-<p>Disaggregation is done for 4 adjacent timespans (<span class="math notranslate nohighlight">\(a_0, a_1, a_2, a_3\)</span>) which generates a new, disaggregated value which is output at the central point of the 4 adjacent timespans.</p>
+<p>Disaggregation is done for four adjacent timespans (<span class="math notranslate nohighlight">\(a_0, a_1, a_2, a_3\)</span>) which generates a new, disaggregated value which is output at the central point of the four adjacent timespans.</p>
<div class="math notranslate nohighlight">
\[\begin{split} p_{ac} &= 0.5 * a_1\\
m &= a_0 + a_2 > 0.\\
@@ -263,15 +269,15 @@ p_{ac}(m) &= a_1(m) * a_2(m) / (a_0(m) + a_2(m))\\
p_{bd} &= 0.5 * a_2\\
m &= a_1 + a_3 > 0.\\
p_{bd}(m) &= a_1(m) * a_2(m) / (a_1(m) + a_3(m))\\\end{split}\]</div>
-<p>This new point <span class="math notranslate nohighlight">\(p\)</span> is used for linear interpolation of the complete timeseries afterwards. If one of the 4 original timespans has a value below 0 it is set to 0 prior to the calculation.</p>
+<p>This new point <span class="math notranslate nohighlight">\(p\)</span> is used for linear interpolation of the complete timeseries afterwards. If one of the four original timespans has a value below 0, it is set to 0 prior to the calculation.</p>
<div class="math notranslate nohighlight">
\[p = p_{ac} + p_{bd}\]</div>
</div>
<div class="section" id="disaggregation-for-precipitation-in-version-7-1">
<h2>Disaggregation for precipitation in version 7.1<a class="headerlink" href="#disaggregation-for-precipitation-in-version-7-1" title="Permalink to this headline">¶</a></h2>
-<p>Due to the problems with generating precipitation in originally dry (or lower) intervals and the temporal smoothing a new algorithm was developed. The approach is based on a one dimensional piecewise linear function with two additional supporting grid points within each grid cell, dividing the interval into three pieces. It fulfils the desired requirements by preserving the integral precipitation in each time interval, guaranteeing continuity at interval boundaries, and maintaining non-negativity. An additional monotonicity filter helps to gain monotonicity.
-The more natural requirements of symmetry, reality, computational efficiency and easy implementation motivates the linear formulation.
-These requirements on the reconstruction algorithm imply that time intervals with no precipitation remain unchanged, i.e. the reconstructed values vanish throughout this whole time interval, too.
+<p>Due to the problems mentioned above, a new algorithm was developed. The approach is based on a one-dimensional, piecewise-linear function with two additional supporting grid points within each grid cell, dividing the interval into three pieces. It fulfils the desired requirements of preserving the integral precipitation in each time interval, guaranteeing continuity at interval boundaries, and maintaining non-negativity. An additional filter improves monotonicity.
+The more natural requirements of symmetry, reality, computational efficiency and easy implementation motivates the use of a linear formulation.
+These requirements for the reconstruction algorithm imply that time intervals with no precipitation remain unchanged, i. e., the reconstructed values vanish throughout this whole time interval, too.
In the simplest scenario of an isolated precipitation event, where in the time interval before and after the data values are zero, the reconstruction algorithm therefore has to vanish at the boundaries of the interval, too.
The additional conditions of continuity and conservation of the precipitation amount then require us to introduce sub-grid points if we want to keep a linear interpolation (Fig. 2).
The height is thereby determined by the condition of conservation of the integral of the function over the time interval.</p>
@@ -295,18 +301,18 @@ The height is thereby determined by the condition of conservation of the integra
\textbf{then}\end{split}\]</div>
<div class="math notranslate nohighlight">
\[ \begin{align}\begin{aligned}f_{i+1}^\diamond=&\frac{18}{13}g_i-\frac{5}{13}f_i\\f_{i+1}^{\diamond\diamond}=&\frac{18}{13}g_{i+1}-\frac{5}{13}f_{i+2}\\f_{i+1} =& \min\left\{3 g_i,\, 3 g_{i+1},\, \sqrt{(f_{i+1}^\diamond\,f_{i+1}^{\diamond\diamond})_+}\right\}\\f_i^{(1)}=& \frac32 g_i -\frac{1}{12}f_{i}-\frac{5}{12}f_{i+1}^{\textrm{mon}}\\f_i^{(2)}=& \frac32 g_i -\frac{5}{12}f_{i}-\frac{1}{12}f_{i+1}^{\textrm{mon}}\\\textbf{endif}\end{aligned}\end{align} \]</div>
-<p>In the case of the new disaggregation method for precipitation, the two new sub grid points are added in the <code class="docutils literal notranslate"><span class="pre">flux</span></code> output files. They are identified by the forecast step parameter <code class="docutils literal notranslate"><span class="pre">step</span></code> which is 0 for the original time interval and 1 or 2 for the two new sub grid points respectively. The filenames do not change.</p>
+<p>In the case of the new disaggregation method for precipitation, the two new sub-grid points are added in the <code class="docutils literal notranslate"><span class="pre">flux</span></code> output files. They are identified by the forecast step parameter <code class="docutils literal notranslate"><span class="pre">step</span></code> which is 0 for the original time interval, and 1 or 2, respectively, for the two new sub-grid points. The filenames do not change.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>The new method for disaggregation was published in the Geoscientific Model Development Journal in 2018:</p>
+<p>The new method for disaggregation was published in the journal Geoscientific Model Development in 2018:</p>
<p>Hittmeir, S., Philipp, A., and Seibert, P.: A conservative reconstruction scheme for the interpolation of extensive quantities in the Lagrangian particle dispersion model FLEXPART, Geosci. Model Dev., 11, 2503-2523, <a class="reference external" href="https://doi.org/10.5194/gmd-11-2503-2018">https://doi.org/10.5194/gmd-11-2503-2018</a>, 2018.</p>
</div>
</div>
-<div class="section" id="disaggregation-for-the-rest-of-the-flux-fields">
-<h2>Disaggregation for the rest of the flux fields<a class="headerlink" href="#disaggregation-for-the-rest-of-the-flux-fields" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="disaggregation-for-the-other-flux-fields">
+<h2>Disaggregation for the other flux fields<a class="headerlink" href="#disaggregation-for-the-other-flux-fields" title="Permalink to this headline">¶</a></h2>
<p>The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times X using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for 4 adjacent timespans (<span class="math notranslate nohighlight">\(p_a, p_b, p_c, p_d\)</span>) which generates a new, disaggregated value which is output at the central point of the 4 adjacent timespans.</p>
+then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent timespans (<span class="math notranslate nohighlight">\(p_a, p_b, p_c, p_d\)</span>) which produces a new, disaggregated value that is the output at the central point of the four adjacent timespans.</p>
<div class="math notranslate nohighlight">
\[\begin{split}p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
@@ -328,10 +334,10 @@ p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.\end{split}\]</div>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="vertco.html" class="btn btn-neutral float-right" title="Vertical Coordinate" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="vertco.html" class="btn btn-neutral float-right" title="Vertical wind" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="output.html" class="btn btn-neutral float-left" title="Output Data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="output.html" class="btn btn-neutral float-left" title="Output data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/input.html b/Documentation/html/Documentation/input.html
index 7eb1b866cdece52ff0090ac56d958a0fa4024793..4a3873de0654b3b5e900ea2bd06b204d6e06f6fc 100644
--- a/Documentation/html/Documentation/input.html
+++ b/Documentation/html/Documentation/input.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Control & Input Data — flex_extract 7.1 alpha documentation</title>
+ <title>Control & input data — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="The Installation Script - setup.sh" href="Input/setup.html" />
- <link rel="prev" title="Program Flow" href="Overview/prog_flow.html" />
+ <link rel="next" title="The installation script - setup.sh" href="Input/setup.html" />
+ <link rel="prev" title="Program flow" href="Overview/prog_flow.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,24 +94,24 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="overview.html">Overview</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Control & Input Data</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="Input/setup.html">The Installation Script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="Input/compilejob.html">The Compilation Jobscript <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="Input/fortran_makefile.html">The Fortran Makefile - <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="Input/run.html">The executable Script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="Input/jobscript.html">The Jobscript <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Control & input data</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="Input/setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Input/compilejob.html">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Input/fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Input/run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Input/jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Input/control.html">The CONTROL file</a></li>
<li class="toctree-l3"><a class="reference internal" href="Input/control_params.html">The CONTROL parameters</a></li>
<li class="toctree-l3"><a class="reference internal" href="Input/examples.html">CONTROL file examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="Input/changes.html">CONTROL file changes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="Input/ecmwf_env.html">ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="Input/ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="Input/templates.html">Templates</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
@@ -167,7 +167,7 @@
<li><a href="../documentation.html">Documentation</a> »</li>
- <li>Control & Input Data</li>
+ <li>Control & input data</li>
<li class="wy-breadcrumbs-aside">
@@ -187,23 +187,23 @@
<div itemprop="articleBody">
<div class="section" id="control-input-data">
-<h1>Control & Input Data<a class="headerlink" href="#control-input-data" title="Permalink to this headline">¶</a></h1>
+<h1>Control & input data<a class="headerlink" href="#control-input-data" title="Permalink to this headline">¶</a></h1>
<dl>
-<dt>Input Data</dt><dd><ul>
+<dt>Input data</dt><dd><ul>
<li><dl>
-<dt><a class="reference internal" href="Input/control.html"><span class="doc">The CONTROL file</span></a></dt><dd><p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> needs a number of controlling parameters to decide on the behaviour and the actual dataset to be retrieved. They are initialized by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with their default values and can be overwritten with definitions set in the so called <a class="reference internal" href="Input/control.html"><span class="doc">The CONTROL file</span></a>.</p>
-<p>To be able to successfully retrieve data from the ECMWF Mars archive it is necessary to understand these parameters and set them to proper and consistent values. They are described in <a class="reference internal" href="Input/control_params.html"><span class="doc">The CONTROL parameters</span></a> section.</p>
-<p>We also have some <a class="reference internal" href="Input/examples.html"><span class="doc">CONTROL file examples</span></a> and description of <a class="reference internal" href="Input/changes.html"><span class="doc">CONTROL file changes</span></a> changes to previous versions and downward compatibilities.</p>
+<dt><a class="reference internal" href="Input/control.html"><span class="doc">The CONTROL file</span></a></dt><dd><p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> needs a number of controlling parameters to decide on the behaviour and the actual data set to be retrieved. They are initialised by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with certain default values which can be overwritten with definitions set in the so-called <a class="reference internal" href="Input/control.html"><span class="doc">The CONTROL file</span></a>.</p>
+<p>For a successfull retrieval of data from the ECMWF MARS archive it is necessary to understand these parameters and to set them to proper and consistent values. They are described in <a class="reference internal" href="Input/control_params.html"><span class="doc">The CONTROL parameters</span></a> section.</p>
+<p>Furthermore, some <a class="reference internal" href="Input/examples.html"><span class="doc">CONTROL file examples</span></a> are provided, and in <a class="reference internal" href="Input/changes.html"><span class="doc">CONTROL file changes</span></a> changes to previous versions and downward compatibilities are described.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
-<dt><a class="reference internal" href="Input/ecmwf_env.html"><span class="doc">ECMWF User Credential file ECMWF_ENV</span></a></dt><dd><p>For <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> it is necessary to be able to reach ECMWF servers in the <strong>remote mode</strong> and the <strong>gateway mode</strong>. Therefore a <a class="reference internal" href="Input/ecmwf_env.html"><span class="doc">ECMWF User Credential file ECMWF_ENV</span></a> is created during the installation process.</p>
+<dt><a class="reference internal" href="Input/ecmwf_env.html"><span class="doc">ECMWF user credential file ECMWF_ENV</span></a></dt><dd><p><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> needs to be able to reach ECMWF servers in the <strong>remote mode</strong> and the <strong>gateway mode</strong>. Therefore a <a class="reference internal" href="Input/ecmwf_env.html"><span class="doc">ECMWF user credential file ECMWF_ENV</span></a> is created during the installation process.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
-<dt><a class="reference internal" href="Input/templates.html"><span class="doc">Templates</span></a></dt><dd><p>A number of files which are created by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are taken from templates. This makes it easy to adapt for example the jobscripts regarding its settings for the batch jobs.</p>
+<dt><a class="reference internal" href="Input/templates.html"><span class="doc">Templates</span></a></dt><dd><p>A number of files which are created by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are taken from templates. This makes it easy to adapt, for example, the job scripts with regard to the settings for the batch jobs.</p>
</dd>
</dl>
</li>
@@ -211,28 +211,30 @@
</dd>
</dl>
<dl id="ref-controlling">
-<dt>Controlling</dt><dd><p>The main tasks and behaviour of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are controlled by its Python scripts. There are two top-level scripts, one for installation called <a class="reference external" href="Input/setup.html#ref-install-script">install</a> and one for execution called <a class="reference external" href="Input/submit.html#ref-submit-script">submit</a>.
-They can interpret a number of command line arguments which can be seen by typing <code class="docutils literal notranslate"><span class="pre">--help</span></code> after the script call. Go to the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> to type:</p>
+<dt>Controlling</dt><dd><p>The main tasks and the behaviour of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are controlled by the Python scripts. There are two top-level scripts, one for installation called <a class="reference external" href="Input/setup.html#ref-install-script">install</a>, and one for execution called <a class="reference external" href="Input/submit.html#ref-submit-script">submit</a>.
+They interpret a number of command-line arguments which can be seen by typing <code class="docutils literal notranslate"><span class="pre">--help</span></code> after the script call. Go to the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> to type:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X
python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
</pre></div>
</div>
-<p>In this new version we provide also the wrapping Shell scripts <a class="reference external" href="Input/setup.html">setup</a> and <a class="reference external" href="Input/run.html">run</a>, which sets the command line parameters, do some checks and execute the corresponing Python scripts <code class="docutils literal notranslate"><span class="pre">install.py</span></code> and <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> respectivley.</p>
-<p>It might be faster and easier for beginners. See <a class="reference internal" href="../quick_start.html"><span class="doc">Quick Start</span></a> for information on how to use them.</p>
-<p>Additionally, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> creates the Korn Shell scripts <a class="reference internal" href="Input/compilejob.html"><span class="doc">The Compilation Jobscript compilejob.ksh</span></a> and <a class="reference internal" href="Input/jobscript.html"><span class="doc">The Jobscript job.ksh</span></a> which will be send to the ECMWF serves in the <strong>remote mode</strong> and the <strong>gateway mode</strong> for starting batch jobs.</p>
-<p>The Fortran program will be compiled during the installation process by the <a class="reference internal" href="Input/fortran_makefile.html"><span class="doc">The Fortran Makefile - calc_etadot</span></a>.</p>
-<p>To sum up, the following scripts controls <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p>
+<dl class="simple">
+<dt>With version 7.1, we provide also wrapper shell scripts <a class="reference external" href="Input/setup.html">setup</a> and <a class="reference external" href="Input/run.html">run</a> which set the command-line parameters, do some checks, and execute the corresponing Python scripts <code class="docutils literal notranslate"><span class="pre">install.py</span></code> and <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>, respectively.</dt><dd><p>It might be faster and easier for beginners if they are used. See <a class="reference internal" href="../quick_start.html"><span class="doc">Quick Start</span></a> for information on how to use them.</p>
+</dd>
+</dl>
+<p><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> also creates the Korn shell scripts <a class="reference internal" href="Input/compilejob.html"><span class="doc">The compilation job script compilejob.ksh</span></a> and <a class="reference internal" href="Input/jobscript.html"><span class="doc">The job script job.ksh</span></a> which will be sent to the ECMWF servers in the <strong>remote mode</strong> and the <strong>gateway mode</strong> for starting batch jobs.</p>
+<p>The Fortran program is compiled during the installation process using the <a class="reference internal" href="Input/fortran_makefile.html"><span class="doc">The Fortran makefile for calc_etadot</span></a>.</p>
+<p>To sum up, the following scripts control <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p>
<dl class="simple">
<dt>Installation</dt><dd><ul class="simple">
-<li><p><a class="reference internal" href="Input/setup.html"><span class="doc">The Installation Script - setup.sh</span></a></p></li>
-<li><p><a class="reference internal" href="Input/compilejob.html"><span class="doc">The Compilation Jobscript compilejob.ksh</span></a></p></li>
-<li><p><a class="reference internal" href="Input/fortran_makefile.html"><span class="doc">The Fortran Makefile - calc_etadot</span></a></p></li>
+<li><p><a class="reference internal" href="Input/setup.html"><span class="doc">The installation script - setup.sh</span></a></p></li>
+<li><p><a class="reference internal" href="Input/compilejob.html"><span class="doc">The compilation job script compilejob.ksh</span></a></p></li>
+<li><p><a class="reference internal" href="Input/fortran_makefile.html"><span class="doc">The Fortran makefile for calc_etadot</span></a></p></li>
</ul>
</dd>
<dt>Execution</dt><dd><ul class="simple">
-<li><p><a class="reference internal" href="Input/run.html"><span class="doc">The executable Script - run.sh</span></a></p></li>
-<li><p><a class="reference internal" href="Input/jobscript.html"><span class="doc">The Jobscript job.ksh</span></a></p></li>
+<li><p><a class="reference internal" href="Input/run.html"><span class="doc">The executable script - run.sh</span></a></p></li>
+<li><p><a class="reference internal" href="Input/jobscript.html"><span class="doc">The job script job.ksh</span></a></p></li>
</ul>
</dd>
</dl>
@@ -250,10 +252,10 @@ python3 Source/Python/submit.py --help
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="Input/setup.html" class="btn btn-neutral float-right" title="The Installation Script - setup.sh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="Input/setup.html" class="btn btn-neutral float-right" title="The installation script - setup.sh" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="Overview/prog_flow.html" class="btn btn-neutral float-left" title="Program Flow" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="Overview/prog_flow.html" class="btn btn-neutral float-left" title="Program flow" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Documentation/output.html b/Documentation/html/Documentation/output.html
index a314c95b836ea3110ec0403eb928929b3849a7a5..e11aa69110d0d4b666fc825817d2028f23186d4c 100644
--- a/Documentation/html/Documentation/output.html
+++ b/Documentation/html/Documentation/output.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Output Data — flex_extract 7.1 alpha documentation</title>
+ <title>Output data — flex_extract 7.1 alpha documentation</title>
@@ -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="Disaggregation of Flux Data" href="disagg.html" />
+ <link rel="next" title="Disaggregation of flux data" href="disagg.html" />
<link rel="prev" title="Templates" href="Input/templates.html" />
</head>
@@ -94,8 +94,8 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="input.html">Control & Input Data</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Output Data</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="input.html">Control & input data</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Output data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#flexpart-input-files"><code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#standard-output-files">Standard output files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#output-files-for-pure-forecast">Output files for pure forecast</a></li>
@@ -108,15 +108,15 @@
<li class="toctree-l4"><a class="reference internal" href="#mars-request-file">MARS request file</a></li>
<li class="toctree-l4"><a class="reference internal" href="#vertical-ec">VERTICAL.EC</a></li>
<li class="toctree-l4"><a class="reference internal" href="#index-file">Index file</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#flux-files">flux files</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#flux-files">Flux files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#fort-files">fort files</a></li>
</ul>
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
@@ -172,7 +172,7 @@
<li><a href="../documentation.html">Documentation</a> »</li>
- <li>Output Data</li>
+ <li>Output data</li>
<li class="wy-breadcrumbs-aside">
@@ -192,8 +192,8 @@
<div itemprop="articleBody">
<div class="section" id="output-data">
-<h1>Output Data<a class="headerlink" href="#output-data" title="Permalink to this headline">¶</a></h1>
-<p>The output data of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are separated mainly into temporary files and the final <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files:</p>
+<h1>Output data<a class="headerlink" href="#output-data" title="Permalink to this headline">¶</a></h1>
+<p>The output data of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> can be divided into the final <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files and temporary files:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 51%" />
@@ -204,14 +204,14 @@
<td><p>Temporary files (saved in debug mode)</p></td>
</tr>
<tr class="row-even"><td><ul class="simple">
-<li><p>Standard output filenames</p></li>
+<li><p>Standard output file names</p></li>
<li><p>Output for pure forecast</p></li>
<li><p>Output for ensemble members</p></li>
<li><p>Output for new precip. disaggregation</p></li>
</ul>
</td>
<td><ul class="simple">
-<li><p>MARS request file (opt)</p></li>
+<li><p>MARS request file (optional)</p></li>
<li><p>flux files</p></li>
<li><p>VERTICAL.EC</p></li>
<li><p>index file</p></li>
@@ -224,17 +224,17 @@
</table>
<div class="section" id="flexpart-input-files">
<h2><code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files<a class="headerlink" href="#flexpart-input-files" title="Permalink to this headline">¶</a></h2>
-<p>The final output files of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are also the meteorological <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files.
-The naming of these files depend on the kind of data extracted by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
+<p>The final output files of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> are the meteorological input files for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>.
+The naming convention for these files depends on the kind of data extracted by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
<div class="section" id="standard-output-files">
<h3>Standard output files<a class="headerlink" href="#standard-output-files" title="Permalink to this headline">¶</a></h3>
-<p>In general, there is a file for each time step with the filename format:</p>
+<p>In general, there is one file for each time named:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><prefix>YYMMDDHH
</pre></div>
</div>
-<p>The <code class="docutils literal notranslate"><span class="pre">prefix</span></code> is by default defined as <code class="docutils literal notranslate"><span class="pre">EN</span></code> and can be re-defined in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.
-Each file contains all meteorological fields needed by <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> for all selected model levels for a specific time step.</p>
-<p>Here is an example output which lists the meteorological fields in a single file called <code class="docutils literal notranslate"><span class="pre">CE00010800</span></code> where we extracted only the lowest model level for demonstration reasons:</p>
+<p>where YY are the last two digits of the year, MM is the month, DD the day, and HH the hour (UTC). <prefix> is by default defined as EN, and can be re-defined in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.
+Each file contains all meteorological fields at all levels as needed by <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>, valid for the time indicated in the file name.</p>
+<p>Here is an example output which lists the meteorological fields in a single file called <code class="docutils literal notranslate"><span class="pre">CE00010800</span></code> (where we extracted only the lowest model level for demonstration purposes):</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ grib_ls CE00010800
edition centre date dataType gridType stepRange typeOfLevel level shortName packingType
@@ -279,25 +279,26 @@ edition centre date dataType gridType stepRange ty
</div>
<div class="section" id="output-files-for-pure-forecast">
<h3>Output files for pure forecast<a class="headerlink" href="#output-files-for-pure-forecast" title="Permalink to this headline">¶</a></h3>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> can retrieve forecasts which can be longer than 23 hours. To avoid collisions of time steps for forecasts of more than one day a new scheme for filenames in pure forecast mode is introduced:</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><prefix>YYMMDD.HH.<FORECAST_STEP>
</pre></div>
</div>
-<p>The <code class="docutils literal notranslate"><span class="pre"><prefix></span></code> is, as in the standard output, by default <code class="docutils literal notranslate"><span class="pre">EN</span></code> and can be re-defined in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file. <code class="docutils literal notranslate"><span class="pre">YYMMDD</span></code> is the date format and <code class="docutils literal notranslate"><span class="pre">HH</span></code> the forecast time which is the starting time for the forecasts. The <code class="docutils literal notranslate"><span class="pre">FORECAST_STEP</span></code> is a 3 digit number which represents the forecast step in hours.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre"><prefix></span></code> is, as in the standard output, by default <code class="docutils literal notranslate"><span class="pre">EN</span></code> and can be re-defined in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file. <code class="docutils literal notranslate"><span class="pre">YYMMDD</span></code> is the date format and <code class="docutils literal notranslate"><span class="pre">HH</span></code> the forecast time which is the starting time for the forecasts. The <code class="docutils literal notranslate"><span class="pre">FORECAST_STEP</span></code> is a 3-digit number which represents the forecast step in hours.</p>
</div>
<div class="section" id="output-files-for-ensemble-predictions">
<h3>Output files for ensemble predictions<a class="headerlink" href="#output-files-for-ensemble-predictions" title="Permalink to this headline">¶</a></h3>
-<p>Ensembles can be retrieved and are addressed by the grib message parameter <code class="docutils literal notranslate"><span class="pre">number</span></code>. The ensembles are saved per file and standard filenames are supplemented by the letter <code class="docutils literal notranslate"><span class="pre">N</span></code> and the ensemble member number in a 3 digit format.</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able to retrieve ensembles data; they are labelled by the grib message parameter <code class="docutils literal notranslate"><span class="pre">number</span></code>. Each ensemble member is saved in a separate file, and standard filenames are supplemented by the letter <code class="docutils literal notranslate"><span class="pre">N</span></code> and the ensemble member number in a 3-digit format.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><prefix>YYMMDDHH.N<ENSEMBLE_MEMBER>
</pre></div>
</div>
</div>
<div class="section" id="additional-fields-with-new-precipitation-disaggregation">
<h3>Additional fields with new precipitation disaggregation<a class="headerlink" href="#additional-fields-with-new-precipitation-disaggregation" title="Permalink to this headline">¶</a></h3>
-<p>The new disaggregation method for precipitation fields produces two additional precipitation fields for each time step and precipitation type. They serve as sub-grid points in the original time interval. For details of the method see <a class="reference internal" href="disagg.html"><span class="doc">Disaggregation of Flux Data</span></a>.
-The two additional fields are marked with the <code class="docutils literal notranslate"><span class="pre">step</span></code> parameter in the Grib messages and are set to “1” and “2” for sub-grid point 1 and 2 respectively.
-The output filenames do not change in this case.
-Below is an example list of precipitation fields in an output file generated with the new disaggregation method:</p>
+<p>The new disaggregation method for precipitation fields produces two additional precipitation fields for each time step and precipitation type (large-scale and convective). They serve as sub-grid points in the original time interval. For details of the method see <a class="reference internal" href="disagg.html"><span class="doc">Disaggregation of flux data</span></a>.
+The two additional fields are addressed using the <code class="docutils literal notranslate"><span class="pre">step</span></code> parameter in the GRIB messages, which
+is set to “1” or “2”, for sub-grid points 1 and 2, respectively.
+The output file names are not altered.
+An example of the list of precipitation fields in an output file generated with the new disaggregation method is found below:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ grib_ls
edition centre date dataType gridType stepRange typeOfLevel level shortName packingType
@@ -313,11 +314,14 @@ edition centre date dataType gridType stepRange ty
</div>
<div class="section" id="temporary-files">
<h2>Temporary files<a class="headerlink" href="#temporary-files" title="Permalink to this headline">¶</a></h2>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> works with a number of temporary data files which are usually deleted after a successful data extraction. They are only stored if the <code class="docutils literal notranslate"><span class="pre">DEBUG</span></code> mode is switched on (see <a class="reference internal" href="Input/control_params.html"><span class="doc">The CONTROL parameters</span></a>).</p>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> creates a number of temporary data files which are usually deleted at the end of a successful run. They are preserved only if the <code class="docutils literal notranslate"><span class="pre">DEBUG</span></code> mode is switched on (see <a class="reference internal" href="Input/control_params.html"><span class="doc">The CONTROL parameters</span></a>).</p>
<div class="section" id="mars-grib-files">
<h3>MARS grib files<a class="headerlink" href="#mars-grib-files" title="Permalink to this headline">¶</a></h3>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> retrieves all meteorological fields from MARS and stores them in files ending with <code class="docutils literal notranslate"><span class="pre">.grb</span></code>.
-Since the request times and data transfer of MARS access are limited and ECMWF asks for efficiency in requesting data from MARS, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> splits the overall data request in several smaller requests. Each request is stored in an extra <code class="docutils literal notranslate"><span class="pre">.grb</span></code> file and the file names are put together by several pieces of information:</p>
+Since there are limits implemented by ECMWF for the time per request and data transfer from MARS,
+and as ECMWF asks for efficient MARS retrievals, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> splits the overall data request
+into several smaller requests. Each request is stored in its own <code class="docutils literal notranslate"><span class="pre">.grb</span></code> file, and the file
+names are composed of several pieces of information:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><field_type><grid_type><temporal_property><level_type>.<date>.<ppid>.<pid>.grb
</pre></div>
@@ -325,21 +329,20 @@ Since the request times and data transfer of MARS access are limited and ECMWF a
</div></blockquote>
<p>Description:</p>
<dl class="simple">
-<dt>Field type:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">AN</span></code> - Analysis, <code class="docutils literal notranslate"><span class="pre">FC</span></code> - Forecast, <code class="docutils literal notranslate"><span class="pre">4V</span></code> - 4d variational analysis, <code class="docutils literal notranslate"><span class="pre">CV</span></code> - Validation forecast, <code class="docutils literal notranslate"><span class="pre">CF</span></code> - Control forecast, <code class="docutils literal notranslate"><span class="pre">PF</span></code> - Perturbed forecast</p>
+<dt>Field type:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">AN</span></code> - Analysis, <code class="docutils literal notranslate"><span class="pre">FC</span></code> - Forecast, <code class="docutils literal notranslate"><span class="pre">4V</span></code> - 4D variational analysis, <code class="docutils literal notranslate"><span class="pre">CV</span></code> - Validation forecast, <code class="docutils literal notranslate"><span class="pre">CF</span></code> - Control forecast, <code class="docutils literal notranslate"><span class="pre">PF</span></code> - Perturbed forecast</p>
</dd>
-<dt>Grid type:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">SH</span></code> - Spherical Harmonics, <code class="docutils literal notranslate"><span class="pre">GG</span></code> - Gaussian Grid, <code class="docutils literal notranslate"><span class="pre">OG</span></code> - Output Grid (typically lat/lon), <code class="docutils literal notranslate"><span class="pre">_OROLSM</span></code> - Orography parameter</p>
+<dt>Grid type:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">SH</span></code> - Spherical Harmonics, <code class="docutils literal notranslate"><span class="pre">GG</span></code> - Gaussian Grid, <code class="docutils literal notranslate"><span class="pre">OG</span></code> - Output Grid (typically lat / lon), <code class="docutils literal notranslate"><span class="pre">_OROLSM</span></code> - Orography parameter</p>
</dd>
<dt>Temporal property:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">__</span></code> - instantaneous fields, <code class="docutils literal notranslate"><span class="pre">_acc</span></code> - accumulated fields</p>
</dd>
-<dt>Level type:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">ML</span></code> - Model Level, <code class="docutils literal notranslate"><span class="pre">SL</span></code> - Surface Level</p>
+<dt>Level type:</dt><dd><p><code class="docutils literal notranslate"><span class="pre">ML</span></code> - model level, <code class="docutils literal notranslate"><span class="pre">SL</span></code> - surface level</p>
</dd>
-<dt>ppid:</dt><dd><p>The process number of the parent process of submitted script.</p>
+<dt>ppid:</dt><dd><p>The process number of the parent process of the script submitted.</p>
</dd>
-<dt>pid:</dt><dd><p>The process number of the submitted script.</p>
+<dt>pid:</dt><dd><p>The process number of the script submitted.</p>
</dd>
</dl>
-<p>The process ids should avoid mixing of fields if several <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> jobs are performed in parallel (which is, however, not recommended). The date format is YYYYMMDDHH.</p>
-<p>Example <code class="docutils literal notranslate"><span class="pre">.grb</span></code> files for a day of CERA-20C data:</p>
+<p>Example <code class="docutils literal notranslate"><span class="pre">.grb</span></code> files for one day of CERA-20C data:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ANOG__ML.20000908.71851.71852.grb
FCOG_acc_SL.20000907.71851.71852.grb
@@ -352,10 +355,12 @@ ANSH__SL.20000908.71851.71852.grb
</div>
<div class="section" id="mars-request-file">
<h3>MARS request file<a class="headerlink" href="#mars-request-file" title="Permalink to this headline">¶</a></h3>
-<p>This file is a <code class="docutils literal notranslate"><span class="pre">csv</span></code> file called <code class="docutils literal notranslate"><span class="pre">mars_requests.csv</span></code> with a list of the actual settings of MARS request parameters (one request per line) in a flex_extract job. It is used for documenting the data which were retrieved and for testing reasons.</p>
-<p>Each request consist of the following parameters, whose meaning mainly can be taken from <a class="reference internal" href="Input/control_params.html"><span class="doc">The CONTROL parameters</span></a> or <a class="reference internal" href="Input/run.html"><span class="doc">The executable Script - run.sh</span></a>:
+<p>This file is a <code class="docutils literal notranslate"><span class="pre">csv</span></code> file called <code class="docutils literal notranslate"><span class="pre">mars_requests.csv</span></code> listing the actual settings of the MARS
+request (one request per line) in a flex_extract job.
+It is used for documenting which data were retrieved, and for testing.</p>
+<p>Each request consists of the following parameters, whose meaning mostly can be taken from <a class="reference internal" href="Input/control_params.html"><span class="doc">The CONTROL parameters</span></a> or <a class="reference internal" href="Input/run.html"><span class="doc">The executable script - run.sh</span></a>:
request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist, levtype, marsclass, number, param, repres, resol, step, stream, target, time, type</p>
-<p>Example output of a one day retrieval of CERA-20c data:</p>
+<p>Example output of a one-day retrieval of CERA-20C data:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist, levtype, marsclass, number, param, repres, resol, step, stream, target, time, <span class="nb">type</span>
<span class="m">1</span>, <span class="m">24</span>, <span class="m">40</span>.0/-5.0/30.0/5.0, None, <span class="m">20000107</span>/to/20000109, <span class="m">1</span>, , <span class="m">1</span>.0/1.0, <span class="m">1</span>, SFC, EP, <span class="m">000</span>, <span class="m">142</span>.128/143.128/146.128/180.128/181.128/176.128, , <span class="m">159</span>, <span class="m">3</span>/to/24/by/3, ENDA, /mnt/nas/Anne/Interpolation/flexextract/flex_extract_v7.1/run/./workspace/CERA_testgrid_local_cds/FCOG_acc_SL.20000107.23903.23904.grb, <span class="m">18</span>, FC
<span class="m">1</span>, <span class="m">24</span>, <span class="m">40</span>.0/-5.0/30.0/5.0, None, <span class="m">20000108</span>/to/20000108, <span class="m">1</span>, , <span class="m">1</span>.0/1.0, <span class="m">85</span>/to/91, ML, EP, <span class="m">000</span>, <span class="m">130</span>.128/133.128/131.128/132.128/077.128/246.128/247.128, , <span class="m">159</span>, <span class="m">00</span>, ENDA, /mnt/nas/Anne/Interpolation/flexextract/flex_extract_v7.1/run/./workspace/CERA_testgrid_local_cds/ANOG__ML.20000108.23903.23904.grb, <span class="m">00</span>/03/06/09/12/15/18/21, AN
@@ -367,22 +372,27 @@ request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist,
</div>
<div class="section" id="vertical-ec">
<h3>VERTICAL.EC<a class="headerlink" href="#vertical-ec" title="Permalink to this headline">¶</a></h3>
-<p>The vertical discretization of model levels. This file contains the <code class="docutils literal notranslate"><span class="pre">A</span></code> and <code class="docutils literal notranslate"><span class="pre">B</span></code> parameters to calculate the model level height in meters.</p>
+<p>This file contains information describing the vertical discretisation (model levels)
+in form of the <code class="docutils literal notranslate"><span class="pre">A</span></code> and <code class="docutils literal notranslate"><span class="pre">B</span></code> parameters which allow to calculate the actual pressure of a model level from the surface pressure.</p>
</div>
<div class="section" id="index-file">
<h3>Index file<a class="headerlink" href="#index-file" title="Permalink to this headline">¶</a></h3>
-<p>This file is usually called <code class="docutils literal notranslate"><span class="pre">date_time_stepRange.idx</span></code>. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.</p>
+<p>This file is called <code class="docutils literal notranslate"><span class="pre">date_time_stepRange.idx</span></code>. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.</p>
+<div class="admonition-todo admonition" id="id1">
+<p class="admonition-title">Todo</p>
+<p>#PS NEEDS MORE DESCRIPTION</p>
+</div>
</div>
<div class="section" id="flux-files">
-<h3>flux files<a class="headerlink" href="#flux-files" title="Permalink to this headline">¶</a></h3>
-<p>The flux files contain the de-accumulated and dis-aggregated flux fields of large scale and convective precipitation, eastward turbulent surface stress, northward turbulent surface stress, surface sensible heat flux and the surface net solar radiation.</p>
+<h3>Flux files<a class="headerlink" href="#flux-files" title="Permalink to this headline">¶</a></h3>
+<p>The flux files contain the de-accumulated and dis-aggregated flux fields of large-scale and convective precipitation, east- and northward turbulent surface stresses, the surface sensible heat flux, and the surface net solar radiation.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>flux<date><span class="o">[</span>.N<xxx><span class="o">][</span>.<xxx><span class="o">]</span>
</pre></div>
</div>
-<p>The date format is YYYYMMDDHH. The optional block <code class="docutils literal notranslate"><span class="pre">[.N<xxx>]</span></code> marks the ensemble forecast number, where <code class="docutils literal notranslate"><span class="pre"><xxx></span></code> is the ensemble member number. The optional block <code class="docutils literal notranslate"><span class="pre">[.<xxx>]</span></code> marks a pure forecast with <code class="docutils literal notranslate"><span class="pre"><xxx></span></code> being the forecast step.</p>
+<p>The date format is YYYYMMDDHH as explained before. The optional block <code class="docutils literal notranslate"><span class="pre">[.N<xxx>]</span></code> is used for the ensemble forecast date, where <code class="docutils literal notranslate"><span class="pre"><xxx></span></code> is the ensemble member number. The optional block <code class="docutils literal notranslate"><span class="pre">[.<xxx>]</span></code> marks a pure forecast with <code class="docutils literal notranslate"><span class="pre"><xxx></span></code> being the forecast step.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>In the case of the new dis-aggregation method for precipitation, two new sub-intervals are added in between each time interval. They are identified by the forecast step parameter which is <code class="docutils literal notranslate"><span class="pre">0</span></code> for the original time interval and <code class="docutils literal notranslate"><span class="pre">1</span></code> or <code class="docutils literal notranslate"><span class="pre">2</span></code> for the two new intervals respectively.</p>
+<p>In the case of the new dis-aggregation method for precipitation, two new sub-intervals are added in between each time interval. They are identified by the forecast step parameter which is <code class="docutils literal notranslate"><span class="pre">0</span></code> for the original time interval, and <code class="docutils literal notranslate"><span class="pre">1</span></code> or <code class="docutils literal notranslate"><span class="pre">2</span></code>, respectively, for the two new intervals.</p>
</div>
</div>
<div class="section" id="fort-files">
@@ -391,11 +401,11 @@ request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist,
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>fort.xx
</pre></div>
</div>
-<p>where <code class="docutils literal notranslate"><span class="pre">xx</span></code> is the number which defines the meteorological fields stored in these files.
-They are generated by the Python part of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> by just splitting the meteorological fields for a unique time stamp from the <code class="docutils literal notranslate"><span class="pre">*.grb</span></code> files into the <code class="docutils literal notranslate"><span class="pre">fort</span></code> files.
-The following table defines the numbers with their corresponding content.</p>
-<table class="colwidths-given docutils align-default" id="id1">
-<caption><span class="caption-text">Content of fort - files</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
+<p>where <code class="docutils literal notranslate"><span class="pre">xx</span></code> is a number which defines the meteorological fields stored in these files.
+They are generated by the Python code in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> by splitting the meteorological fields for a unique time stamp from the <code class="docutils literal notranslate"><span class="pre">*.grb</span></code> files, storing them under the names <code class="docutils literal notranslate"><span class="pre">fort.<XX></span></code> where <XX> represents some number.
+The following table defines the numbers and the corresponding content:</p>
+<table class="colwidths-given docutils align-default" id="id2">
+<caption><span class="caption-text">Content of fort - files</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
@@ -425,23 +435,23 @@ The following table defines the numbers with their corresponding content.</p>
<td><p>specific humidity</p></td>
</tr>
<tr class="row-even"><td><p>18</p></td>
-<td><p>surface specific humidity (reduced gaussian)</p></td>
+<td><p>surface specific humidity (reduced Gaussian grid)</p></td>
</tr>
<tr class="row-odd"><td><p>19</p></td>
-<td><p>vertical velocity (pressure) (optional)</p></td>
+<td><p>omega (vertical velocity in pressure coordinates) (optional)</p></td>
</tr>
<tr class="row-even"><td><p>21</p></td>
<td><p>eta-coordinate vertical velocity (optional)</p></td>
</tr>
<tr class="row-odd"><td><p>22</p></td>
-<td><p>total cloud water content (optional)</p></td>
+<td><p>total cloud-water content (optional)</p></td>
</tr>
</tbody>
</table>
-<p>Some of the fields are solely retrieved with specific settings, e.g. the eta-coordinate vertical velocity is not available in ERA-Interim datasets and the total cloud water content is an optional field for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span> <span class="pre">v10</span></code> and newer.</p>
+<p>Some of the fields are solely retrieved with specific settings, e. g., the eta-coordinate vertical velocity is not available in ERA-Interim datasets, and the total cloud-water content is an optional field which is useful for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span> <span class="pre">v10</span></code> and newer.</p>
<p>The <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> program saves its results in file <code class="docutils literal notranslate"><span class="pre">fort.15</span></code> which typically contains:</p>
-<table class="colwidths-given docutils align-default" id="id2">
-<caption><span class="caption-text">Output file of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
+<table class="colwidths-given docutils align-default" id="id3">
+<caption><span class="caption-text">Output file of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
@@ -457,10 +467,10 @@ The following table defines the numbers with their corresponding content.</p>
</tr>
</tbody>
</table>
-<p>More details about the content of <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> can be found in <a class="reference internal" href="vertco.html"><span class="doc">Vertical Coordinate</span></a>.</p>
+<p>More details about the content of <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> can be found in <a class="reference internal" href="vertco.html"><span class="doc">Vertical wind</span></a>.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>The <code class="docutils literal notranslate"><span class="pre">fort.4</span></code> file is the namelist file to drive the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>. It is therefore also an input file.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">fort.4</span></code> file is the namelist file to control the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>. It is therefore also an input file.</p>
<p>Example of a namelist:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="p">&</span>NAMGEN
<span class="nv">maxl</span> <span class="o">=</span> <span class="m">11</span>,
@@ -498,7 +508,7 @@ The following table defines the numbers with their corresponding content.</p>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="disagg.html" class="btn btn-neutral float-right" title="Disaggregation of Flux Data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="disagg.html" class="btn btn-neutral float-right" title="Disaggregation of flux data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Input/templates.html" class="btn btn-neutral float-left" title="Templates" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/Documentation/overview.html b/Documentation/html/Documentation/overview.html
index 89c60de4bf677eb06516816a3a16cfbc9f1d1dbf..62075620ccd53e6f9ab6f30c42fe0e573d56dbaf 100644
--- a/Documentation/html/Documentation/overview.html
+++ b/Documentation/html/Documentation/overview.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="Application Modes" href="Overview/app_modes.html" />
+ <link rel="next" title="Application modes" href="Overview/app_modes.html" />
<link rel="prev" title="Documentation" href="../documentation.html" />
</head>
@@ -94,15 +94,15 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">Overview</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="Overview/app_modes.html">Application Modes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="Overview/prog_flow.html">Program Flow</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Overview/app_modes.html">Application modes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Overview/prog_flow.html">Program flow</a></li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
@@ -179,20 +179,20 @@
<div class="section" id="overview">
<h1>Overview<a class="headerlink" href="#overview" 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 <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> Atmospheric Transport Modelling system.
-<code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> was created explicitly for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> users who wants to use meteorological data from ECMWF to drive the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> model.
-The software retrieves the minimal number of parameters <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> needs to work and provides the data in the explicity format <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> understands.</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 European Centre for Medium-Range Weather Forecasts (ECMWF) MARS archive to serve as input files for the <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> atmospheric transport modelling system.
+<code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> was created explicitly for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> users who want to use meteorological data from ECMWF to drive the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> model.
+The software retrieves the minimum set of parameters needed by <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> to work, and provides the data in the specific format required by <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>.</p>
<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> consists of 2 main parts:</dt><dd><ol class="arabic simple">
-<li><p>a Python part, where the reading of parameter settings, retrieving data from MARS and preparing the data for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> is done and</p></li>
-<li><p>a Fortran part, where the calculation of the vertical velocity is done and if necessary the conversion from spectral to regular latitude/longitude grids.</p></li>
+<dt><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> consists of two main parts:</dt><dd><ol class="arabic simple">
+<li><p>a Python part which reads the parameter settings, retrieves the data from MARS, and prepares them for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>, and</p></li>
+<li><p>a Fortran part which calculates the vertical velocity and, if necessary, converts variables from the spectral representation to regular latitude/longitude grids.</p></li>
</ol>
</dd>
</dl>
-<p>Additionally, it has some Korn shell scripts which are used to set the environment and batch job features on ECMWF servers for the <em>gateway</em> and <em>remote</em> mode. See <a class="reference internal" href="Overview/app_modes.html"><span class="doc">Application Modes</span></a> for information of application modes.</p>
+<p>In addition, there are some Korn shell scripts to set the environment and batch job features on ECMWF servers for the <em>gateway</em> and <em>remote</em> mode. See <a class="reference internal" href="Overview/app_modes.html"><span class="doc">Application modes</span></a> for information of application modes.</p>
<p>A number of Shell scripts are wrapped around the software package for easy installation and fast job submission.</p>
-<p>The software depends on a number of third-party libraries which can be found in <a class="reference internal" href="../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a>.</p>
-<p>Some details on the tasks and program worksteps are described in <a class="reference internal" href="Overview/prog_flow.html"><span class="doc">Program Flow</span></a>.</p>
+<p>The software depends on some third-party libraries as listed in <a class="reference internal" href="../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a>.</p>
+<p>Details of the tasks and program work steps are described in <a class="reference internal" href="Overview/prog_flow.html"><span class="doc">Program flow</span></a>.</p>
<div class="toctree-wrapper compound">
</div>
</div>
@@ -205,7 +205,7 @@ The software retrieves the minimal number of parameters <code class="docutils li
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="Overview/app_modes.html" class="btn btn-neutral float-right" title="Application Modes" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="Overview/app_modes.html" class="btn btn-neutral float-right" title="Application modes" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="../documentation.html" class="btn btn-neutral float-left" title="Documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/Documentation/vertco.html b/Documentation/html/Documentation/vertco.html
index 51dae94c4a4aed69a66fb381d0f405f6aa634db1..7635340bcb92e7840d388b2ced60923a08cb8c46 100644
--- a/Documentation/html/Documentation/vertco.html
+++ b/Documentation/html/Documentation/vertco.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Vertical Coordinate — flex_extract 7.1 alpha documentation</title>
+ <title>Vertical wind — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Auto Generated Documentation" href="api.html" />
- <link rel="prev" title="Disaggregation of Flux Data" href="disagg.html" />
+ <link rel="next" title="Auto-generated documentation" href="api.html" />
+ <link rel="prev" title="Disaggregation of flux data" href="disagg.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,18 +94,18 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../documentation.html">Documentation</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Vertical Coordinate</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#calculation-of-vertical-velocity-and-preparation-of-output-files">Calculation of vertical velocity and preparation of Output-files</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#calculation-of-vertical-velocity-from-horizontal-wind-using-the-continuity-equation">Calculation of vertical velocity from horizontal wind using the continuity equation</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#calculation-of-vertical-velocity-from-pre-calculated-mars-parameter-77">Calculation of vertical velocity from pre-calculated MARS parameter 77</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Vertical wind</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#calculation-of-vertical-velocity-and-preparation-of-output-files">Calculation of vertical velocity and preparation of output files</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#calculation-of-the-vertical-velocity-from-the-horizontal-wind-using-the-continuity-equation">Calculation of the vertical velocity from the horizontal wind using the continuity equation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#calculation-of-the-vertical-velocity-from-the-pre-calculated-mars-parameter-77">Calculation of the vertical velocity from the pre-calculated MARS parameter 77</a><ul class="simple">
</ul>
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
@@ -161,7 +161,7 @@
<li><a href="../documentation.html">Documentation</a> »</li>
- <li>Vertical Coordinate</li>
+ <li>Vertical wind</li>
<li class="wy-breadcrumbs-aside">
@@ -180,14 +180,14 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="vertical-coordinate">
-<h1>Vertical Coordinate<a class="headerlink" href="#vertical-coordinate" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="vertical-wind">
+<h1>Vertical wind<a class="headerlink" href="#vertical-wind" title="Permalink to this headline">¶</a></h1>
<div class="section" id="calculation-of-vertical-velocity-and-preparation-of-output-files">
-<h2>Calculation of vertical velocity and preparation of Output-files<a class="headerlink" href="#calculation-of-vertical-velocity-and-preparation-of-output-files" title="Permalink to this headline">¶</a></h2>
+<h2>Calculation of vertical velocity and preparation of output files<a class="headerlink" href="#calculation-of-vertical-velocity-and-preparation-of-output-files" title="Permalink to this headline">¶</a></h2>
<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> has two ways to calculate the vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>:</dt><dd><ol class="lowerroman simple">
+<dt>Two methods are provided in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> for the calculation of the vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>:</dt><dd><ol class="lowerroman simple">
<li><p>from the horizontal wind field,</p></li>
-<li><p>from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets <strong>ERA5</strong> and <strong>CERA-20C</strong>.</p></li>
+<li><p>from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets <strong>ERA5</strong> and <strong>CERA-20C</strong>, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.</p></li>
</ol>
</dd>
</dl>
@@ -199,42 +199,41 @@ give a vertical velocity in Pa/s as needed by <code class="docutils literal notr
<p>Calculation from the horizontal wind field is still required for historical case studies using
<strong>ERA-40</strong>, <strong>ERA-Interim</strong> or operational data prior to September 2008.</p>
</div>
-<div class="section" id="calculation-of-vertical-velocity-from-horizontal-wind-using-the-continuity-equation">
-<h2>Calculation of vertical velocity from horizontal wind using the continuity equation<a class="headerlink" href="#calculation-of-vertical-velocity-from-horizontal-wind-using-the-continuity-equation" title="Permalink to this headline">¶</a></h2>
-<p>The vertical velocity is computed by the FORTRAN90 program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> in the ECMWF
-vertical coordinate system by applying the equation of continuity and thereby ensuring mass consistent 3D wind fields. A detailed description of <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> can be found in the
+<div class="section" id="calculation-of-the-vertical-velocity-from-the-horizontal-wind-using-the-continuity-equation">
+<h2>Calculation of the vertical velocity from the horizontal wind using the continuity equation<a class="headerlink" href="#calculation-of-the-vertical-velocity-from-the-horizontal-wind-using-the-continuity-equation" title="Permalink to this headline">¶</a></h2>
+<p>The vertical velocity in the ECMWF’s eta vertical coordinate system is computed by the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>, using the continuity equation and thereby ensuring mass-consistent 3D wind fields. A detailed description of <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> can be found in the
documents v20_update_protocol.pdf, V30_update_protocol.pdf and
V40_update_protocol.pdf. The computational demand and accuracy of <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> is highly
dependent on the specification of parameters <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> and <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code>. The
following guidance can be given for choosing the right parameters:</p>
<blockquote>
<div><ul class="simple">
-<li><p>For very fine output grids (0.25 degree or finer) the full resolution T799 or even T1279 of the operational model is required (<code class="docutils literal notranslate"><span class="pre">RESOL=799</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code>). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on <em>ecgate</em>, the computation of the vertical velocity is feasible only on the lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.</p></li>
+<li><p>For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (<code class="docutils literal notranslate"><span class="pre">RESOL=799</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code>). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on <em>ecgate</em>, the computation of the vertical velocity is feasible only on the lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.</p></li>
<li><dl class="simple">
<dt>For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:</dt><dd><ul>
<li><p>For 1.0 degree grids: <code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL=255</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=179</span></code></p></li>
<li><p>For 0.5 degree grids: <code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL=399</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=359</span></code></p></li>
<li><p>Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.</p></li>
-<li><p>If <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> is set to 1, only the following choices are possible for <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> on <em>ecgate</em>: 159,255,319,399,511,799, (on the HPC also 1279, 2047 in future models). This choice is restricted because a reduced Gaussian grid is defined in then ECMWF EMOSLIB only for these spectral resolutions. For <code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> can be any value below the operational resolution.</p></li>
-<li><p>For <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> any resolution lower than <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> is possible. If no smoothing is desired, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code> should be chosen. <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> has no effect if vertical velocity is calculated on lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>).</p></li>
+<li><p>If <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> is set to 1, only the following choices are possible for <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> on <em>ecgate</em>: 159,255,319,399,511,799, (on the HPC also 1279; 2047 in future model versions). This choice is restricted because a reduced Gaussian grid is defined in the ECMWF EMOSLIB only for these spectral resolutions. For <code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> can be any value below the operational resolution.</p></li>
+<li><p>For <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code>, any resolution lower than <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> is possible. If no smoothing is desired, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code> should be chosen. <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> has no effect if the vertical velocity is calculated on a lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>).</p></li>
</ul>
</dd>
</dl>
</li>
-<li><p>The on demand scripts send an error message for settings where <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> (if set) and <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> are larger than 360./<code class="docutils literal notranslate"><span class="pre">GRID</span></code>/2, since in this case, the output grid cannot resolve the highest wave numbers. The scripts continue operations, however.</p></li>
+<li><p>The on-demand scripts send an error message for settings where <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> (if set) and <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> are larger than 360./<code class="docutils literal notranslate"><span class="pre">GRID</span></code>/2, since in this case, the output grid cannot resolve the highest wave numbers. The scripts continue operations, however.</p></li>
<li><p>Regional grids are not cyclic in zonal directions, but global grids are. The software assumes a cyclic grid if <code class="docutils literal notranslate"><span class="pre">RIGHT</span></code>-<code class="docutils literal notranslate"><span class="pre">LEFT</span></code> is equal to <code class="docutils literal notranslate"><span class="pre">GRID</span></code> or is equal to <code class="docutils literal notranslate"><span class="pre">GRID</span></code>-360.</p></li>
-<li><p>Finally, model and flux data as well as the vertical velocity computed are written to files <code class="docutils literal notranslate"><span class="pre"><prefix>yymmddhh</span></code> for application in ATM modelling. If the parameters <code class="docutils literal notranslate"><span class="pre">OMEGA</span></code> or <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span></code> are set, also files <code class="docutils literal notranslate"><span class="pre">OMEGAyymmddhh</span></code> are created, containing the pressure vertical velocity (omega) and the difference between omega from <code class="docutils literal notranslate"><span class="pre">MARS</span></code> and the surface pressure tendency. <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span></code> should be zero except for debugging, since it triggers expensive calculations on the Gaussian grid.</p></li>
+<li><p>Finally, model and flux data as well as the vertical velocity computed are written to files <code class="docutils literal notranslate"><span class="pre"><prefix>yymmddhh</span></code> (the standard <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output files) If the parameters <code class="docutils literal notranslate"><span class="pre">OMEGA</span></code> or <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span></code> are set, also files <code class="docutils literal notranslate"><span class="pre">OMEGAyymmddhh</span></code> are created, containing the pressure vertical velocity (omega) and the difference between omega from <code class="docutils literal notranslate"><span class="pre">MARS</span></code> and from the surface pressure tendency. <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span></code> should be set to zero except for debugging, since it triggers expensive calculations on the Gaussian grid.</p></li>
</ul>
</div></blockquote>
</div>
-<div class="section" id="calculation-of-vertical-velocity-from-pre-calculated-mars-parameter-77">
-<h2>Calculation of vertical velocity from pre-calculated MARS parameter 77<a class="headerlink" href="#calculation-of-vertical-velocity-from-pre-calculated-mars-parameter-77" title="Permalink to this headline">¶</a></h2>
-<p>Since November 2008, the parameter 77 (deta/dt) is stored in <code class="docutils literal notranslate"><span class="pre">MARS</span></code> on full model levels. <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> in its current version requires <code class="docutils literal notranslate"><span class="pre">deta/dt</span></code> on model half levels, multiplied by <code class="docutils literal notranslate"><span class="pre">dp/deta</span></code>. In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, the program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> assumes that this parameter is available if the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> parameter <code class="docutils literal notranslate"><span class="pre">ETA</span></code> is set to 1.</p>
+<div class="section" id="calculation-of-the-vertical-velocity-from-the-pre-calculated-mars-parameter-77">
+<h2>Calculation of the vertical velocity from the pre-calculated MARS parameter 77<a class="headerlink" href="#calculation-of-the-vertical-velocity-from-the-pre-calculated-mars-parameter-77" title="Permalink to this headline">¶</a></h2>
+<p>Since November 2008, the parameter 77 (deta/dt) is stored in <code class="docutils literal notranslate"><span class="pre">MARS</span></code> on full model levels. <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> in its current version requires <code class="docutils literal notranslate"><span class="pre">deta/dt</span></code> on model half levels, multiplied by <code class="docutils literal notranslate"><span class="pre">dp/deta</span></code>. In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, the program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> assumes that parameter 77 is available if the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> parameter <code class="docutils literal notranslate"><span class="pre">ETA</span></code> is set to 1.</p>
<p>It is recommended to use the pre-calculated parameter 77 by setting <code class="docutils literal notranslate"><span class="pre">ETA</span></code> to 1 whenever possible.</p>
-<p>Setting parameter <code class="docutils literal notranslate"><span class="pre">ETA</span></code> to 1 normally disables calculation of vertical velocity from the horizontal wind field, which saves a lot of computational time.</p>
+<p>Setting the parameter <code class="docutils literal notranslate"><span class="pre">ETA</span></code> to 1 disables calculation of vertical velocity from the horizontal wind field, which saves a lot of computational time.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>However, the calculation on the Gaussian grid are avoided only if both <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> and <code class="docutils literal notranslate"><span class="pre">ETADIFF</span></code> are set to 0. Please set <code class="docutils literal notranslate"><span class="pre">ETADIFF</span></code> to 1 only if you are really need it for debugging since this is a very expensive option. In this case <code class="docutils literal notranslate"><span class="pre">ETAyymmddhh</span></code> files are produced that contain the vertical velocity from horizontal winds and the difference to the pre-calculated vertical velocity.</p>
+<p>However, the calculations on the Gaussian grid are avoided only if both <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> and <code class="docutils literal notranslate"><span class="pre">ETADIFF</span></code> are set to 0. Please set <code class="docutils literal notranslate"><span class="pre">ETADIFF</span></code> to 1 only if you are really need it for debugging since this is a very expensive option. In this case, <code class="docutils literal notranslate"><span class="pre">ETAyymmddhh</span></code> files are produced that contain the vertical velocity from horizontal winds and the difference to the pre-calculated vertical velocity.</p>
</div>
<p>The parameters <code class="docutils literal notranslate"><span class="pre">RESOL</span></code>, <code class="docutils literal notranslate"><span class="pre">GRID</span></code>, <code class="docutils literal notranslate"><span class="pre">UPPER</span></code>, <code class="docutils literal notranslate"><span class="pre">LOWER</span></code>, <code class="docutils literal notranslate"><span class="pre">LEFT</span></code>, <code class="docutils literal notranslate"><span class="pre">RIGHT</span></code> still apply. As for calculations on the Gaussian grid, the spectral resolution parameter <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> should be compatible with the grid resolution (see previous subsection).</p>
<div class="toctree-wrapper compound">
@@ -250,10 +249,10 @@ following guidance can be given for choosing the right parameters:</p>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="api.html" class="btn btn-neutral float-right" title="Auto Generated Documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="api.html" class="btn btn-neutral float-right" title="Auto-generated documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="disagg.html" class="btn btn-neutral float-left" title="Disaggregation of Flux Data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="disagg.html" class="btn btn-neutral float-left" title="Disaggregation of flux data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Ecmwf/access.html b/Documentation/html/Ecmwf/access.html
index 80e61ef78cdba06e42fe811091ec7c7ef1e6ee8d..0d880c714fe3fdf7fa864a7b6d92285e98873c32 100644
--- a/Documentation/html/Ecmwf/access.html
+++ b/Documentation/html/Ecmwf/access.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Access Modes — flex_extract 7.1 alpha documentation</title>
+ <title>Access modes — flex_extract 7.1 alpha documentation</title>
@@ -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="Available Datasets for Member State users" href="msdata.html" />
+ <link rel="next" title="Available data sets for member-state users" href="msdata.html" />
<link rel="prev" title="ECMWF Data" href="../ecmwf_data.html" />
</head>
@@ -92,13 +92,13 @@
<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a><ul class="current">
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Access Modes</a><ul class="simple">
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Access modes</a><ul class="simple">
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available Datasets for Member State users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available Datasets for Public users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints to specify dataset retrieval</a></li>
-<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link Collection for Quick finder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available data sets for member-state users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available data sets for public users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints for data set selection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link collection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
@@ -155,7 +155,7 @@
<li><a href="../ecmwf_data.html">ECMWF Data</a> »</li>
- <li>Access Modes</li>
+ <li>Access modes</li>
<li class="wy-breadcrumbs-aside">
@@ -175,17 +175,17 @@
<div itemprop="articleBody">
<div class="section" id="access-modes">
-<h1>Access Modes<a class="headerlink" href="#access-modes" title="Permalink to this headline">¶</a></h1>
-<p>Access to the ECMWF Mars archive is divided into two groups: <strong>member state</strong> users and <strong>public</strong> users.</p>
+<h1>Access modes<a class="headerlink" href="#access-modes" title="Permalink to this headline">¶</a></h1>
+<p>Access to the ECMWF MARS archive is divided into two groups: <strong>member state</strong> users and <strong>public</strong> users.</p>
<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>
+<dt><strong>Member-state user</strong>:</dt><dd><p>This access mode allows the user to work directly on a ECMWF member-state Linux server or via the <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code> Web-Access Toolkit 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 no access to the latest forecasts. In case such data are needed, this has to be agreed upon with the national <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, which, however, 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 to extract the re-analysis datasets such as ERA-Interim and CERA-20C for use with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> (tested). 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, only a 6-hourly temporal resolution is available 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 data set 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">
<p class="admonition-title">Note</p>
-<p>The availability of the public dataset <em>ERA5</em> with the ECMWF Web API was cancelled in March 2019. The oportunity of local retrieval of this dataset was moved to the <a class="reference external" href="https://cds.climate.copernicus.eu">Climate Data Store</a> which uses another Web API named <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a>. This Data Store stores the data on explicit webservers for faster and easier access. Unfortunately, for <em>ERA5</em> there are only surface level and pressure level data available for <em>public users</em>. In the case of a <em>member user</em> it is possible to bypass the request to the MARS archive from ECMWF to retrieve the data. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is already modified to use this API so <em>member user</em> can already retrieve <em>ERA5</em> data while <em>public users</em> have to wait until model level are available.</p>
+<p>The availability of the public dataset <em>ERA5</em> with the ECMWF Web API was cancelled by ECWMF in March 2019. Local retrieval of this dataset now has to use the <a class="reference external" href="https://cds.climate.copernicus.eu">Climate Data Store</a> (CDS) with a different Web API called <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a>. CDS stores the data on dedicated web servers for faster and easier access. Unfortunately, for <em>ERA5</em>, only surface level and pressure level data are available for <em>public users</em> which is not enough to run FLEXPART. For a <em>member user</em>, it is possible to pass the request to the MARS archive to retrieve the data. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is already modified to use this API so a <em>member user</em> can already retrieve <em>ERA5</em> data for FLEXPART while <em>public users</em> have to wait until model level are made available.</p>
</div>
<p>For information on how to register see <a class="reference internal" href="../installation.html#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a>.</p>
<div class="toctree-wrapper compound">
@@ -200,7 +200,7 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="msdata.html" class="btn btn-neutral float-right" title="Available Datasets for Member State users" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="msdata.html" class="btn btn-neutral float-right" title="Available data sets for member-state users" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="../ecmwf_data.html" class="btn btn-neutral float-left" title="ECMWF Data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/Ecmwf/ec-links.html b/Documentation/html/Ecmwf/ec-links.html
index 42da733c33585d8cc38578de3f58fe23f3caa67b..ef9cad81013cce4873182563f1431e2faea5af15 100644
--- a/Documentation/html/Ecmwf/ec-links.html
+++ b/Documentation/html/Ecmwf/ec-links.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Link Collection for Quick finder — flex_extract 7.1 alpha documentation</title>
+ <title>Link collection — flex_extract 7.1 alpha documentation</title>
@@ -39,7 +39,7 @@
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Documentation" href="../documentation.html" />
- <link rel="prev" title="Hints to specify dataset retrieval" href="hintsecmwf.html" />
+ <link rel="prev" title="Hints for data set selection" href="hintsecmwf.html" />
</head>
<body class="wy-body-for-nav">
@@ -92,11 +92,11 @@
<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="access.html">Access Modes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available Datasets for Member State users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available Datasets for Public users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints to specify dataset retrieval</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Link Collection for Quick finder</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="access.html">Access modes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available data sets for member-state users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available data sets for public users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints for data set selection</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Link collection</a><ul class="simple">
</ul>
</li>
</ul>
@@ -155,7 +155,7 @@
<li><a href="../ecmwf_data.html">ECMWF Data</a> »</li>
- <li>Link Collection for Quick finder</li>
+ <li>Link collection</li>
<li class="wy-breadcrumbs-aside">
@@ -174,47 +174,47 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="link-collection-for-quick-finder">
-<h1>Link Collection for Quick finder<a class="headerlink" href="#link-collection-for-quick-finder" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="link-collection">
+<h1>Link collection<a class="headerlink" href="#link-collection" title="Permalink to this headline">¶</a></h1>
<dl>
-<dt>ECMWF - General Overview</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/">ECMWF Home</a></p>
-<p><a class="reference external" href="https://www.ecmwf.int/en/learning">ECMWF Training</a></p>
-<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/UDOC/User+Documentation">General User Documentation</a></p>
-<p><a class="reference external" href="https://confluence.ecmwf.int/display/SUP">Software Support</a></p>
+<dt>ECMWF - General overview</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/">ECMWF Home</a></p>
+<p><a class="reference external" href="https://www.ecmwf.int/en/learning">ECMWF training</a></p>
+<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/UDOC/User+Documentation">General user documentation</a></p>
+<p><a class="reference external" href="https://confluence.ecmwf.int/display/SUP">Software support</a></p>
</dd>
<dt>MARS</dt><dd><p><a class="reference external" href="https://confluence.ecmwf.int//display/UDOC/MARS+user+documentation">MARS user documentation</a></p>
-<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords">MARS Keywords</a></p>
-<p><a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/MARS+content">MARS Content</a></p>
-<p><a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/MARS+actions">MARS Actions</a></p>
-<p><a class="reference external" href="https://apps.ecmwf.int/codes/grib/param-db">Parameter Database</a></p>
+<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords">MARS keywords</a></p>
+<p><a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/MARS+content">MARS content</a></p>
+<p><a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/MARS+actions">MARS actions</a></p>
+<p><a class="reference external" href="https://apps.ecmwf.int/codes/grib/param-db">Parameter database</a></p>
</dd>
-<dt>Registration</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Contact of Computing Representative’s</a></p>
+<dt>Registration</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Contacts of Computing Representatives</a></p>
<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/WEBAPI/Access+MARS">Public registration for ECMWF Web API</a></p>
-<p><a class="reference external" href="https://cds.climate.copernicus.eu/user/register">CDS Registration</a></p>
+<p><a class="reference external" href="https://cds.climate.copernicus.eu/user/register">CDS registration</a></p>
</dd>
-<dt>Available Member State Datasets</dt><dd><p><a class="reference external" href="http://apps.ecmwf.int/archive-catalogue/">Web Interface for accessing member state datasets</a></p>
-<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets">Available datasets for member state users</a></p>
+<dt>Member-State data sets available</dt><dd><p><a class="reference external" href="http://apps.ecmwf.int/archive-catalogue/">Web interface for accessing member-state data sets</a></p>
+<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets">Data sets available for member state users</a></p>
</dd>
-<dt>Available Public Datasets</dt><dd><p><a class="reference external" href="http://apps.ecmwf.int/datasets/">Web Interface for accessing public datasets</a></p>
-<p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">ECMWF’s public datasets</a></p>
-<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets">Public dataset Licences</a></p>
-<p><a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset">ERA5 public dataset Licence</a></p>
+<dt>Public data sets available</dt><dd><p><a class="reference external" href="http://apps.ecmwf.int/datasets/">Web interface for accessing public data sets</a></p>
+<p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">ECMWF’s public data sets</a></p>
+<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets">Public data set licences</a></p>
+<p><a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset">ERA5 public dataset licence</a></p>
</dd>
<dt>Datasets</dt><dd><dl>
-<dt>Overview</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets">Complete list of datasets</a></p>
+<dt>Overview</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets">Complete list of data sets</a></p>
<p><a class="reference external" href="https://www.ecmwf.int/en/research/climate-reanalysis">What is climate reanalysis</a></p>
<p><a class="reference external" href="https://confluence.ecmwf.int/display/FUG/1+Introduction">Forecast user guide</a></p>
</dd>
<dt>Real-time (Operational)</dt><dd><p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/catalogue-ecmwf-real-time-products">List of real_time datasets</a></p>
-<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/set-i">Atmospheric model - HRES (our typical operational dataset)</a></p>
+<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/set-i">Atmospheric model - HRES (typical operational dataset)</a></p>
<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/set-iii">Atmospheric model - ENS (15-day ensemble forecast)</a></p>
</dd>
<dt>ERA-Interim</dt><dd><p><a class="reference external" href="https://confluence.ecmwf.int/display/CKB/What+is+ERA-Interim">What is ERA-Interim</a></p>
<p><a class="reference external" href="https://www.ecmwf.int/en/elibrary/8174-era-interim-archive-version-20">ERA-Interim documentation</a></p>
-<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/era-interim">ERA-Interim dataset</a></p>
+<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/era-interim">ERA-Interim data set</a></p>
</dd>
<dt>CERA-20C</dt><dd><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/CKB/What+is+CERA-20C">What is CERA-20C</a></p>
-<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/cera-20c">CERA-20C dataset</a></p>
+<p><a class="reference external" href="https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/cera-20c">CERA-20C data set</a></p>
</dd>
<dt>ERA5</dt><dd><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/CKB/What+is+ERA5">What is ERA5</a></p>
<p><a class="reference external" href="https://confluence.ecmwf.int/pages/viewpage.action?pageId=74764925">What are the changes from ERA-Interim to ERA5</a></p>
@@ -224,7 +224,7 @@
</dd>
</dl>
</dd>
-<dt>Third Party Libraries</dt><dd><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API Home</a></p>
+<dt>Third-party libraries</dt><dd><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API home</a></p>
<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran">Building ECMWF software with gfortran</a></p>
<p><a class="reference external" href="http://www.fftw.org">FFTW</a></p>
<p><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">EMOSLIB</a></p>
@@ -234,16 +234,16 @@
</dd>
<dt>Plotting GRIB fields:</dt><dd><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/CKB/How+to+plot+GRIB+files+with+Python+and+matplotlib">Example Python script to plot GRIB files</a></p>
</dd>
-<dt>Scientific Information</dt><dd><p><a class="reference external" href="https://confluence.ecmwf.int/display/FCST/Introducing+the+octahedral+reduced+Gaussian+grid">Octahedral reduced Gaussian Grid</a></p>
+<dt>Scientific information</dt><dd><p><a class="reference external" href="https://confluence.ecmwf.int/display/FCST/Introducing+the+octahedral+reduced+Gaussian+grid">Octahedral reduced Gaussian grid</a></p>
<p><a class="reference external" href="https://www.ecmwf.int/en/newsletter/147/meteorology/use-high-density-observations-precipitation-verification">Precipitation</a></p>
</dd>
</dl>
-<p>Technical Information of ECMWF serves</p>
+<p>Technical information for ECMWF servers</p>
<blockquote>
-<div><p><a class="reference external" href="https://confluence.ecmwf.int/download/attachments/73008494/intro-slurm-2017.pdf?version=1&modificationDate=1488574096323&api=v2">Introduction presentation to SLURM</a></p>
+<div><p><a class="reference external" href="https://confluence.ecmwf.int/download/attachments/73008494/intro-slurm-2017.pdf?version=1&modificationDate=1488574096323&api=v2">Introductary presentation of SLURM</a></p>
</div></blockquote>
<dl class="simple">
-<dt>Troubleshooting</dt><dd><p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Web-API+Troubleshooting">ECMWF Web API Troubleshooting</a></p>
+<dt>Trouble-shooting</dt><dd><p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Web-API+Troubleshooting">ECMWF Web API trouble-shooting</a></p>
</dd>
</dl>
<div class="toctree-wrapper compound">
@@ -261,7 +261,7 @@
<a href="../documentation.html" class="btn btn-neutral float-right" title="Documentation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="hintsecmwf.html" class="btn btn-neutral float-left" title="Hints to specify dataset retrieval" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="hintsecmwf.html" class="btn btn-neutral float-left" title="Hints for data set selection" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Ecmwf/hintsecmwf.html b/Documentation/html/Ecmwf/hintsecmwf.html
index f25c6a6e72235768ec69204fa0ba7d14168265f4..697c36c17c49bb41279207761bb3369f6eb05cd3 100644
--- a/Documentation/html/Ecmwf/hintsecmwf.html
+++ b/Documentation/html/Ecmwf/hintsecmwf.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Hints to specify dataset retrieval — flex_extract 7.1 alpha documentation</title>
+ <title>Hints for data set selection — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Link Collection for Quick finder" href="ec-links.html" />
- <link rel="prev" title="Available Datasets for Public users" href="pubdata.html" />
+ <link rel="next" title="Link collection" href="ec-links.html" />
+ <link rel="prev" title="Available data sets for public users" href="pubdata.html" />
</head>
<body class="wy-body-for-nav">
@@ -92,16 +92,16 @@
<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="access.html">Access Modes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available Datasets for Member State users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available Datasets for Public users</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Hints to specify dataset retrieval</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#how-can-i-find-out-what-data-is-available">How can I find out what data is available?</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="access.html">Access modes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available data sets for member-state users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available data sets for public users</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Hints for data set selection</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#how-can-i-find-out-what-data-are-available">How can I find out what data are available?</a><ul class="simple">
</ul>
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link Collection for Quick finder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link collection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
@@ -158,7 +158,7 @@
<li><a href="../ecmwf_data.html">ECMWF Data</a> »</li>
- <li>Hints to specify dataset retrieval</li>
+ <li>Hints for data set selection</li>
<li class="wy-breadcrumbs-aside">
@@ -177,18 +177,18 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="hints-to-specify-dataset-retrieval">
-<h1>Hints to specify dataset retrieval<a class="headerlink" href="#hints-to-specify-dataset-retrieval" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="hints-for-data-set-selection">
+<h1>Hints for data set selection<a class="headerlink" href="#hints-for-data-set-selection" title="Permalink to this headline">¶</a></h1>
<div class="contents local topic" id="contents">
<ul class="simple">
-<li><p><a class="reference internal" href="#how-can-i-find-out-what-data-is-available" id="id1">How can I find out what data is available?</a></p></li>
+<li><p><a class="reference internal" href="#how-can-i-find-out-what-data-are-available" id="id1">How can I find out what data are available?</a></p></li>
</ul>
</div>
-<div class="section" id="how-can-i-find-out-what-data-is-available">
-<h2><a class="toc-backref" href="#id1">How can I find out what data is available?</a><a class="headerlink" href="#how-can-i-find-out-what-data-is-available" title="Permalink to this headline">¶</a></h2>
-<p>Go to the <a class="reference external" href="http://apps.ecmwf.int/archive-catalogue/">Web Interface for accessing member state datasets</a>
+<div class="section" id="how-can-i-find-out-what-data-are-available">
+<h2><a class="toc-backref" href="#id1">How can I find out what data are available?</a><a class="headerlink" href="#how-can-i-find-out-what-data-are-available" title="Permalink to this headline">¶</a></h2>
+<p>Go to the <a class="reference external" href="http://apps.ecmwf.int/archive-catalogue/">Web Interface for accessing member-state data sets</a>
and click yourself through the steps to define your set of data and see what is available to you.</p>
-<p>For public users there is the <a class="reference external" href="http://apps.ecmwf.int/datasets/">Web Interface for accessing public datasets</a>.</p>
+<p>For public users there is the <a class="reference external" href="http://apps.ecmwf.int/datasets/">Web Interface for accessing public data sets</a>.</p>
<div class="toctree-wrapper compound">
</div>
</div>
@@ -202,10 +202,10 @@ and click yourself through the steps to define your set of data and see what is
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="ec-links.html" class="btn btn-neutral float-right" title="Link Collection for Quick finder" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="ec-links.html" class="btn btn-neutral float-right" title="Link collection" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="pubdata.html" class="btn btn-neutral float-left" title="Available Datasets for Public users" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="pubdata.html" class="btn btn-neutral float-left" title="Available data sets for public users" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Ecmwf/msdata.html b/Documentation/html/Ecmwf/msdata.html
index 7d80d2e0e55075ad04db6e4c6a69364b4d30768a..9e5eefb49aa90d036e010e0397bb0c1d142a7732 100644
--- a/Documentation/html/Ecmwf/msdata.html
+++ b/Documentation/html/Ecmwf/msdata.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Available Datasets for Member State users — flex_extract 7.1 alpha documentation</title>
+ <title>Available data sets for member-state users — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Available Datasets for Public users" href="pubdata.html" />
- <link rel="prev" title="Access Modes" href="access.html" />
+ <link rel="next" title="Available data sets for public users" href="pubdata.html" />
+ <link rel="prev" title="Access modes" href="access.html" />
</head>
<body class="wy-body-for-nav">
@@ -92,17 +92,17 @@
<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="access.html">Access Modes</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Available Datasets for Member State users</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#model-level-data">Model level data</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#surface-level-data">Surface level data</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="access.html">Access modes</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Available data sets for member-state users</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#model-level-data">Model-level data</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#surface-data">Surface data</a><ul class="simple">
</ul>
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available Datasets for Public users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints to specify dataset retrieval</a></li>
-<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link Collection for Quick finder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pubdata.html">Available data sets for public users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints for data set selection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link collection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
@@ -159,7 +159,7 @@
<li><a href="../ecmwf_data.html">ECMWF Data</a> »</li>
- <li>Available Datasets for Member State users</li>
+ <li>Available data sets for member-state users</li>
<li class="wy-breadcrumbs-aside">
@@ -178,16 +178,16 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="available-datasets-for-member-state-users">
-<h1>Available Datasets for Member State users<a class="headerlink" href="#available-datasets-for-member-state-users" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="available-data-sets-for-member-state-users">
+<h1>Available data sets for member-state users<a class="headerlink" href="#available-data-sets-for-member-state-users" title="Permalink to this headline">¶</a></h1>
<div class="section" id="model-level-data">
-<h2>Model level data<a class="headerlink" href="#model-level-data" title="Permalink to this headline">¶</a></h2>
+<h2>Model-level data<a class="headerlink" href="#model-level-data" title="Permalink to this headline">¶</a></h2>
<div class="figure align-default">
<img alt="../_images/ECMWF_FPparameter_ml.png" src="../_images/ECMWF_FPparameter_ml.png" />
</div>
</div>
-<div class="section" id="surface-level-data">
-<h2>Surface level data<a class="headerlink" href="#surface-level-data" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="surface-data">
+<h2>Surface data<a class="headerlink" href="#surface-data" title="Permalink to this headline">¶</a></h2>
<div class="figure align-default">
<img alt="../_images/ECMWF_FPparameter_sfc-0.png" src="../_images/ECMWF_FPparameter_sfc-0.png" />
</div>
@@ -207,10 +207,10 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="pubdata.html" class="btn btn-neutral float-right" title="Available Datasets for Public users" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="pubdata.html" class="btn btn-neutral float-right" title="Available data sets for public users" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="access.html" class="btn btn-neutral float-left" title="Access Modes" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="access.html" class="btn btn-neutral float-left" title="Access modes" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Ecmwf/pubdata.html b/Documentation/html/Ecmwf/pubdata.html
index 0357524ed95091ca534c1f114b3bd16ddd359f6b..32205a99dcf89cbe97f4baca0b75930f587ce857 100644
--- a/Documentation/html/Ecmwf/pubdata.html
+++ b/Documentation/html/Ecmwf/pubdata.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Available Datasets for Public users — flex_extract 7.1 alpha documentation</title>
+ <title>Available data sets for public users — flex_extract 7.1 alpha documentation</title>
@@ -38,8 +38,8 @@
<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="Hints to specify dataset retrieval" href="hintsecmwf.html" />
- <link rel="prev" title="Available Datasets for Member State users" href="msdata.html" />
+ <link rel="next" title="Hints for data set selection" href="hintsecmwf.html" />
+ <link rel="prev" title="Available data sets for member-state users" href="msdata.html" />
</head>
<body class="wy-body-for-nav">
@@ -92,13 +92,13 @@
<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="access.html">Access Modes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available Datasets for Member State users</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Available Datasets for Public users</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="access.html">Access modes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="msdata.html">Available data sets for member-state users</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Available data sets for public users</a><ul class="simple">
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints to specify dataset retrieval</a></li>
-<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link Collection for Quick finder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hintsecmwf.html">Hints for data set selection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ec-links.html">Link collection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
@@ -155,7 +155,7 @@
<li><a href="../ecmwf_data.html">ECMWF Data</a> »</li>
- <li>Available Datasets for Public users</li>
+ <li>Available data sets for public users</li>
<li class="wy-breadcrumbs-aside">
@@ -174,10 +174,10 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="available-datasets-for-public-users">
-<h1>Available Datasets for Public users<a class="headerlink" href="#available-datasets-for-public-users" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="available-data-sets-for-public-users">
+<h1>Available data sets for public users<a class="headerlink" href="#available-data-sets-for-public-users" title="Permalink to this headline">¶</a></h1>
<blockquote>
-<div><p>IN PREPARATION</p>
+<div><p>UNDER PREPARATION</p>
</div></blockquote>
<div class="toctree-wrapper compound">
</div>
@@ -191,10 +191,10 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="hintsecmwf.html" class="btn btn-neutral float-right" title="Hints to specify dataset retrieval" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="hintsecmwf.html" class="btn btn-neutral float-right" title="Hints for data set selection" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="msdata.html" class="btn btn-neutral float-left" title="Available Datasets for Member State users" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="msdata.html" class="btn btn-neutral float-left" title="Available data sets for member-state users" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Evaluation/staticcode.html b/Documentation/html/Evaluation/staticcode.html
index c7a1afb7242d837e9436a0e1c1d695a8be070878..4dd23bc397b9b59621d607ca9f1838568ce0c891 100644
--- a/Documentation/html/Evaluation/staticcode.html
+++ b/Documentation/html/Evaluation/staticcode.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Static Code Analysis — flex_extract 7.1 alpha documentation</title>
+ <title>Static code analysis — flex_extract 7.1 alpha documentation</title>
@@ -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="Testcases" href="testcases.html" />
+ <link rel="next" title="Test cases" href="testcases.html" />
<link rel="prev" title="Evaluation" href="../evaluation.html" />
</head>
@@ -94,10 +94,10 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../evaluation.html">Evaluation</a><ul class="current">
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Static Code Analysis</a><ul class="simple">
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Static code analysis</a><ul class="simple">
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="testcases.html">Testcases</a></li>
+<li class="toctree-l2"><a class="reference internal" href="testcases.html">Test cases</a></li>
<li class="toctree-l2"><a class="reference internal" href="metrics.html">Metrics</a></li>
</ul>
</li>
@@ -153,7 +153,7 @@
<li><a href="../evaluation.html">Evaluation</a> »</li>
- <li>Static Code Analysis</li>
+ <li>Static code analysis</li>
<li class="wy-breadcrumbs-aside">
@@ -173,7 +173,7 @@
<div itemprop="articleBody">
<div class="section" id="static-code-analysis">
-<h1>Static Code Analysis<a class="headerlink" href="#static-code-analysis" title="Permalink to this headline">¶</a></h1>
+<h1>Static code analysis<a class="headerlink" href="#static-code-analysis" title="Permalink to this headline">¶</a></h1>
<blockquote>
<div><p>UNDER CONSTRUCTION</p>
</div></blockquote>
@@ -189,7 +189,7 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="testcases.html" class="btn btn-neutral float-right" title="Testcases" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="testcases.html" class="btn btn-neutral float-right" title="Test cases" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="../evaluation.html" class="btn btn-neutral float-left" title="Evaluation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/Evaluation/testcases.html b/Documentation/html/Evaluation/testcases.html
index 3561b860ad298a89f272c21283d35b9aa711f13f..944014427f685da329c5f0c6d130e7fbc3d02680 100644
--- a/Documentation/html/Evaluation/testcases.html
+++ b/Documentation/html/Evaluation/testcases.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Testcases — flex_extract 7.1 alpha documentation</title>
+ <title>Test cases — flex_extract 7.1 alpha documentation</title>
@@ -39,7 +39,7 @@
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Metrics" href="metrics.html" />
- <link rel="prev" title="Static Code Analysis" href="staticcode.html" />
+ <link rel="prev" title="Static code analysis" href="staticcode.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,10 +94,10 @@
<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="../evaluation.html">Evaluation</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="staticcode.html">Static Code Analysis</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Testcases</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="staticcode.html">Static code analysis</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Test cases</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#comparison-of-mars-requests">Comparison of MARS requests</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#comparison-of-grib-files">Comparison of grib files</a><ul class="simple">
+<li class="toctree-l3"><a class="reference internal" href="#comparison-of-grib-files">Comparison of GRIB files</a><ul class="simple">
</ul>
</li>
</ul>
@@ -157,7 +157,7 @@
<li><a href="../evaluation.html">Evaluation</a> »</li>
- <li>Testcases</li>
+ <li>Test cases</li>
<li class="wy-breadcrumbs-aside">
@@ -176,8 +176,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="testcases">
-<h1>Testcases<a class="headerlink" href="#testcases" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="test-cases">
+<h1>Test cases<a class="headerlink" href="#test-cases" title="Permalink to this headline">¶</a></h1>
<div class="section" id="comparison-of-mars-requests">
<h2>Comparison of MARS requests<a class="headerlink" href="#comparison-of-mars-requests" title="Permalink to this headline">¶</a></h2>
<blockquote>
@@ -185,7 +185,7 @@
</div></blockquote>
</div>
<div class="section" id="comparison-of-grib-files">
-<h2>Comparison of grib files<a class="headerlink" href="#comparison-of-grib-files" title="Permalink to this headline">¶</a></h2>
+<h2>Comparison of GRIB files<a class="headerlink" href="#comparison-of-grib-files" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>UNDER CONSTRUCTION</p>
</div></blockquote>
@@ -205,7 +205,7 @@
<a href="metrics.html" class="btn btn-neutral float-right" title="Metrics" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="staticcode.html" class="btn btn-neutral float-left" title="Static Code Analysis" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="staticcode.html" class="btn btn-neutral float-left" title="Static code analysis" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/Installation/local.html b/Documentation/html/Installation/local.html
index 71c6bcd6884884b2f3a583db8f279755aa037830..7684e468c09f9c6513fdd15f30d7bbdf9b5a28d1 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">
@@ -99,8 +99,8 @@
<li class="toctree-l3"><a class="reference internal" href="gateway.html">Gateway mode installation</a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">Local mode installation</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#local-mode-dependencies">Local mode - dependencies</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#prepare-local-environment">Prepare local environment</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#test-local-environment">Test local environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#preparing-the-local-environment">Preparing the local environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#testing-the-local-environment">Testing the local environment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#local-installation">Local installation</a></li>
</ul>
</li>
@@ -192,7 +192,7 @@
<div class="section" id="local-mode-dependencies">
<span id="ref-req-local"></span><span id="ref-local-mode"></span><h2>Local mode - dependencies<a class="headerlink" href="#local-mode-dependencies" title="Permalink to this headline">¶</a></h2>
<p>The installation is the same for the access modes <strong>member</strong> and <strong>public</strong>.</p>
-<p>The environment on your local system has to provide these software packages
+<p>The environment on your local system has to provide the following software packages
and libraries, since the preparation of the extraction and the post-processing is done on the local machine:</p>
<table class="docutils align-default">
<colgroup>
@@ -203,32 +203,33 @@ and libraries, since the preparation of the extraction and the post-processing i
<tr class="row-odd"><td><p>Python part</p></td>
<td><p>Fortran part</p></td>
</tr>
-<tr class="row-even"><td><ul class="simple">
+<tr class="row-even"><td><ol class="arabic simple">
<li><p><a class="reference external" href="https://www.python.org/downloads/">Python3</a></p></li>
<li><p><a class="reference external" href="http://www.numpy.org/">numpy</a></p></li>
<li><p><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></p></li>
<li><p><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></p></li>
<li><p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</p></li>
<li><p><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5 and member user)</p></li>
-</ul>
+</ol>
</td>
-<td><ul class="simple">
+<td><ol class="arabic simple">
<li><p><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></p></li>
<li><p><a class="reference external" href="http://www.fftw.org">fftw3</a></p></li>
<li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></p></li>
<li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></p></li>
-</ul>
+</ol>
</td>
</tr>
</tbody>
</table>
</div>
-<div class="section" id="prepare-local-environment">
-<span id="ref-prep-local"></span><h2>Prepare local environment<a class="headerlink" href="#prepare-local-environment" title="Permalink to this headline">¶</a></h2>
-<p>The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights.
+<div class="section" id="preparing-the-local-environment">
+<span id="ref-prep-local"></span><h2>Preparing the local environment<a class="headerlink" href="#preparing-the-local-environment" title="Permalink to this headline">¶</a></h2>
+<p>The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights.
The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p>
-<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager):</span>
-<span class="c1"># (if not already available):</span>
+<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Debian or Debian-derived (e. g. Ubuntu) system,</span>
+<span class="c1"># you may use the following commands (or equivalent commands of your preferred package manager):</span>
+<span class="c1"># (if respective packages are not already available):</span>
apt-get install python3 <span class="o">(</span>usually already available on GNU/Linux systems<span class="o">)</span>
apt-get install python3-eccodes
apt-get install python3-genshi
@@ -237,10 +238,12 @@ The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubu
apt-get install fftw3-dev
apt-get install libeccodes-dev
apt-get install libemos-dev
-<span class="c1"># Some of these packages will pull in further packages as dependencies. This is fine, and some are even needed by ``flex_extract''.</span>
-
+<span class="c1"># Some of these packages will pull in further packages as dependencies.</span>
+<span class="c1"># This is fine, and some are even needed by ``flex_extract''.</span>
-<span class="c1"># As currently the CDS and ECMWF API packages are not available as Debian packages, they need to be installed outside of the Debian (Ubuntu etc.) package management system. The recommended way is:</span>
+<span class="c1"># As currently the CDS and ECMWF API packages are not available as Debian packages,</span>
+<span class="c1"># they need to be installed outside of the Debian (Ubuntu etc.) package management system.</span>
+<span class="c1"># The recommended way is:</span>
apt-get install pip
pip install cdsapi
pip install ecmwf-api-client
@@ -248,39 +251,41 @@ The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubu
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>In case you would like to use Anaconda Python we recommend you follow the installation instructions of
-<a class="reference external" href="https://docs.anaconda.com/anaconda/install/linux/">Anaconda Python Installation for Linux</a> and then install the
-<code class="docutils literal notranslate"><span class="pre">eccodes</span></code> package from <code class="docutils literal notranslate"><span class="pre">conda</span></code> with:</p>
+<p>If you are using Anaconda Python, we recommend to follow the installation instructions of
+<a class="reference external" href="https://docs.anaconda.com/anaconda/install/linux/">Anaconda Python Installation for Linux</a>
+and then install the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> package from <code class="docutils literal notranslate"><span class="pre">conda</span></code> with:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install conda-forge::python-eccodes
</pre></div>
</div>
</div>
-<p>The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.</p>
+<p>The CDS API (<code class="docutils literal notranslate"><span class="pre">cdsapi</span></code>) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>Since <strong>public users</strong> currently don’t have access to the full <em>ERA5</em> dataset they can skip the installation of the <code class="docutils literal notranslate"><span class="pre">CDS</span> <span class="pre">API</span></code>.</p>
+<p>Since <strong>public users</strong> currently don’t have access to the full <em>ERA5</em> dataset, they can skip the installation of the CDS API.</p>
</div>
-<p>Both user groups have to provide keys with their credentials for the Web API’s in their home directory. Therefore, follow these instructions:</p>
+<p>Both user groups have to provide keys with their credentials for the Web APIs in their home directory, following these instructions:</p>
<dl class="simple">
-<dt>ECMWF Web API:</dt><dd><p>Go to <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, on this site in section “Install ECMWF KEY” the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file <cite>.ecmwfapirc</cite> in your home directory).</p>
+<dt>ECMWF Web API:</dt><dd><p>Go to the <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, go to the section “Install ECMWF KEY”, where the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file <code class="docutils literal notranslate"><span class="pre">.ecmwfapirc</span></code> in your home directory).</p>
</dd>
-<dt>CDS API:</dt><dd><p>Go to <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">CDS API registration</a> and register there too. Log in at the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> website and follow the instructions at section “Install the CDS API key” to save your credentials in a <cite>.cdsapirc</cite> file.</p>
+<dt>CDS API:</dt><dd><p>Go to <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">CDS API registration</a> and register there, too. Log in on the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> website and follow the instructions in the section “Install the CDS API key” to save your credentials in file <code class="docutils literal notranslate"><span class="pre">.cdsapirc</span></code>.</p>
</dd>
</dl>
</div>
-<div class="section" id="test-local-environment">
-<span id="ref-test-local"></span><h2>Test local environment<a class="headerlink" href="#test-local-environment" title="Permalink to this headline">¶</a></h2>
-<p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell. If there are no error messages, you succeeded in setting up the environment.</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
-<span class="kn">import</span> <span class="nn">eccodes</span>
-<span class="kn">import</span> <span class="nn">genshi</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-<span class="kn">import</span> <span class="nn">cdsapi</span>
-<span class="kn">import</span> <span class="nn">ecmwfapi</span>
-</pre></div>
-</div>
-<div class="section" id="test-the-web-api-s">
-<h3>Test the Web API’s<a class="headerlink" href="#test-the-web-api-s" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="testing-the-local-environment">
+<span id="ref-test-local"></span><h2>Testing the local environment<a class="headerlink" href="#testing-the-local-environment" title="Permalink to this headline">¶</a></h2>
+<p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell:
+.. code-block:: python</p>
+<blockquote>
+<div><p># check in python3 console
+import eccodes
+import genshi
+import numpy
+import cdsapi
+import ecmwfapi</p>
+</div></blockquote>
+<p>If there are no error messages, you succeeded in setting up the environment.</p>
+<div class="section" id="testing-the-web-apis">
+<h3>Testing the Web APIs<a class="headerlink" href="#testing-the-web-apis" title="Permalink to this headline">¶</a></h3>
<p>You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> later on.</p>
<div class="section" id="ecmwf-web-api">
<h4>ECMWF Web API<a class="headerlink" href="#ecmwf-web-api" title="Permalink to this headline">¶</a></h4>
@@ -290,8 +295,8 @@ The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubu
<col style="width: 50%" />
</colgroup>
<tbody>
-<tr class="row-odd"><td><p>Please use this piece of Python code for <strong>Member user</strong>:</p></td>
-<td><p>Please use this piece of Python code for <strong>Public user</strong>:</p></td>
+<tr class="row-odd"><td><p>Please use this Python code snippet as a <strong>Member user</strong>:</p></td>
+<td><p>Please use this Python code snippet as a <strong>Public user</strong>:</p></td>
</tr>
<tr class="row-even"><td><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ecmwfapi</span> <span class="kn">import</span> <span class="n">ECMWFService</span>
@@ -340,7 +345,7 @@ The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubu
<div class="section" id="cds-api">
<h4>CDS API<a class="headerlink" href="#cds-api" title="Permalink to this headline">¶</a></h4>
<p>Extraction of ERA5 data via CDS API might take time as currently there is a high demand for ERA5 data. Therefore, as a simple test for the API just retrieve pressure-level data (even if that is NOT what we need for FLEXPART), as they are stored on disk and don’t need to be retrieved from MARS (which is the time-consuming action):</p>
-<p>Please use this piece of Python code to retrieve a small sample of <em>ERA5</em> pressure levels:</p>
+<p>Please use the following Python code snippet to retrieve a small sample of <em>ERA5</em> pressure level data:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">cdsapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span>
@@ -360,7 +365,7 @@ The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubu
</pre></div>
</div>
<p>If you know that your CDS API works, you can try to extract some data from MARS.</p>
-<p>Please use this piece of Python code to retrieve a small <em>ERA5</em> data sample as a <strong>member-state user</strong>! The <strong>Public user</strong> do not have access to the full <em>ERA5</em> dataset!</p>
+<p>Please use the following Python code snippet to retrieve a small <em>ERA5</em> data sample as a <strong>member-state user</strong>! The <strong>Public user</strong> do not have access to the full <em>ERA5</em> dataset!</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">cdsapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span>
@@ -388,22 +393,20 @@ The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubu
</div>
<div class="section" id="local-installation">
<span id="ref-install-local"></span><h2>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline">¶</a></h2>
-<p>First prepare the Fortran <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for your environment and set it in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script. (See section <a class="reference internal" href="../Documentation/Input/fortran_makefile.html#ref-convert"><span class="std std-ref">Fortran Makefile</span></a> for more information.)
-<code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> comes with two <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> prepared for the <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> compiler. One for the normal use <code class="docutils literal notranslate"><span class="pre">makefile_fast</span></code> and one for debugging <code class="docutils literal notranslate"><span class="pre">makefile_debug</span></code> which is usually only resonable for developers.</p>
-<p>They assume that <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> and <code class="docutils literal notranslate"><span class="pre">emoslib</span></code> are installed as distribution packages and can be found at <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p>
+<p>First, adapt the Fortran <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for your environment (if necessary) and insert it into <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script (see <a class="reference internal" href="../Documentation/Input/fortran_makefile.html#ref-convert"><span class="std std-ref">Fortran Makefile</span></a> for more information).
+They can be found at <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran/</span></code>, where <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted by the current flex_extract version number.</p>
<div class="admonition caution">
<p class="admonition-title">Caution</p>
<p>It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> in these
<code class="docutils literal notranslate"><span class="pre">makefiles</span></code> if other than standard paths are used.</p>
</div>
-<p>So starting from the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>,
-go to the <code class="docutils literal notranslate"><span class="pre">Fortran</span></code> source directory and open the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> of your
-choice to modify with an editor of your choice. We use the <code class="docutils literal notranslate"><span class="pre">nedit</span></code> in this case.</p>
+<p>Thus, go to the <code class="docutils literal notranslate"><span class="pre">Fortran</span></code> source directory and open the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> of your
+choice, and check / modify with an editor of your choice:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X/Source/Fortran
nedit makefile_fast
</pre></div>
</div>
-<p>Edit the paths to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine.</p>
+<p>Set the paths to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine, if necessary.</p>
<div class="admonition caution">
<p class="admonition-title">Caution</p>
<p>This can vary from system to system.
@@ -416,18 +419,18 @@ $ dpkg -L libeccodes-dev <span class="p">|</span> grep libeccodes.so
</div>
<p>to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p>
</div>
-<p>Substitute these paths in the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for parameters <strong>ECCODES_INCLUDE_DIR</strong>
-and <strong>ECCODES_LIB</strong> and save it.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># these are the paths on a current Debian 10 Testing system (May 2019)</span>
+<p>Assign these paths to the parameters <strong>ECCODES_INCLUDE_DIR</strong>
+and <strong>ECCODES_LIB</strong> in the makefile, and save it.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># these are the paths on Debian Buster:</span>
<span class="nv">ECCODES_INCLUDE_DIR</span><span class="o">=</span>/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
<span class="nv">ECCODES_LIB</span><span class="o">=</span> -L/usr/lib -leccodes_f90 -leccodes -lm
</pre></div>
</div>
<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during the
-installation process.Therefore the name of the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> to be used needs to be given in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p>
+installation process. Therefore, the name of the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> to be used needs to be given in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p>
<p>In the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, open the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script
-and adapt the installation parameters in the section labelled with
-“AVAILABLE COMMANDLINE ARGUMENTS TO SET” like shown below.</p>
+with an editor and adapt the installation parameters in the section labelled with
+“AVAILABLE COMMANDLINE ARGUMENTS TO SET” as shown below:</p>
<div class="literal-block-wrapper docutils container" id="setup-sh">
<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-sh" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
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/Documentation/Api/api_fortran.rst.txt b/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt
index 1bb81d5baf120630908ebec4a5bac9a6f4c624e2..16ad7c833688202b6aa5bce8814cc99aba7f1062 100644
--- a/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt
+++ b/Documentation/html/_sources/Documentation/Api/api_fortran.rst.txt
@@ -1,26 +1,14 @@
-**************************************
-Fortran's Auto Generated Documentation
-**************************************
+******************************************************
+Auto-generated documentation for the Fortran programme
+******************************************************
.. contents::
:local:
-
-
-Link to other documentation!
-
+
+`Fortran API <Fortran/index.html>`_
-
-
-.... f:autoprogram:: preconvert
-
-
-
.. toctree::
:hidden:
:maxdepth: 2
-
-
-
-
diff --git a/Documentation/html/_sources/Documentation/Api/api_python.rst.txt b/Documentation/html/_sources/Documentation/Api/api_python.rst.txt
index 724892ec33987c1c962692b2f10896a6a6641cc1..3be98adfa342acb7df40be76f0bca567bd5490d7 100644
--- a/Documentation/html/_sources/Documentation/Api/api_python.rst.txt
+++ b/Documentation/html/_sources/Documentation/Api/api_python.rst.txt
@@ -1,6 +1,6 @@
-*************************************
-Python's Auto Generated Documentation
-*************************************
+***************************************************
+Auto-generated documentation for the Python scripts
+***************************************************
.. contents::
:local:
diff --git a/Documentation/html/_sources/Documentation/Input/changes.rst.txt b/Documentation/html/_sources/Documentation/Input/changes.rst.txt
index 4f11b051c9cd9d394a88fc99a7e2e9dddc768a8e..0c3b257f5e674fd0c609c1c1106cfeee73f736df 100644
--- a/Documentation/html/_sources/Documentation/Input/changes.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/changes.rst.txt
@@ -7,8 +7,8 @@ Changes from version 7.0.4 to version 7.1
- grid resolution not in 1/1000 degress anymore (but is still available for downward compatibility)
- comments available with ``#``
- only parameters which are needed to override the default values are necessary
- - number of type/step/time elements do not have to be 24 any more. Just select the interval you need.
- - the ``dtime`` parameter needs to be consistent with ``type/step/time``. For example ``dtime`` can be coarser as ``time`` intervals are available, but not finer.
+ - number of type/step/time elements does not have to be 24 anymore. Just provide what you need.
+ - the ``dtime`` parameter needs to be consistent with ``type/step/time``, for example, ``dtime`` can be coarser than the ``time`` intervals available, but not finer.
diff --git a/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt b/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
index 9c7c3000a35657801bc7de9b7f1cb51c4d5bb999..7eac32c0626ae8e63276c2a80f30eb6dc12eaed3 100644
--- a/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
@@ -1,14 +1,14 @@
-********************************************
-The Compilation Jobscript ``compilejob.ksh``
-********************************************
+*********************************************
+The compilation job script ``compilejob.ksh``
+*********************************************
-The compilejob is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
+The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
-``Flex_extract`` uses the python package `genshi <https://genshi.edgewall.org/>`_ to generate
+``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
-The jobscript has a number of settings for the batch system which are fixed and differentiates between the *ecgate* and the *cca/ccb*
+The job script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
The submission is done by the ``ECaccess`` tool from within ``flex_extract`` with the command ``ecaccess-job-submit``.
@@ -18,13 +18,13 @@ The submission is done by the ``ECaccess`` tool from within ``flex_extract`` wit
What does the compilation script do?
------------------------------------
- #. It sets necessary batch system parameters
+ #. It sets the necessary batch-system parameters
#. It prepares the job environment at the ECMWF servers by loading the necessary library modules
- #. It sets some environment variabels for the single session
+ #. It sets some environment variables for the single session
#. It creates the ``flex_extract`` root directory in the ``$HOME`` path of the user
- #. It untars the tar-ball into the root directory.
- #. It compiles the Fortran programs's ``Makefile``.
- #. At the end it checks if the script returned an error or not and send the log file via email to the user.
+ #. It untars the tarball into the root directory.
+ #. It compiles the Fortran program using ``Makefile``.
+ #. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
diff --git a/Documentation/html/_sources/Documentation/Input/control.rst.txt b/Documentation/html/_sources/Documentation/Input/control.rst.txt
index fb770de664ca9a11a62bc68d4b912119711d4817..13e5baa2d05c50773145b0218b05ed9fcaf2c279 100644
--- a/Documentation/html/_sources/Documentation/Input/control.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/control.rst.txt
@@ -9,34 +9,34 @@ The CONTROL file
This file is an input file for :literal:`flex_extract's` main script :literal:`submit.py`.
-It contains the controlling parameters :literal:`flex_extract` needs to decide on dataset specifications,
-handling of the retrieved data and general bahaviour. The naming convention is usually (but not necessary):
+It contains the controlling parameters which :literal:`flex_extract` needs to decide on data set specifications,
+handling of the data retrieved, and general behaviour. The naming convention is usually (but not necessarily):
:literal:`CONTROL_<Dataset>[.optionalIndications]`
-The tested datasets are the operational dataset and the re-analysis datasets CERA-20C, ERA5 and ERA-Interim.
-The optional extra indications for the re-analysis datasets mark the files for *public users*
-and *global* domain. For the operational datasets (*OD*) the file names contain also information of
-the stream, the field type for forecasts, the method for extracting the vertical coordinate and other things like time or horizontal resolution.
+There are a number of data sets for which the procedures have been tested, the operational data and the re-analysis datasets CERA-20C, ERA5, and ERA-Interim.
+The optional indications for the re-analysis data sets mark the files for *public users*
+and *global* domain. For the operational data sets (*OD*), the file names contain also information of
+the stream, the field type for forecasts, the method for extracting the vertical wind, and other information such as temporal or horizontal resolution.
Format of CONTROL files
----------------------------------
The first string of each line is the parameter name, the following string(s) (separated by spaces) is (are) the parameter values.
-The parameters can be sorted in any order with one parameter per line.
+The parameters can be listed in any order with one parameter per line.
Comments are started with a '#' - sign. Some of these parameters can be overruled by the command line
parameters given to the :literal:`submit.py` script.
-All parameters have default values. Only those parameters which have to be changed
-must be listed in the :literal:`CONTROL` files.
+All parameters have default values; only those parameters which deviate from default
+have be listed in the :literal:`CONTROL` files.
Example CONTROL files
--------------------------------
A number of example files can be found in the directory :literal:`flex_extract_vX.X/Run/Control/`.
-They can be used as a template for adaptations and understand what's possible to
-retrieve from ECMWF's archive.
-For each main dataset there is an example and additionally some variances in resolution, type of field or type of retrieving the vertical coordinate.
+They can be used as a template for adaptation, and to understand what can be
+retrievee from ECMWF's archives.
+There is an example for each main data set, and in addition, some more varied with respect to resolution, type of field, or way of retrieving the vertical wind.
@@ -44,8 +44,9 @@ For each main dataset there is an example and additionally some variances in res
CONTROL file
------------
The file :literal:`CONTROL.documentation` documents the available parameters
-in grouped sections with their default values. In :doc:`control_params` you can find a more
-detailed description with additional hints, possible values and some useful information about
+in grouped sections together with their default values.
+In :doc:`control_params`, you can find a more
+detailed description with additional hints, possible values, and further information about
the setting of these parameters.
.. literalinclude:: ../../../../../Run/Control/CONTROL.documentation
diff --git a/Documentation/html/_sources/Documentation/Input/control_params.rst.txt b/Documentation/html/_sources/Documentation/Input/control_params.rst.txt
index d505c9871963f4773e523aa8e1125e98c789304a..60fa4dc03e5041ff380b1a5ce126af415ceee380 100644
--- a/Documentation/html/_sources/Documentation/Input/control_params.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/control_params.rst.txt
@@ -10,7 +10,7 @@ The CONTROL parameters
User Section
************
-.. exceltable:: User parameter in CONTROL file
+.. exceltable:: User parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: UserSection
:header: 1
@@ -20,7 +20,7 @@ User Section
General Section
***************
-.. exceltable:: General parameter in CONTROL file
+.. exceltable:: General parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: GeneralSection
:header: 1
@@ -30,7 +30,7 @@ General Section
Time Section
************
-.. exceltable:: Time parameter in CONTROL file
+.. exceltable:: Time parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: TimeSection
:header: 1
@@ -41,7 +41,7 @@ Time Section
Data Section
************
-.. exceltable:: Data parameter in CONTROL file
+.. exceltable:: Data parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: DataSection
:header: 1
@@ -52,7 +52,7 @@ Data Section
Data field Section
******************
-.. exceltable:: Data field parameter in CONTROL file
+.. exceltable:: Data field parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: DatafieldsSection
:header: 1
@@ -63,7 +63,7 @@ Data field Section
Flux data Section
*****************
-.. exceltable:: Flux data parameter in CONTROL file
+.. exceltable:: Flux data parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: FluxDataSection
:header: 1
@@ -74,7 +74,7 @@ Flux data Section
Domain Section
**************
-.. exceltable:: Domain parameter in CONTROL file
+.. exceltable:: Domain parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: DomainSection
:header: 1
@@ -98,7 +98,7 @@ Vertical wind Section
Additional data Section
***********************
-.. exceltable:: Additional data parameter in CONTROL file
+.. exceltable:: Additional data parameters in CONTROL file
:file: ../../_files/CONTROLparameter.xls
:sheet: AddDataSection
:header: 1
diff --git a/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt b/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt
index 057136caee885f01651f2490160f433584883fba..565b5a9c7af88b675defbaed8aff931bd794631e 100644
--- a/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt
@@ -1,5 +1,5 @@
****************************************
-ECMWF User Credential file ``ECMWF_ENV``
+ECMWF user credential file ``ECMWF_ENV``
****************************************
This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/Run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
@@ -15,7 +15,7 @@ This file is based on the template ``ECMWF_ENV.template`` which is located in th
Content of ``ECMWF_ENV``
------------------------
-The following shows an example of the content of an ``ECMWF_ENV`` file:
+An example of the content of an ``ECMWF_ENV`` file is shown below:
.. code-block:: bash
diff --git a/Documentation/html/_sources/Documentation/Input/examples.rst.txt b/Documentation/html/_sources/Documentation/Input/examples.rst.txt
index c61b1a54076329f417b4ebc258b2dbf899db2ff1..f69fd02641edbf9e42e102092decaf1b8286a96a 100644
--- a/Documentation/html/_sources/Documentation/Input/examples.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/examples.rst.txt
@@ -2,12 +2,12 @@
CONTROL file examples
**********************
-``Flex_extract`` has a couple of example ``CONTROL`` files for a number of different data set constellations in the directory path ``flex_extract_vX.X/Run/Control``.
+``Flex_extract`` comes with a number of example ``CONTROL`` files for a number of different data set constellations in the directory path ``flex_extract_vX.X/Run/Control``.
-Here is a list of the example files and a description of the data set:
+Here is a list of the example files:
CONTROL.documentation
- This file is not intended to be used with ``flex_extract``. It has a list of all possible parameters and their default values for a quick overview.
+ This file is not intended to be used with ``flex_extract``. It just contains a list of all possible parameters and their default values for a quick overview.
.. code-block:: bash
@@ -32,10 +32,13 @@ CONTROL.documentation
CONTROL_OD.OPER.FC.eta.highres
CONTROL_OD.OPER.FC.gauss.highres
CONTROL_OD.OPER.FC.operational
- CONTROL_OD.OPER.FC.twiceaday.1hourly
- CONTROL_OD.OPER.FC.twiceaday.3hourly
+ CONTROL_OD.OPER.FC.twicedaily.1hourly
+ CONTROL_OD.OPER.FC.twicedaily.3hourly
-
+.. todo::
+
+ #PS some information to be added.
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/Documentation/html/_sources/Documentation/Input/fortran_makefile.rst.txt b/Documentation/html/_sources/Documentation/Input/fortran_makefile.rst.txt
index e176135d4d176861cf1c168a68953ada23851f47..b88cbd41a0633cf36994cf752db41039504e9080 100644
--- a/Documentation/html/_sources/Documentation/Input/fortran_makefile.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/fortran_makefile.rst.txt
@@ -1,40 +1,35 @@
-**************************************
-The Fortran Makefile - ``calc_etadot``
-**************************************
+****************************************
+The Fortran makefile for ``calc_etadot``
+****************************************
.. _ref-convert:
-``Flex_extract``'s Fortran program will be compiled during
-the installation process to get the executable named ``calc_etadot``.
+The Fortran program ``calc_etadot`` will be compiled during
+the installation process to produce the executable called ``calc_etadot``.
-``Flex_extract`` has a couple of ``makefiles`` prepared which can be found in the directory
-``flex_extract_vX.X/Source/Fortran``, where ``vX.X`` should be substituted with the current version number.
-A list of these ``makefiles`` are shown below:
+``Flex_extract`` includes several ``makefiles`` which can be found in the directory
+``flex_extract_vX.X/Source/Fortran``, where ``vX.X`` should be substituted by the current flex_extract version number.
+A list of these ``makefiles`` is shown below:
| **Remote/Gateway mode**:
| Files to be used as they are!
- | **makefile_ecgate**
- | For the use on ECMWF's server **ecgate**.
-
- | **makefile_cray**
- | For the use on ECMWF's server **cca/ccb**.
+ | **makefile_ecgate**: For use on ECMWF's server **ecgate**.
+ | **makefile_cray**: For use on ECMWF's server **cca/ccb**.
| **Local mode**
-| It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB**
+| It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** if they don't correspond to the standard paths pre-set in the makefiles.
- | **makefile_fast**
- | For the use with gfortran compiler and optimization mode.
-
- | **makefile_debug**
- | For the use with gfortran compiler in debugging mode.
+ | **makefile_fast**: For use with the gfortran compiler and optimisation mode.
+ | **makefile_debug**: For use with the gfortran compiler and debugging mode. Primarily for developers.
+If you want to use another compiler than gfortran locally, you can still take ``makefile_fast``,
+and adapt everything that is compiler-specific in this file.
-For instructions on how to adapt the ``makefiles`` for the local application mode
+For instructions on how to adapt the ``makefile`` (local application mode only),
please see :ref:`ref-install-local`.
-
.. toctree::
:hidden:
diff --git a/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt b/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
index 466c91f34ae0c36d5afbca74fdb276d37a6c8c0d..24ef07e50e18d14a50b0976fa50a222ed3e2f0fc 100644
--- a/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
@@ -1,33 +1,33 @@
-*************************
-The Jobscript ``job.ksh``
-*************************
+**************************
+The job script ``job.ksh``
+**************************
-The jobscript is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
+The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
-It is based on the ``job.temp`` template file which is stored in the ``Templates`` directory.
-This template is by itself generated in the installation process from a ``job.template`` template file.
+It is based on the ``job.temp`` template file stored in the ``Templates`` directory.
+This template is generated in the installation process from a ``job.template`` template file.
-``Flex_extract`` uses the python package `genshi <https://genshi.edgewall.org/>`_ to generate
+``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
+These individual parameters are marked by ``$$`` in ``job.temp``.
-The jobscript has a number of settings for the batch system which are fixed and differentiates between the *ecgate* and the *cca/ccb*
+The job script has a number of settings for the batch system which are fixed, and differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
The submission is done by the ``ECaccess`` tool from within ``flex_extract`` with the command ``ecaccess-job-submit``.
-What does the jobscript do?
----------------------------
+What does the job script do?
+----------------------------
- #. It sets necessary batch system parameters
- #. It prepares the job environment at the ECMWF servers by loading the necessary library modules
- #. It sets some environment variabels for the single session
- #. It creates the directory structure in the users ``$SCRATCH`` file system
- #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are given to the jobscript with its default or the user defined values. It also sets the ``CONTROL`` as an environment variable.
- #. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new pathes for input and output directory and the recently generated ``CONTROL`` file.
- #. At the end it checks if the script returned an error or not and send the log file via email to the user.
+ #. It sets necessary batch system parameters.
+ #. It prepares the job environment at the ECMWF servers by loading the necessary library modules.
+ #. It sets some environment variables for the single session.
+ #. It creates the directory structure in the user's ``$SCRATCH`` file system.
+ #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
+ #. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new paths for input and output directories and the recently generated ``CONTROL`` file.
+ #. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
diff --git a/Documentation/html/_sources/Documentation/Input/run.rst.txt b/Documentation/html/_sources/Documentation/Input/run.rst.txt
index 658b89275a0eea08a37f2d53b15326a690ef2ce0..1e3ad685d5b5d23c1adea0e66b36a64a5f65aab1 100644
--- a/Documentation/html/_sources/Documentation/Input/run.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/run.rst.txt
@@ -1,23 +1,23 @@
**********************************
-The executable Script - ``run.sh``
+The executable script - ``run.sh``
**********************************
-The execution of ``flex_extract`` is done by the ``run.sh`` Shell script, which is a wrapping script for the top-level Python script ``submit.py``.
+The execution of ``flex_extract`` is done by the ``run.sh`` shell script, which is a wrapper script for the top-level Python script ``submit.py``.
The Python script constitutes the entry point to ECMWF data retrievals with ``flex_extract`` and controls the program flow.
-``submit.py`` has two (three) sources for input parameters with information about program flow and ECMWF data selection, the so-called ``CONTROL`` file,
-the command line parameters and the so-called ``ECMWF_ENV`` file. Whereby, the command line parameters will override the ``CONTROL`` file parameters.
+``submit.py`` has two (or three) sources for input parameters with information about program flow and ECMWF data selection, the so-called ``CONTROL`` file,
+the command line parameters, and the so-called ``ECMWF_ENV`` file. Command line parameters will override parameters specified in the ``CONTROL`` file.
-Based on these input information ``flex_extract`` applies one of the application modes to either retrieve the ECMWF data via a Web API on a local maschine or submit a jobscript to ECMWF servers and retrieve the data there with sending the files to the local system eventually.
+Based on this input information, ``flex_extract`` applies one of the application modes to either retrieve the ECMWF data via a web API on a local maschine, or submit a job script to an ECMWF server and retrieve the data there, and at the end sends the files to the local system.
-Submission Parameter
---------------------
+Submission parameters
+---------------------
-.. exceltable:: Parameter for Submission
+.. exceltable:: Parameters for submission
:file: ../../_files/SubmitParameters.xls
:header: 1
:sheet: 0
@@ -33,14 +33,14 @@ Content of ``run.sh``
:caption: run.sh
-.. _ref-install-script:
+
Usage of ``submit.py`` (optional)
---------------------------------
-It is also possible to start ``flex_extract`` directly from command line by using the ``submit.py`` script instead of the wrapping Shell script ``run.sh``. This top-level script is located in
-``flex_extract_vX.X/Source/Python`` and is executable. With the ``help`` parameter we see again all possible
-command line parameter.
+It is also possible to start ``flex_extract`` directly from command line by using the ``submit.py`` script instead of the wrapper shell script ``run.sh``. This top-level script is located in
+``flex_extract_vX.X/Source/Python`` and is executable. With the ``--help`` parameter
+we see again all possible command line parameters.
.. code-block:: bash
diff --git a/Documentation/html/_sources/Documentation/Input/setup.rst.txt b/Documentation/html/_sources/Documentation/Input/setup.rst.txt
index 05fce15064106a3afe4b0821d66974bb74cb6867..7160ae88978f273a89365d45e73b7564e4a4c306 100644
--- a/Documentation/html/_sources/Documentation/Input/setup.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/setup.rst.txt
@@ -1,25 +1,24 @@
**************************************
-The Installation Script - ``setup.sh``
+The installation script - ``setup.sh``
**************************************
+The installation of ``flex_extract`` is done by the shell script ``setup.sh`` located in the root directory of ``flex_extract``.
+It calls the top-level Python script ``install.py`` which does all the necessary operations to prepare the application environment selected. This includes:
-The installation of ``flex_extract`` is done by the Shell script ``setup.sh`` which is located in the root directory of ``flex_extract``.
-It calls the top-level Python script ``install.py`` which does all necessary operations to prepare the selected application environment. This includes:
-
-- preparing the file ``ECMWF_ENV`` with the user credentials for member state access to ECMWF servers (in **remote** and **gateway** mode)
+- preparing the file ``ECMWF_ENV`` with the user credentials for member-state access to ECMWF servers (in **remote** and **gateway** mode)
- preparation of a compilation Korn-shell script (in **remote** and **gateway** mode)
- preparation of a job template with user credentials (in **remote** and **gateway** mode)
-- create a tar-ball of all necessary files
-- copying tar-ball to target location (depending on application mode and installation path)
-- submit compilation script to batch queue at ECMWF servers (in **remote** and **gateway** mode) or just untar tar-ball at target location (**local mode**)
-- compilation of the FORTRAN90 program ``calc_etadot``
+- create a tarball of all necessary files
+- copying the tarball to the target location (depending on application mode and installation path)
+- submit the compilation script to the batch queue at ECMWF servers (in **remote** and **gateway** mode) or just untar the tarball at target location (**local mode**)
+- compilation of the Fortran program ``calc_etadot``
-The Python installation script ``install.py`` has a couple of command line arguments which are defined in ``setup.sh`` in the section labelled with "*AVAILABLE COMMANDLINE ARGUMENTS TO SET*". The user has to adapt these parameters for his personal use. The parameters are listed and described in :ref:`ref-instparams`. The script also does some checks to guarantee necessary parameters were set.
+The Python installation script ``install.py`` has several command line arguments defined in ``setup.sh``, in the section labelled "*AVAILABLE COMMANDLINE ARGUMENTS TO SET*". The user has to adapt these parameters according to his/her personal needs. The parameters are listed and described in :ref:`ref-instparams`. The script also does some checks to guarantee that the necessary parameters were set.
After the installation process, some tests can be conducted. They are described in section :ref:`ref-testinstallfe`.
-The following diagram sketches the involved files and scripts in the installation process:
+The following diagram sketches the files and scripts involved in the installation process:
.. _ref-install-blockdiag:
@@ -114,7 +113,7 @@ The following diagram sketches the involved files and scripts in the installatio
.. blockdiag::
- :caption: Diagram of data flow during the installation process. The trapezoids are input files with the light blue area being the template files. The edge-rounded, orange boxes are the executable files which start the installation process and reads the input files. The rectangular, green boxes are the output files. The light green files are files which are only needed in the remota and gateway mode.
+ :caption: Diagram of data flow during the installation process. Trapezoids are input files with the light blue area being the template files. Round-edge orange boxes are executable files which start the installation process and read the input files. Rectangular green boxes are output files. Light green files are needed only in the remota and gateway mode.
blockdiag {
@@ -132,8 +131,8 @@ The following diagram sketches the involved files and scripts in the installatio
.. _ref-instparams:
-Installation Parameter
-----------------------
+Installation parameters
+-----------------------
.. exceltable:: Parameter for Installation
:file: ../../_files/InstallationParameter.xls
@@ -154,9 +153,9 @@ Content of ``setup.sh``
Usage of ``install.py`` (optional)
----------------------------------
-It is also possible to start the installation process of ``flex_extract`` directly from command line by using the ``install.py`` script instead of the wrapping Shell script ``setup.sh``. This top-level script is located in
-``flex_extract_vX.X/Source/Python`` and is executable. With the ``help`` parameter we see again all possible
-command line parameter.
+It is also possible to start the installation process of ``flex_extract`` directly from the command line by using the ``install.py`` script instead of the wrapper shell script ``setup.sh``. This top-level script is located in
+``flex_extract_vX.X/Source/Python`` and is executable. With the ``--help`` parameter,
+we see again all possible command line parameters.
.. code-block:: bash
@@ -178,7 +177,7 @@ command line parameter.
program (default: None)
--ecuid ECUID The user id at ECMWF. (default: None)
--ecgid ECGID The group id at ECMWF. (default: None)
- --gateway GATEWAY The name of the local gateway server. (default: None)
+ --gateway GATEWAY The IP name (or IP address) of the local gateway server. (default: None)
--destination DESTINATION
The ecaccess association, e.g. myUser@genericSftp
(default: None)
diff --git a/Documentation/html/_sources/Documentation/Input/templates.rst.txt b/Documentation/html/_sources/Documentation/Input/templates.rst.txt
index 109175a39fa211a778cc407bd264f6a0ea593660..786679efaf40d9bb6eaced866ba44a1cb59800e3 100644
--- a/Documentation/html/_sources/Documentation/Input/templates.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/templates.rst.txt
@@ -2,19 +2,19 @@
Templates
*********
-In ``flex_extract`` we use the Python package `genshi <https://genshi.edgewall.org/>`_ to create specific files from templates. It is the most efficient way to be able to quickly adapt e.g. the job scripts send to the ECMWF batch queue system or the namelist file für the Fortran program without the need to change the program code.
+In ``flex_extract``, the Python package `genshi <https://genshi.edgewall.org/>`_ is used to create specific files from templates. It is the most efficient way to be able to quickly adapt, e. g., the job scripts sent to the ECMWF batch queue system, or the namelist file für the Fortran program, without the need to change the program code.
.. note::
- Usually it is not recommended to change anything in these files without being able to understand the effects.
+ Do not change anything in these files unless you understand the effects!
-Each template file has its content framework and keeps so-called placeholder variables in the positions where the values needs to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used the ``$`` sign needs to be doubled to `escape` and keep a single ``$`` sign as it is.
+Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
-The following templates are used and can be found in directory ``flex_extract_vX.X/Templates``:
+The following templates are used; they can be found in the directory ``flex_extract_vX.X/Templates``:
convert.nl
----------
- This is the template for a Fortran namelist file called ``fort.4`` which will be read by ``calc_etadot``.
+ This is the template for a Fortran namelist file called ``fort.4`` read by ``calc_etadot``.
It contains all the parameters ``calc_etadot`` needs.
.. code-block:: fortran
@@ -56,13 +56,13 @@ compilejob.template
This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**.
- At the beginning some directives for the batch system are set.
- On the **ecgate** server the ``SBATCH`` comments are the directives for the SLURM workload manager. A description of the single lines can be found at `SLURM directives <https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs>`_.
- For the high performance computers **cca** and **ccb** the ``PBS`` comments are necessary and can be view at `PBS directives <https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS>`_.
+ At the beginning, some directives for the batch system are set.
+ On the **ecgate** server, the ``SBATCH`` comments are the directives for the SLURM workload manager. A description of the single lines can be found at `SLURM directives <https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs>`_.
+ For the high-performance computers **cca** and **ccb**, the ``PBS`` comments are necessary; for details see `PBS directives <https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS>`_.
- The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending in the ``HOST``. It should not be changed without testing.
+ The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending on the ``HOST``. It should not be changed without testing.
- Afterwards the installation steps as such are done. Including the generation of the root directory, putting files in place, compiling the Fortran program and sending a log file via email.
+ Afterwards, the installation steps as such are done. They included the generation of the root directory, putting files in place, compiling the Fortran program, and sending a log file by email.
.. code-block:: ksh
@@ -144,13 +144,14 @@ job.temp
This template is used to create the actual job script file called ``job.ksh`` for the execution of ``flex_extract`` in the application modes **remote** and **gateway**.
- At the beginning some directives for the batch system are set.
- On the **ecgate** server the ``SBATCH`` comments are the directives for the SLURM workload manager. A description of the single lines can be found at `SLURM directives <https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs>`_.
- For the high performance computers **cca** and **ccb** the ``PBS`` comments are necessary and can be view at `PBS directives <https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS>`_.
+ At the beginning, some directives for the batch system are set.
+ On the **ecgate** server, the ``SBATCH`` comments are the directives for the SLURM workload manager. A description of the single lines can be found at `SLURM directives <https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs>`_.
+ For the high performance computers **cca** and **ccb**, the ``PBS`` comments are necessary;
+ for details see `PBS directives <https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS>`_.
- The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending in the ``HOST``. It should not be changed without testing.
+ The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending on the ``HOST``. It should not be changed without testing.
- Afterwards the run directory and the ``CONTROL`` file are created and ``flex_extract`` is executed. In the end a log file is send via email.
+ Afterwards, the run directory and the ``CONTROL`` file are created and ``flex_extract`` is executed. In the end, a log file is send by email.
.. code-block:: ksh
@@ -238,7 +239,7 @@ job.temp
job.template
------------
- This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. A couple of parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
+ This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
.. code-block:: ksh
@@ -324,21 +325,6 @@ job.template
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
.. toctree::
diff --git a/Documentation/html/_sources/Documentation/Overview/app_modes.rst.txt b/Documentation/html/_sources/Documentation/Overview/app_modes.rst.txt
index 27fd4c1ebaa21a36dd2faee8889e8187c85740ee..5d8d44bb899dbdada34c5c0f98d7ff785a5a934e 100644
--- a/Documentation/html/_sources/Documentation/Overview/app_modes.rst.txt
+++ b/Documentation/html/_sources/Documentation/Overview/app_modes.rst.txt
@@ -1,5 +1,5 @@
*****************
-Application Modes
+Application modes
*****************
.. role:: underline
@@ -12,25 +12,25 @@ Application Modes
.. _ref-app-modes:
-Arising from the two user groups described in :doc:`../../Ecmwf/access`, ``flex_extract`` has 4 different :underline:`user application modes`:
+Arising from the two user groups described in :doc:`../../Ecmwf/access`, ``flex_extract`` has four different :underline:`user application modes`:
.. _ref-remote-desc:
1. Remote (member)
- In the **Remote mode** the user works directly on ECMWF Linux member state server, such as ``ecgate`` or ``cca/ccb``. The software will be installed in the ``$HOME`` directory. The user does not need to install any of the additional third-party libraries mentioned in :ref:`ref-requirements` as ECMWF provides everything with environment modules. The module selection will be done automatically in ``flex_extract``.
+ In the **Remote mode** the user works directly on a ECMWF member-state Linux server, such as ``ecgate`` or ``cca/ccb``. The software will be installed in the ``$HOME`` directory. The user does not need to install any of the third-party libraries mentioned in :ref:`ref-requirements`, as ECMWF provides everything with environment modules. The module selection will be done automatically by ``flex_extract``.
.. _ref-gateway-desc:
2. Gateway (member)
- The **Gateway mode** can be used if a local member state gateway server is in place. Then the job scripts can be submitted to the ECMWF Linux member state server via the ECMWF web access tool ``ecaccess``. The installation script of ``flex_extract`` must be executed at the local gateway server such that the software will be installed in the ``$HOME`` directory at the ECMWF server and some extra setup is done in the local ``flex_extract`` directory at the local gateway server. For more information about establishing a gateway server please see `ECMWF's instructions on gateway server`_. For the **Gateway mode** the necessary environment has to be established which is described in :ref:`ref-prep-gateway`.
+ The **Gateway mode** can be used if a local member-state gateway server is in place. Then, the job scripts can be submitted to the ECMWF member-state Linux server via the ECMWF web access tool ``ecaccess``. The installation script of ``flex_extract`` must be executed on the local gateway server such that the software will be installed in the ``$HOME`` directory at the ECMWF server and that some extra setup is done in the ``flex_extract`` directory on the local gateway server. For more information about establishing a gateway server, please refer to `ECMWF's instructions on gateway server`_. For the **Gateway mode** the necessary environment has to be established which is described in :ref:`ref-prep-gateway`.
.. _ref-local-desc:
3. Local member
- Scripts are installed and executed on a local machine, either in the current ``flex_extract`` directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API's have to be installed to access ECMWF server. The complete installation process is described in :ref:`ref-local-mode`.
+ Scripts are installed and executed on a local machine, either in the current ``flex_extract`` directory or in a path given to the installation script. Under this scenario, a software environment similar to that at ECMWF is required. Additionally, web API's have to be installed to access ECMWF server. The complete installation process is described in :ref:`ref-local-mode`.
4. Local public
- Scripts are installed and executed on a local machine, either in the current ``flex_extract`` directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API's have to be installed to access ECMWF server. The complete installation process is described in :ref:`ref-local-mode`. In this case a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.
+ Scripts are installed and executed on a local machine, either in the current ``flex_extract`` directory or in a path given to the installation script. Under this scenario, a software environment similar to that at ECMWF is required. Additionally, web API's have to be installed to access ECMWF servers. The complete installation process is described in :ref:`ref-local-mode`. In this case, a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.
An overview is sketched in figure :ref:`ref-fig-marsaccess`.
diff --git a/Documentation/html/_sources/Documentation/Overview/prog_flow.rst.txt b/Documentation/html/_sources/Documentation/Overview/prog_flow.rst.txt
index 074d414c625e265e2dadb6d25fc79d0a802beeb9..eeced25f4c7c61afea8542dfdfa4fa240bf89270 100644
--- a/Documentation/html/_sources/Documentation/Overview/prog_flow.rst.txt
+++ b/Documentation/html/_sources/Documentation/Overview/prog_flow.rst.txt
@@ -1,5 +1,5 @@
************
-Program Flow
+Program flow
************
@@ -15,24 +15,24 @@ The following flow diagram shows the general steps performed by ``flex_extract``
.. figure:: ../../_files/submit.png
- Overview of the call of python's ``submit.py`` script and raw sequence of working steps done in ``flex_extract``.
+ Overview of the call of the``submit.py`` Python script and raw sequence of work steps in ``flex_extract``.
-The ``submit.py`` Python program is called by the Shell script ``run.sh`` or ``run_local.sh`` and accomplish the following steps:
+The ``submit.py`` Python script is called by the shell script ``run.sh`` or ``run_local.sh`` and accomplishes the following steps:
- 1. Setup the control data:
- It gets all command-line and ``CONTROL`` file parameters as well as optionally the ECMWF user credentials. Depending the :doc:`app_modes`, it might also prepare a job script which is then send to the ECMWF queue.
- 2. Retrieves data from MARS:
- It creates and sends MARS-requests either on the local machine or on ECMWF server, that receives the data and stores them in a specific format in GRIB files. If the parameter ``REQUEST`` was set ``1`` the data are not received but a file ``mars_requests.csv`` is created with a list of MARS requests and their settings. If it is set to ``2`` the file is created in addition to retrieving the data. The requests are created in an optimised way by splitting in time, jobs and parameters.
- 3. Post-process data to create final ``FLEXPART`` input files:
- After all data is retrieved, the disaggregation of flux fields (`see here <../disagg.html>`_ ) is done as well as the calculation of vertical velocity (`see here <../vertco.html>`_) by the Fortran program ``calc_etadot``. Eventually, the GRIB fields are merged together such that a single grib file per time step is available with all fields for ``FLEXPART``. Since model level fields are typically in *GRIB2* format whereas surface level fields are still in *GRIB1* format, they can be converted into GRIB2 if parameter ``FORMAT`` is set to *GRIB2*. Please note, however, that older versions of FLEXPART may have difficulties reading pure *GRIB2* files since some parameter IDs change in *GRIB2*. If the retrieval is executed remotely at ECMWF, the resulting files can be communicated to the local gateway server via the ``ECtrans`` utility if the parameter ``ECTRANS`` is set to ``1`` and the parameters ``GATEWAY``, ``DESTINATION`` have been set properly during installation. The status of the transfer can be checked with the command ``ecaccess-ectrans-list`` (on the local gateway server). If the script is executed locally the progress of the script can be followed with the usual Linux tools.
+ 1. Setup of control data:
+ Command-line and ``CONTROL``-file parameters are read, as well as (optionally) the ECMWF user credentials. Depending the :doc:`app_modes`, a job script might be prepared which is then sent to the ECMWF queue.
+ 2. Retrieval of data from MARS:
+ MARS requests are created either on the local machine or on the ECMWF server and then submitted which retrieve the data and store them in GRIB files. If the parameter ``REQUEST`` was set ``1``, the data are not retrieved and instead a file ``mars_requests.csv`` is created, which contains a list of the MARS requests and their settings. If ``REQEST`` is set to ``2``, the csv file is created in addition to retrieving the data. The requests are created in an optimised way by splitting with respect to time, jobs and parameters.
+ 3. Post-processing of data to create final ``FLEXPART`` input files:
+ After all data have been retrieved, flux fields are disaggregated (`see here <../disagg.html>`_ ) and the vertical velocity is calculated (`see here <../vertco.html>`_) by the Fortran program ``calc_etadot``. Finally, the GRIB fields are merged into a single grib file per time step containing all the fields for ``FLEXPART``. Since model-level fields are typically in *GRIB2* format, whereas surface-level fields are still in *GRIB1* format, they will be converted into GRIB2 if parameter ``FORMAT`` is set to *GRIB2*. Please note, however, that older versions of FLEXPART may have difficulties to read these *GRIB2* files since some parameter IDs have been change in *GRIB2*. If the retrieval is executed remotely at ECMWF, the resulting files will be sent to the local gateway server via the ``ECtrans`` utility if the parameter ``ECTRANS`` is set to ``1`` and the parameters ``GATEWAY``, ``DESTINATION`` have been set properly during installation. The status of the transfer can be checked with the command ``ecaccess-ectrans-list`` (on the local gateway server). If the script is executed locally, the progress of the script can be followed with the usual Linux tools.
Workflows of different application modes
========================================
-More details on how different the program flow is for the different :doc:`app_modes` is sketched in the following diagrams:
+The following diagrams show how different the program flow is for the different :doc:`app_modes`:
+-------------------------------------------------+------------------------------------------------+
| .. figure:: ../../_files/mode_remote.png | .. figure:: ../../_files/mode_gateway.png |
diff --git a/Documentation/html/_sources/Documentation/api.rst.txt b/Documentation/html/_sources/Documentation/api.rst.txt
index 5c0bff7d88c9354d70df4de575aa4fb853191c2c..4494165114752802da0472037da11916a80e3552 100644
--- a/Documentation/html/_sources/Documentation/api.rst.txt
+++ b/Documentation/html/_sources/Documentation/api.rst.txt
@@ -1,5 +1,5 @@
****************************
-Auto Generated Documentation
+Auto-generated documentation
****************************
diff --git a/Documentation/html/_sources/Documentation/disagg.rst.txt b/Documentation/html/_sources/Documentation/disagg.rst.txt
index deb420864c82f618b2142df0a954e4816214136c..5a035f8be97175182318fbe97ca1d8f8e4edcd8f 100644
--- a/Documentation/html/_sources/Documentation/disagg.rst.txt
+++ b/Documentation/html/_sources/Documentation/disagg.rst.txt
@@ -1,12 +1,17 @@
***************************
-Disaggregation of Flux Data
+Disaggregation of flux data
***************************
-``FLEXPART`` interpolates meteorological input data linearly to the position of computational particles in time and space. This method requires point values in the discrete input fields. However, flux data (as listed in table :ref:`ref-table-fluxpar`) from the ECMWF represent cell averages or integrals and are accumulated over a specific time interval, depending on the dataset. Hence, to conserve the integral quantity with ``FLEXPART``'s linear interpolation a pre-processing scheme has to be applied.
+``FLEXPART`` interpolates meteorological input data linearly to the position of computational
+particles in time and space. This method requires point values in the discrete input fields.
+However, flux data (as listed in table :ref:`ref-table-fluxpar` below) from the ECMWF represent cell
+averages or integrals and are accumulated over a specific time interval, depending on the data
+set. Hence, to conserve the integral quantity with the linear interpolation used in ``FLEXPART``,
+pre-processing has to be applied.
.. _ref-table-fluxpar:
-.. csv-table:: flux fields
+.. csv-table:: Flux fields
:header: "Short Name", "Name", "Units", "Interpolation Type"
:align: center
:widths: 5,15,5,10
@@ -19,25 +24,25 @@ Disaggregation of Flux Data
SSR, "surface net solar radiation", ":math:`J m^{-2}`", "bicubic interpolation"
-The first step is to *de-accumulate* the fields in time so that each value represents an integral in x, y, t space.
-Afterwards, a *disaggregation* scheme is applied which means to break down the integral value into point values.
-In order to be able to carry out the disaggregation procedure proposed by Paul James, additional flux data is retrieved automatically for one day at the beginning and one day at the end of the period specified. Thus, data for flux computation will be requested for the period START_DATE-1 to END_DATE+1. Note that these (additional) dates are used only for interpolation within ``flex_extract`` and are not communicated to the final ``FLEXPART`` input files.
+The first step is to *de-accumulate* the fields in time so that each value represents non-overlapping integrals in x-, y-, and t-space.
+Afterwards, a *disaggregation* scheme is applied which means to convert the integral value to corresponding point values to be used late for the interpolation.
+The disaggregation procedure as proposed by Paul James (currently, the standard) requires additional flux data for one day at the beginning and one day at the end of the period specified.
+They are retrieved automatically. Thus, data for flux computation will be requested for the period START_DATE-1 to END_DATE+1. Note that these (additional) dates are used only for interpolation within ``flex_extract`` and are not contained in the final ``FLEXPART`` input files.
-The flux disaggregation produces files named ``fluxYYYYMMDDHH``, where ``YYYYMMDDHH`` is the date format. Note, that the first two and last two flux files do not contain any data.
+The flux disaggregation produces files named ``fluxYYYYMMDDHH``, where ``YYYYMMDDHH`` is the date format. Note that the first two and last two flux files do not contain any data.
.. note::
- Note also that for operational retrievals (``BASETIME`` set to 00 or 12) forecast fluxes are only available until ``BASETIME``, so that no polynomial interpolation is possible in the last two time intervals. This is the reason why setting ``BASETIME`` is not recommended for on demand scripts.
+ Note also that for operational retrievals (``BASETIME`` set to 00 or 12), forecast fluxes are only available until ``BASETIME``, so that no polynomial interpolation is possible in the last two time intervals. This is the reason why setting ``BASETIME`` is not recommended for on-demand scripts.
Disaggregation for precipitation in older versions
--------------------------------------------------
-In ``flex_extract`` up to version 5 the disaggregation was done with a Fortran program (FLXACC2). In version 6 this part was converted to Python.
+In ``flex_extract`` up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.
-
-In the old versions (below 7.1) a relatively simple method processes the precipitation fields in a way that is consistent with the scheme applied in ``FLEXPART`` for all variables: linear interpolation between times where input fields are available.
-At first the accumulated values are divided by the number of hours (i.e., 3 or 6).
+In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in ``FLEXPART`` for all variables.
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -52,11 +57,11 @@ However, the supporting points in space are not shifted between precipitation an
.. figure:: ../_files/old_disagg.png
:figclass: align-center
- Fig. 1: Example of disaggregation scheme as implemented in older versions for an isolated precipitation event lasting one time interval (thick blue line). The amount of original precipitation after de-accumulation is given by the blue-shaded area. The green circles represent the discrete grid points after disaggregation and linearly interpolate in between them as indicated by the green line and the green-shaded area. Note that supporting points for the interpolation are shifted by a half-time interval compared to the times when other meteorological fields are available (Hittmeir et al. 2018).
+ Fig. 1: Example of disaggregation scheme as implemented in older versions for an isolated precipitation event lasting one time interval (thick blue line). The amount of original precipitation after de-accumulation is given by the blue-shaded area. The green circles represent the discrete grid points after disaggregation and linearly interpolate in between them as indicated by the green line and the green-shaded area. Note that supporting points for the interpolation are shifted by half a time interval compared to the times when other meteorological fields are available (Hittmeir et al. 2018).
-Disaggregation is done for 4 adjacent timespans (:math:`a_0, a_1, a_2, a_3`) which generates a new, disaggregated value which is output at the central point of the 4 adjacent timespans.
+Disaggregation is done for four adjacent timespans (:math:`a_0, a_1, a_2, a_3`) which generates a new, disaggregated value which is output at the central point of the four adjacent timespans.
.. math::
@@ -68,7 +73,7 @@ Disaggregation is done for 4 adjacent timespans (:math:`a_0, a_1, a_2, a_3`) whi
p_{bd}(m) &= a_1(m) * a_2(m) / (a_1(m) + a_3(m))\\
-This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards. If one of the 4 original timespans has a value below 0 it is set to 0 prior to the calculation.
+This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards. If one of the four original timespans has a value below 0, it is set to 0 prior to the calculation.
.. math::
@@ -77,14 +82,12 @@ This new point :math:`p` is used for linear interpolation of the complete timese
-
-
Disaggregation for precipitation in version 7.1
-----------------------------------------------
-Due to the problems with generating precipitation in originally dry (or lower) intervals and the temporal smoothing a new algorithm was developed. The approach is based on a one dimensional piecewise linear function with two additional supporting grid points within each grid cell, dividing the interval into three pieces. It fulfils the desired requirements by preserving the integral precipitation in each time interval, guaranteeing continuity at interval boundaries, and maintaining non-negativity. An additional monotonicity filter helps to gain monotonicity.
-The more natural requirements of symmetry, reality, computational efficiency and easy implementation motivates the linear formulation.
-These requirements on the reconstruction algorithm imply that time intervals with no precipitation remain unchanged, i.e. the reconstructed values vanish throughout this whole time interval, too.
+Due to the problems mentioned above, a new algorithm was developed. The approach is based on a one-dimensional, piecewise-linear function with two additional supporting grid points within each grid cell, dividing the interval into three pieces. It fulfils the desired requirements of preserving the integral precipitation in each time interval, guaranteeing continuity at interval boundaries, and maintaining non-negativity. An additional filter improves monotonicity.
+The more natural requirements of symmetry, reality, computational efficiency and easy implementation motivates the use of a linear formulation.
+These requirements for the reconstruction algorithm imply that time intervals with no precipitation remain unchanged, i. e., the reconstructed values vanish throughout this whole time interval, too.
In the simplest scenario of an isolated precipitation event, where in the time interval before and after the data values are zero, the reconstruction algorithm therefore has to vanish at the boundaries of the interval, too.
The additional conditions of continuity and conservation of the precipitation amount then require us to introduce sub-grid points if we want to keep a linear interpolation (Fig. 2).
The height is thereby determined by the condition of conservation of the integral of the function over the time interval.
@@ -141,27 +144,24 @@ The following lists the equations of the new algorithm.
\textbf{endif}
-In the case of the new disaggregation method for precipitation, the two new sub grid points are added in the ``flux`` output files. They are identified by the forecast step parameter ``step`` which is 0 for the original time interval and 1 or 2 for the two new sub grid points respectively. The filenames do not change.
+In the case of the new disaggregation method for precipitation, the two new sub-grid points are added in the ``flux`` output files. They are identified by the forecast step parameter ``step`` which is 0 for the original time interval, and 1 or 2, respectively, for the two new sub-grid points. The filenames do not change.
.. note::
- The new method for disaggregation was published in the Geoscientific Model Development Journal in 2018:
+ The new method for disaggregation was published in the journal Geoscientific Model Development in 2018:
Hittmeir, S., Philipp, A., and Seibert, P.: A conservative reconstruction scheme for the interpolation of extensive quantities in the Lagrangian particle dispersion model FLEXPART, Geosci. Model Dev., 11, 2503-2523, https://doi.org/10.5194/gmd-11-2503-2018, 2018.
-
-
-
-Disaggregation for the rest of the flux fields
+Disaggregation for the other flux fields
----------------------------------------------
The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times X using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for 4 adjacent timespans (:math:`p_a, p_b, p_c, p_d`) which generates a new, disaggregated value which is output at the central point of the 4 adjacent timespans.
+then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent timespans (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent timespans.
.. math::
diff --git a/Documentation/html/_sources/Documentation/input.rst.txt b/Documentation/html/_sources/Documentation/input.rst.txt
index 1dbfe31f6fbfc5f447fa2bacb2a522023185e5a6..0a0e11d66cd7bdffa7762fdb86eaafe2c59302de 100644
--- a/Documentation/html/_sources/Documentation/input.rst.txt
+++ b/Documentation/html/_sources/Documentation/input.rst.txt
@@ -1,22 +1,20 @@
********************
-Control & Input Data
+Control & input data
********************
-Input Data
+Input data
- :doc:`Input/control`
- ``Flex_extract`` needs a number of controlling parameters to decide on the behaviour and the actual dataset to be retrieved. They are initialized by ``flex_extract`` with their default values and can be overwritten with definitions set in the so called :doc:`Input/control`.
+ ``Flex_extract`` needs a number of controlling parameters to decide on the behaviour and the actual data set to be retrieved. They are initialised by ``flex_extract`` with certain default values which can be overwritten with definitions set in the so-called :doc:`Input/control`.
- To be able to successfully retrieve data from the ECMWF Mars archive it is necessary to understand these parameters and set them to proper and consistent values. They are described in :doc:`Input/control_params` section.
+ For a successfull retrieval of data from the ECMWF MARS archive it is necessary to understand these parameters and to set them to proper and consistent values. They are described in :doc:`Input/control_params` section.
- We also have some :doc:`Input/examples` and description of :doc:`Input/changes` changes to previous versions and downward compatibilities.
+ Furthermore, some :doc:`Input/examples` are provided, and in :doc:`Input/changes` changes to previous versions and downward compatibilities are described.
- :doc:`Input/ecmwf_env`
- For ``flex_extract`` it is necessary to be able to reach ECMWF servers in the **remote mode** and the **gateway mode**. Therefore a :doc:`Input/ecmwf_env` is created during the installation process.
+ ``flex_extract`` needs to be able to reach ECMWF servers in the **remote mode** and the **gateway mode**. Therefore a :doc:`Input/ecmwf_env` is created during the installation process.
- :doc:`Input/templates`
- A number of files which are created by ``flex_extract`` are taken from templates. This makes it easy to adapt for example the jobscripts regarding its settings for the batch jobs.
-
-
+ A number of files which are created by ``flex_extract`` are taken from templates. This makes it easy to adapt, for example, the job scripts with regard to the settings for the batch jobs.
@@ -28,8 +26,8 @@ Input Data
.. _ref-controlling:
Controlling
- The main tasks and behaviour of ``flex_extract`` are controlled by its Python scripts. There are two top-level scripts, one for installation called install_ and one for execution called submit_.
- They can interpret a number of command line arguments which can be seen by typing ``--help`` after the script call. Go to the root directory of ``flex_extract`` to type:
+ The main tasks and the behaviour of ``flex_extract`` are controlled by the Python scripts. There are two top-level scripts, one for installation called install_, and one for execution called submit_.
+ They interpret a number of command-line arguments which can be seen by typing ``--help`` after the script call. Go to the root directory of ``flex_extract`` to type:
.. code-block:: bash
@@ -37,15 +35,14 @@ Controlling
python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
- In this new version we provide also the wrapping Shell scripts setup_ and run_, which sets the command line parameters, do some checks and execute the corresponing Python scripts ``install.py`` and ``submit.py`` respectivley.
-
- It might be faster and easier for beginners. See :doc:`../quick_start` for information on how to use them.
+ With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively.
+ It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
- Additionally, ``flex_extract`` creates the Korn Shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be send to the ECMWF serves in the **remote mode** and the **gateway mode** for starting batch jobs.
+ ``flex_extract`` also creates the Korn shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be sent to the ECMWF servers in the **remote mode** and the **gateway mode** for starting batch jobs.
- The Fortran program will be compiled during the installation process by the :doc:`Input/fortran_makefile`.
+ The Fortran program is compiled during the installation process using the :doc:`Input/fortran_makefile`.
- To sum up, the following scripts controls ``flex_extract``:
+ To sum up, the following scripts control ``flex_extract``:
Installation
- :doc:`Input/setup`
diff --git a/Documentation/html/_sources/Documentation/output.rst.txt b/Documentation/html/_sources/Documentation/output.rst.txt
index 40e8310376aaa02364364b18498cb9457d3a3328..8a25f252022e118e62de2570426b24f7619e6899 100644
--- a/Documentation/html/_sources/Documentation/output.rst.txt
+++ b/Documentation/html/_sources/Documentation/output.rst.txt
@@ -1,13 +1,13 @@
***********
-Output Data
+Output data
***********
-The output data of ``flex_extract`` are separated mainly into temporary files and the final ``FLEXPART`` input files:
+The output data of ``flex_extract`` can be divided into the final ``FLEXPART`` input files and temporary files:
+-----------------------------------------------+----------------------------------------------+
| ``FLEXPART`` input files | Temporary files (saved in debug mode) |
+-----------------------------------------------+----------------------------------------------+
-| - Standard output filenames | - MARS request file (opt) |
+| - Standard output file names | - MARS request file (optional) |
| - Output for pure forecast | - flux files |
| - Output for ensemble members | - VERTICAL.EC |
| - Output for new precip. disaggregation | - index file |
@@ -20,22 +20,22 @@ The output data of ``flex_extract`` are separated mainly into temporary files an
``FLEXPART`` input files
========================
-The final output files of ``flex_extract`` are also the meteorological ``FLEXPART`` input files.
-The naming of these files depend on the kind of data extracted by ``flex_extract``.
+The final output files of ``flex_extract`` are the meteorological input files for ``FLEXPART``.
+The naming convention for these files depends on the kind of data extracted by ``flex_extract``.
Standard output files
---------------------
-In general, there is a file for each time step with the filename format:
+In general, there is one file for each time named:
.. code-block:: bash
<prefix>YYMMDDHH
-The ``prefix`` is by default defined as ``EN`` and can be re-defined in the ``CONTROL`` file.
-Each file contains all meteorological fields needed by ``FLEXPART`` for all selected model levels for a specific time step.
+where YY are the last two digits of the year, MM is the month, DD the day, and HH the hour (UTC). <prefix> is by default defined as EN, and can be re-defined in the ``CONTROL`` file.
+Each file contains all meteorological fields at all levels as needed by ``FLEXPART``, valid for the time indicated in the file name.
-Here is an example output which lists the meteorological fields in a single file called ``CE00010800`` where we extracted only the lowest model level for demonstration reasons:
+Here is an example output which lists the meteorological fields in a single file called ``CE00010800`` (where we extracted only the lowest model level for demonstration purposes):
.. code-block:: bash
@@ -83,19 +83,19 @@ Here is an example output which lists the meteorological fields in a single file
Output files for pure forecast
------------------------------
-``Flex_extract`` can retrieve forecasts which can be longer than 23 hours. To avoid collisions of time steps for forecasts of more than one day a new scheme for filenames in pure forecast mode is introduced:
+``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:
.. code-block:: bash
<prefix>YYMMDD.HH.<FORECAST_STEP>
-The ``<prefix>`` is, as in the standard output, by default ``EN`` and can be re-defined in the ``CONTROL`` file. ``YYMMDD`` is the date format and ``HH`` the forecast time which is the starting time for the forecasts. The ``FORECAST_STEP`` is a 3 digit number which represents the forecast step in hours.
+The ``<prefix>`` is, as in the standard output, by default ``EN`` and can be re-defined in the ``CONTROL`` file. ``YYMMDD`` is the date format and ``HH`` the forecast time which is the starting time for the forecasts. The ``FORECAST_STEP`` is a 3-digit number which represents the forecast step in hours.
Output files for ensemble predictions
-------------------------------------
-Ensembles can be retrieved and are addressed by the grib message parameter ``number``. The ensembles are saved per file and standard filenames are supplemented by the letter ``N`` and the ensemble member number in a 3 digit format.
+``Flex_extract`` is able to retrieve ensembles data; they are labelled by the grib message parameter ``number``. Each ensemble member is saved in a separate file, and standard filenames are supplemented by the letter ``N`` and the ensemble member number in a 3-digit format.
.. code-block:: bash
@@ -105,10 +105,11 @@ Ensembles can be retrieved and are addressed by the grib message parameter ``num
Additional fields with new precipitation disaggregation
-------------------------------------------------------
-The new disaggregation method for precipitation fields produces two additional precipitation fields for each time step and precipitation type. They serve as sub-grid points in the original time interval. For details of the method see :doc:`disagg`.
-The two additional fields are marked with the ``step`` parameter in the Grib messages and are set to "1" and "2" for sub-grid point 1 and 2 respectively.
-The output filenames do not change in this case.
-Below is an example list of precipitation fields in an output file generated with the new disaggregation method:
+The new disaggregation method for precipitation fields produces two additional precipitation fields for each time step and precipitation type (large-scale and convective). They serve as sub-grid points in the original time interval. For details of the method see :doc:`disagg`.
+The two additional fields are addressed using the ``step`` parameter in the GRIB messages, which
+is set to "1" or "2", for sub-grid points 1 and 2, respectively.
+The output file names are not altered.
+An example of the list of precipitation fields in an output file generated with the new disaggregation method is found below:
.. code-block:: bash
@@ -128,13 +129,16 @@ Below is an example list of precipitation fields in an output file generated wit
Temporary files
===============
-``Flex_extract`` works with a number of temporary data files which are usually deleted after a successful data extraction. They are only stored if the ``DEBUG`` mode is switched on (see :doc:`Input/control_params`).
+``Flex_extract`` creates a number of temporary data files which are usually deleted at the end of a successful run. They are preserved only if the ``DEBUG`` mode is switched on (see :doc:`Input/control_params`).
MARS grib files
---------------
``Flex_extract`` retrieves all meteorological fields from MARS and stores them in files ending with ``.grb``.
-Since the request times and data transfer of MARS access are limited and ECMWF asks for efficiency in requesting data from MARS, ``flex_extract`` splits the overall data request in several smaller requests. Each request is stored in an extra ``.grb`` file and the file names are put together by several pieces of information:
+Since there are limits implemented by ECMWF for the time per request and data transfer from MARS,
+and as ECMWF asks for efficient MARS retrievals, ``flex_extract`` splits the overall data request
+into several smaller requests. Each request is stored in its own ``.grb`` file, and the file
+names are composed of several pieces of information:
.. code-block:: bash
@@ -143,21 +147,20 @@ Since the request times and data transfer of MARS access are limited and ECMWF a
Description:
Field type:
- ``AN`` - Analysis, ``FC`` - Forecast, ``4V`` - 4d variational analysis, ``CV`` - Validation forecast, ``CF`` - Control forecast, ``PF`` - Perturbed forecast
+ ``AN`` - Analysis, ``FC`` - Forecast, ``4V`` - 4D variational analysis, ``CV`` - Validation forecast, ``CF`` - Control forecast, ``PF`` - Perturbed forecast
Grid type:
- ``SH`` - Spherical Harmonics, ``GG`` - Gaussian Grid, ``OG`` - Output Grid (typically lat/lon), ``_OROLSM`` - Orography parameter
+ ``SH`` - Spherical Harmonics, ``GG`` - Gaussian Grid, ``OG`` - Output Grid (typically lat / lon), ``_OROLSM`` - Orography parameter
Temporal property:
``__`` - instantaneous fields, ``_acc`` - accumulated fields
Level type:
- ``ML`` - Model Level, ``SL`` - Surface Level
+ ``ML`` - model level, ``SL`` - surface level
ppid:
- The process number of the parent process of submitted script.
+ The process number of the parent process of the script submitted.
pid:
- The process number of the submitted script.
+ The process number of the script submitted.
-The process ids should avoid mixing of fields if several ``flex_extract`` jobs are performed in parallel (which is, however, not recommended). The date format is YYYYMMDDHH.
-Example ``.grb`` files for a day of CERA-20C data:
+Example ``.grb`` files for one day of CERA-20C data:
.. code-block:: bash
@@ -171,12 +174,14 @@ Example ``.grb`` files for a day of CERA-20C data:
MARS request file
-----------------
-This file is a ``csv`` file called ``mars_requests.csv`` with a list of the actual settings of MARS request parameters (one request per line) in a flex_extract job. It is used for documenting the data which were retrieved and for testing reasons.
+This file is a ``csv`` file called ``mars_requests.csv`` listing the actual settings of the MARS
+request (one request per line) in a flex_extract job.
+It is used for documenting which data were retrieved, and for testing.
-Each request consist of the following parameters, whose meaning mainly can be taken from :doc:`Input/control_params` or :doc:`Input/run`:
+Each request consists of the following parameters, whose meaning mostly can be taken from :doc:`Input/control_params` or :doc:`Input/run`:
request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist, levtype, marsclass, number, param, repres, resol, step, stream, target, time, type
-Example output of a one day retrieval of CERA-20c data:
+Example output of a one-day retrieval of CERA-20C data:
.. code-block:: bash
@@ -191,29 +196,34 @@ Example output of a one day retrieval of CERA-20c data:
VERTICAL.EC
-----------
-The vertical discretization of model levels. This file contains the ``A`` and ``B`` parameters to calculate the model level height in meters.
+This file contains information describing the vertical discretisation (model levels)
+in form of the ``A`` and ``B`` parameters which allow to calculate the actual pressure of a model level from the surface pressure.
Index file
----------
-This file is usually called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
+This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
+.. todo::
-flux files
+ #PS NEEDS MORE DESCRIPTION
+
+
+Flux files
----------
-The flux files contain the de-accumulated and dis-aggregated flux fields of large scale and convective precipitation, eastward turbulent surface stress, northward turbulent surface stress, surface sensible heat flux and the surface net solar radiation.
+The flux files contain the de-accumulated and dis-aggregated flux fields of large-scale and convective precipitation, east- and northward turbulent surface stresses, the surface sensible heat flux, and the surface net solar radiation.
.. code-block:: bash
flux<date>[.N<xxx>][.<xxx>]
-The date format is YYYYMMDDHH. The optional block ``[.N<xxx>]`` marks the ensemble forecast number, where ``<xxx>`` is the ensemble member number. The optional block ``[.<xxx>]`` marks a pure forecast with ``<xxx>`` being the forecast step.
+The date format is YYYYMMDDHH as explained before. The optional block ``[.N<xxx>]`` is used for the ensemble forecast date, where ``<xxx>`` is the ensemble member number. The optional block ``[.<xxx>]`` marks a pure forecast with ``<xxx>`` being the forecast step.
.. note::
- In the case of the new dis-aggregation method for precipitation, two new sub-intervals are added in between each time interval. They are identified by the forecast step parameter which is ``0`` for the original time interval and ``1`` or ``2`` for the two new intervals respectively.
+ In the case of the new dis-aggregation method for precipitation, two new sub-intervals are added in between each time interval. They are identified by the forecast step parameter which is ``0`` for the original time interval, and ``1`` or ``2``, respectively, for the two new intervals.
fort files
@@ -225,9 +235,9 @@ There are a number of input files for the ``calc_etadot`` Fortran program named
fort.xx
-where ``xx`` is the number which defines the meteorological fields stored in these files.
-They are generated by the Python part of ``flex_extract`` by just splitting the meteorological fields for a unique time stamp from the ``*.grb`` files into the ``fort`` files.
-The following table defines the numbers with their corresponding content.
+where ``xx`` is a number which defines the meteorological fields stored in these files.
+They are generated by the Python code in ``flex_extract`` by splitting the meteorological fields for a unique time stamp from the ``*.grb`` files, storing them under the names ``fort.<XX>`` where <XX> represents some number.
+The following table defines the numbers and the corresponding content:
.. csv-table:: Content of fort - files
:header: "Number", "Content"
@@ -239,12 +249,12 @@ The following table defines the numbers with their corresponding content.
"13", "divergence (optional)"
"16", "surface fields"
"17", "specific humidity"
- "18", "surface specific humidity (reduced gaussian)"
- "19", "vertical velocity (pressure) (optional)"
+ "18", "surface specific humidity (reduced Gaussian grid)"
+ "19", "omega (vertical velocity in pressure coordinates) (optional)"
"21", "eta-coordinate vertical velocity (optional)"
- "22", "total cloud water content (optional)"
+ "22", "total cloud-water content (optional)"
-Some of the fields are solely retrieved with specific settings, e.g. the eta-coordinate vertical velocity is not available in ERA-Interim datasets and the total cloud water content is an optional field for ``FLEXPART v10`` and newer.
+Some of the fields are solely retrieved with specific settings, e. g., the eta-coordinate vertical velocity is not available in ERA-Interim datasets, and the total cloud-water content is an optional field which is useful for ``FLEXPART v10`` and newer.
The ``calc_etadot`` program saves its results in file ``fort.15`` which typically contains:
@@ -258,7 +268,7 @@ More details about the content of ``calc_etadot`` can be found in :doc:`vertco`.
.. note::
- The ``fort.4`` file is the namelist file to drive the Fortran program ``calc_etadot``. It is therefore also an input file.
+ The ``fort.4`` file is the namelist file to control the Fortran program ``calc_etadot``. It is therefore also an input file.
Example of a namelist:
diff --git a/Documentation/html/_sources/Documentation/overview.rst.txt b/Documentation/html/_sources/Documentation/overview.rst.txt
index 1e9af1b4f5f8aa4bd6f92b237d8dbcbeee82a436..0409ac22fe138183d9f7c47352e9ec001bd55ef0 100644
--- a/Documentation/html/_sources/Documentation/overview.rst.txt
+++ b/Documentation/html/_sources/Documentation/overview.rst.txt
@@ -2,21 +2,21 @@
Overview
========
-``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`` was created explicitly for ``FLEXPART`` users who wants to use meteorological data from ECMWF to drive the ``FLEXPART`` model.
-The software retrieves the minimal number of parameters ``FLEXPART`` needs to work and provides the data in the explicity format ``FLEXPART`` understands.
+``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`` was created explicitly for ``FLEXPART`` users who want to use meteorological data from ECMWF to drive the ``FLEXPART`` model.
+The software retrieves the minimum set of parameters needed by ``FLEXPART`` to work, and provides the data in the specific format required by ``FLEXPART``.
-``Flex_extract`` consists of 2 main parts:
- 1. a Python part, where the reading of parameter settings, retrieving data from MARS and preparing the data for ``FLEXPART`` is done and
- 2. a Fortran part, where the calculation of the vertical velocity is done and if necessary the conversion from spectral to regular latitude/longitude grids.
+``Flex_extract`` consists of two main parts:
+ 1. a Python part which reads the parameter settings, retrieves the data from MARS, and prepares them for ``FLEXPART``, and
+ 2. a Fortran part which calculates the vertical velocity and, if necessary, converts variables from the spectral representation to regular latitude/longitude grids.
-Additionally, it has some Korn shell scripts which are used to set the environment and batch job features on ECMWF servers for the *gateway* and *remote* mode. See :doc:`Overview/app_modes` for information of application modes.
+In addition, there are some Korn shell scripts to set the environment and batch job features on ECMWF servers for the *gateway* and *remote* mode. See :doc:`Overview/app_modes` for information of application modes.
A number of Shell scripts are wrapped around the software package for easy installation and fast job submission.
-The software depends on a number of third-party libraries which can be found in :ref:`ref-requirements`.
+The software depends on some third-party libraries as listed in :ref:`ref-requirements`.
-Some details on the tasks and program worksteps are described in :doc:`Overview/prog_flow`.
+Details of the tasks and program work steps are described in :doc:`Overview/prog_flow`.
.. - directory structure (new diagramm!)
diff --git a/Documentation/html/_sources/Documentation/vertco.rst.txt b/Documentation/html/_sources/Documentation/vertco.rst.txt
index e0d1d6633392a6d31ac9f34002d86fe8b132d8b5..fcc1d14faabe35e602a735b786c52f96c711c4d5 100644
--- a/Documentation/html/_sources/Documentation/vertco.rst.txt
+++ b/Documentation/html/_sources/Documentation/vertco.rst.txt
@@ -1,13 +1,13 @@
*******************
-Vertical Coordinate
+Vertical wind
*******************
-Calculation of vertical velocity and preparation of Output-files
+Calculation of vertical velocity and preparation of output files
================================================================
-``flex_extract`` has two ways to calculate the vertical velocity for ``FLEXTRA``/``FLEXPART``:
+Two methods are provided in ``flex_extract`` for the calculation of the vertical velocity for ``FLEXTRA``/``FLEXPART``:
(i) from the horizontal wind field,
- (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**.
+ (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
Especially for high resolution data, use of the ``MARS`` parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
@@ -19,39 +19,38 @@ Calculation from the horizontal wind field is still required for historical case
**ERA-40**, **ERA-Interim** or operational data prior to September 2008.
-Calculation of vertical velocity from horizontal wind using the continuity equation
-===================================================================================
+Calculation of the vertical velocity from the horizontal wind using the continuity equation
+===========================================================================================
-The vertical velocity is computed by the FORTRAN90 program ``calc_etadot`` in the ECMWF
-vertical coordinate system by applying the equation of continuity and thereby ensuring mass consistent 3D wind fields. A detailed description of ``calc_etadot`` can be found in the
+The vertical velocity in the ECMWF's eta vertical coordinate system is computed by the Fortran program ``calc_etadot``, using the continuity equation and thereby ensuring mass-consistent 3D wind fields. A detailed description of ``calc_etadot`` can be found in the
documents v20_update_protocol.pdf, V30_update_protocol.pdf and
V40_update_protocol.pdf. The computational demand and accuracy of ``calc_etadot`` is highly
dependent on the specification of parameters ``GAUSS``, ``RESOL`` and ``SMOOTH``. The
following guidance can be given for choosing the right parameters:
- * For very fine output grids (0.25 degree or finer) the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
+ * For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
* For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:
- For 1.0 degree grids: ``GAUSS=1``, ``RESOL=255``, ``SMOOTH=179``
- For 0.5 degree grids: ``GAUSS=1``, ``RESOL=399``, ``SMOOTH=359``
- Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.
- - If ``GAUSS`` is set to 1, only the following choices are possible for ``RESOL`` on *ecgate*: 159,255,319,399,511,799, (on the HPC also 1279, 2047 in future models). This choice is restricted because a reduced Gaussian grid is defined in then ECMWF EMOSLIB only for these spectral resolutions. For ``GAUSS=0``, ``RESOL`` can be any value below the operational resolution.
- - For ``SMOOTH`` any resolution lower than ``RESOL`` is possible. If no smoothing is desired, ``SMOOTH=0`` should be chosen. ``SMOOTH`` has no effect if vertical velocity is calculated on lat\/lon grid (``GAUSS=0``).
- * The on demand scripts send an error message for settings where ``SMOOTH`` (if set) and ``RESOL`` are larger than 360./``GRID``/2, since in this case, the output grid cannot resolve the highest wave numbers. The scripts continue operations, however.
+ - If ``GAUSS`` is set to 1, only the following choices are possible for ``RESOL`` on *ecgate*: 159,255,319,399,511,799, (on the HPC also 1279; 2047 in future model versions). This choice is restricted because a reduced Gaussian grid is defined in the ECMWF EMOSLIB only for these spectral resolutions. For ``GAUSS=0``, ``RESOL`` can be any value below the operational resolution.
+ - For ``SMOOTH``, any resolution lower than ``RESOL`` is possible. If no smoothing is desired, ``SMOOTH=0`` should be chosen. ``SMOOTH`` has no effect if the vertical velocity is calculated on a lat\/lon grid (``GAUSS=0``).
+ * The on-demand scripts send an error message for settings where ``SMOOTH`` (if set) and ``RESOL`` are larger than 360./``GRID``/2, since in this case, the output grid cannot resolve the highest wave numbers. The scripts continue operations, however.
* Regional grids are not cyclic in zonal directions, but global grids are. The software assumes a cyclic grid if ``RIGHT``-``LEFT`` is equal to ``GRID`` or is equal to ``GRID``-360.
- * Finally, model and flux data as well as the vertical velocity computed are written to files ``<prefix>yymmddhh`` for application in ATM modelling. If the parameters ``OMEGA`` or ``OMEGADIFF`` are set, also files ``OMEGAyymmddhh`` are created, containing the pressure vertical velocity (omega) and the difference between omega from ``MARS`` and the surface pressure tendency. ``OMEGADIFF`` should be zero except for debugging, since it triggers expensive calculations on the Gaussian grid.
+ * Finally, model and flux data as well as the vertical velocity computed are written to files ``<prefix>yymmddhh`` (the standard ``flex_extract`` output files) If the parameters ``OMEGA`` or ``OMEGADIFF`` are set, also files ``OMEGAyymmddhh`` are created, containing the pressure vertical velocity (omega) and the difference between omega from ``MARS`` and from the surface pressure tendency. ``OMEGADIFF`` should be set to zero except for debugging, since it triggers expensive calculations on the Gaussian grid.
-Calculation of vertical velocity from pre-calculated MARS parameter 77
-======================================================================
+Calculation of the vertical velocity from the pre-calculated MARS parameter 77
+==============================================================================
-Since November 2008, the parameter 77 (deta/dt) is stored in ``MARS`` on full model levels. ``FLEXTRA``/``FLEXPART`` in its current version requires ``deta/dt`` on model half levels, multiplied by ``dp/deta``. In ``flex_extract``, the program ``calc_etadot`` assumes that this parameter is available if the ``CONTROL`` parameter ``ETA`` is set to 1.
+Since November 2008, the parameter 77 (deta/dt) is stored in ``MARS`` on full model levels. ``FLEXTRA``/``FLEXPART`` in its current version requires ``deta/dt`` on model half levels, multiplied by ``dp/deta``. In ``flex_extract``, the program ``calc_etadot`` assumes that parameter 77 is available if the ``CONTROL`` parameter ``ETA`` is set to 1.
It is recommended to use the pre-calculated parameter 77 by setting ``ETA`` to 1 whenever possible.
-Setting parameter ``ETA`` to 1 normally disables calculation of vertical velocity from the horizontal wind field, which saves a lot of computational time.
+Setting the parameter ``ETA`` to 1 disables calculation of vertical velocity from the horizontal wind field, which saves a lot of computational time.
.. note::
- However, the calculation on the Gaussian grid are avoided only if both ``GAUSS`` and ``ETADIFF`` are set to 0. Please set ``ETADIFF`` to 1 only if you are really need it for debugging since this is a very expensive option. In this case ``ETAyymmddhh`` files are produced that contain the vertical velocity from horizontal winds and the difference to the pre-calculated vertical velocity.
+ However, the calculations on the Gaussian grid are avoided only if both ``GAUSS`` and ``ETADIFF`` are set to 0. Please set ``ETADIFF`` to 1 only if you are really need it for debugging since this is a very expensive option. In this case, ``ETAyymmddhh`` files are produced that contain the vertical velocity from horizontal winds and the difference to the pre-calculated vertical velocity.
The parameters ``RESOL``, ``GRID``, ``UPPER``, ``LOWER``, ``LEFT``, ``RIGHT`` still apply. As for calculations on the Gaussian grid, the spectral resolution parameter ``RESOL`` should be compatible with the grid resolution (see previous subsection).
diff --git a/Documentation/html/_sources/Ecmwf/access.rst.txt b/Documentation/html/_sources/Ecmwf/access.rst.txt
index 6c2930e90bf32d0a9586b907fee286dc5f9b8be7..4edd8ca954282a6cff5e5020bb51d8b56fc302b9 100644
--- a/Documentation/html/_sources/Ecmwf/access.rst.txt
+++ b/Documentation/html/_sources/Ecmwf/access.rst.txt
@@ -1,5 +1,5 @@
************
-Access Modes
+Access modes
************
.. _public datasets: https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets
@@ -7,18 +7,18 @@ Access Modes
.. _Climate Data Store: https://cds.climate.copernicus.eu
.. _CDS API: https://cds.climate.copernicus.eu/api-how-to
-Access to the ECMWF Mars archive is divided into two groups: **member state** users and **public** users.
+Access to the ECMWF MARS archive is divided into two groups: **member state** users and **public** users.
-**Member state user**:
- This access mode allows the user to work directly on the ECMWF Linux Member State Servers or via a Web Access Toolkit ``ecaccess`` 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 `Computing Representative`_. This user group is also able to work from their local facilities without a gateway server in the same way a **public** user would. The only difference is the connection with the Web API. However, this is automatically selected by ``flex_extract``.
+**Member-state user**:
+ This access mode allows the user to work directly on a ECMWF member-state Linux server or via the ``ecaccess`` Web-Access Toolkit 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 no access to the latest forecasts. In case such data are needed, this has to be agreed upon with the national `Computing Representative`_. This user group is also able to work from their local facilities without a gateway server in the same way a **public** user would. The only difference is the connection with the Web API, which, however, is automatically selected by ``flex_extract``.
**Public user**:
- This access mode allows every user to access the ECMWF `public datasets`_ from their local facilities. ``Flex_extract`` is able (tested for the use with ``FLEXPART``) to extract the re-analysis datasets such as ERA-Interim and CERA-20C. The main difference to the **member state user** 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 ``CONTROL`` 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 :ref:`ref-licence`.
+ This access mode allows every user to access the ECMWF `public datasets`_ from their local facilities. ``Flex_extract`` is able to extract the re-analysis datasets such as ERA-Interim and CERA-20C for use with ``FLEXPART`` (tested). The main difference to the **member-state user** is the method of access with the Web API and the availability of data. For example, in ERA-Interim, only a 6-hourly temporal resolution is available 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 ``CONTROL`` file. Also, the user has to explicitly accept the license of the data set to be retrieved. This can be done as described in the installation process at section :ref:`ref-licence`.
.. note::
- The availability of the public dataset *ERA5* with the ECMWF Web API was cancelled in March 2019. The oportunity of local retrieval of this dataset was moved to the `Climate Data Store`_ which uses another Web API named `CDS API`_. This Data Store stores the data on explicit webservers for faster and easier access. Unfortunately, for *ERA5* there are only surface level and pressure level data available for *public users*. In the case of a *member user* it is possible to bypass the request to the MARS archive from ECMWF to retrieve the data. ``Flex_extract`` is already modified to use this API so *member user* can already retrieve *ERA5* data while *public users* have to wait until model level are available.
+ The availability of the public dataset *ERA5* with the ECMWF Web API was cancelled by ECWMF in March 2019. Local retrieval of this dataset now has to use the `Climate Data Store`_ (CDS) with a different Web API called `CDS API`_. CDS stores the data on dedicated web servers for faster and easier access. Unfortunately, for *ERA5*, only surface level and pressure level data are available for *public users* which is not enough to run FLEXPART. For a *member user*, it is possible to pass the request to the MARS archive to retrieve the data. ``Flex_extract`` is already modified to use this API so a *member user* can already retrieve *ERA5* data for FLEXPART while *public users* have to wait until model level are made available.
For information on how to register see :ref:`ref-registration`.
diff --git a/Documentation/html/_sources/Ecmwf/ec-links.rst.txt b/Documentation/html/_sources/Ecmwf/ec-links.rst.txt
index 4095813c39f14a3449beb1fdd9d5d3e8fb34b6de..c596a00571e931ec6aa1e7013c0a59c5afb9975c 100644
--- a/Documentation/html/_sources/Ecmwf/ec-links.rst.txt
+++ b/Documentation/html/_sources/Ecmwf/ec-links.rst.txt
@@ -1,53 +1,53 @@
################################
-Link Collection for Quick finder
+Link collection
################################
-ECMWF - General Overview
+ECMWF - General overview
`ECMWF Home <https://www.ecmwf.int/>`_
- `ECMWF Training <https://www.ecmwf.int/en/learning>`_
+ `ECMWF training <https://www.ecmwf.int/en/learning>`_
- `General User Documentation <https://software.ecmwf.int/wiki/display/UDOC/User+Documentation>`_
+ `General user documentation <https://software.ecmwf.int/wiki/display/UDOC/User+Documentation>`_
- `Software Support <https://confluence.ecmwf.int/display/SUP>`_
+ `Software support <https://confluence.ecmwf.int/display/SUP>`_
MARS
`MARS user documentation <https://confluence.ecmwf.int//display/UDOC/MARS+user+documentation>`_
- `MARS Keywords <https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords>`_
+ `MARS keywords <https://software.ecmwf.int/wiki/display/UDOC/MARS+keywords>`_
- `MARS Content <https://confluence.ecmwf.int/display/UDOC/MARS+content>`_
+ `MARS content <https://confluence.ecmwf.int/display/UDOC/MARS+content>`_
- `MARS Actions <https://confluence.ecmwf.int/display/UDOC/MARS+actions>`_
+ `MARS actions <https://confluence.ecmwf.int/display/UDOC/MARS+actions>`_
- `Parameter Database <https://apps.ecmwf.int/codes/grib/param-db>`_
+ `Parameter database <https://apps.ecmwf.int/codes/grib/param-db>`_
Registration
- `Contact of Computing Representative's <https://www.ecmwf.int/en/about/contact-us/computing-representatives>`_
+ `Contacts of Computing Representatives <https://www.ecmwf.int/en/about/contact-us/computing-representatives>`_
`Public registration for ECMWF Web API <https://software.ecmwf.int/wiki/display/WEBAPI/Access+MARS>`_
- `CDS Registration <https://cds.climate.copernicus.eu/user/register>`_
+ `CDS registration <https://cds.climate.copernicus.eu/user/register>`_
-Available Member State Datasets
- `Web Interface for accessing member state datasets <http://apps.ecmwf.int/archive-catalogue/>`_
+Member-State data sets available
+ `Web interface for accessing member-state data sets <http://apps.ecmwf.int/archive-catalogue/>`_
- `Available datasets for member state users <https://www.ecmwf.int/en/forecasts/datasets>`_
+ `Data sets available for member state users <https://www.ecmwf.int/en/forecasts/datasets>`_
-Available Public Datasets
- `Web Interface for accessing public datasets <http://apps.ecmwf.int/datasets/>`_
+Public data sets available
+ `Web interface for accessing public data sets <http://apps.ecmwf.int/datasets/>`_
- `ECMWF's public datasets <https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets>`_
+ `ECMWF's public data sets <https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets>`_
- `Public dataset Licences <https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets>`_
+ `Public data set licences <https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets>`_
- `ERA5 public dataset Licence <https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset>`_
+ `ERA5 public dataset licence <https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset>`_
Datasets
Overview
- `Complete list of datasets <https://www.ecmwf.int/en/forecasts/datasets>`_
+ `Complete list of data sets <https://www.ecmwf.int/en/forecasts/datasets>`_
`What is climate reanalysis <https://www.ecmwf.int/en/research/climate-reanalysis>`_
@@ -56,7 +56,7 @@ Datasets
Real-time (Operational)
`List of real_time datasets <https://www.ecmwf.int/en/forecasts/datasets/catalogue-ecmwf-real-time-products>`_
- `Atmospheric model - HRES (our typical operational dataset) <https://www.ecmwf.int/en/forecasts/datasets/set-i>`_
+ `Atmospheric model - HRES (typical operational dataset) <https://www.ecmwf.int/en/forecasts/datasets/set-i>`_
`Atmospheric model - ENS (15-day ensemble forecast) <https://www.ecmwf.int/en/forecasts/datasets/set-iii>`_
@@ -65,12 +65,12 @@ Datasets
`ERA-Interim documentation <https://www.ecmwf.int/en/elibrary/8174-era-interim-archive-version-20>`_
- `ERA-Interim dataset <https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/era-interim>`_
+ `ERA-Interim data set <https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/era-interim>`_
CERA-20C
`What is CERA-20C <https://software.ecmwf.int/wiki/display/CKB/What+is+CERA-20C>`_
- `CERA-20C dataset <https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/cera-20c>`_
+ `CERA-20C data set <https://www.ecmwf.int/en/forecasts/datasets/archive-datasets/reanalysis-datasets/cera-20c>`_
ERA5
`What is ERA5 <https://software.ecmwf.int/wiki/display/CKB/What+is+ERA5>`_
@@ -83,8 +83,8 @@ Datasets
`ERA5 Documentation <https://software.ecmwf.int/wiki/display/CKB/ERA5+data+documentation>`_
-Third Party Libraries
- `ECMWF Web API Home <https://software.ecmwf.int/wiki/display/WEBAPI/ECMWF+Web+API+Home>`_
+Third-party libraries
+ `ECMWF Web API home <https://software.ecmwf.int/wiki/display/WEBAPI/ECMWF+Web+API+Home>`_
`Building ECMWF software with gfortran <https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran>`_
@@ -102,18 +102,18 @@ Plotting GRIB fields:
`Example Python script to plot GRIB files <https://software.ecmwf.int/wiki/display/CKB/How+to+plot+GRIB+files+with+Python+and+matplotlib>`_
-Scientific Information
- `Octahedral reduced Gaussian Grid <https://confluence.ecmwf.int/display/FCST/Introducing+the+octahedral+reduced+Gaussian+grid>`_
+Scientific information
+ `Octahedral reduced Gaussian grid <https://confluence.ecmwf.int/display/FCST/Introducing+the+octahedral+reduced+Gaussian+grid>`_
`Precipitation <https://www.ecmwf.int/en/newsletter/147/meteorology/use-high-density-observations-precipitation-verification>`_
-Technical Information of ECMWF serves
+Technical information for ECMWF servers
- `Introduction presentation to SLURM <https://confluence.ecmwf.int/download/attachments/73008494/intro-slurm-2017.pdf?version=1&modificationDate=1488574096323&api=v2>`_
+ `Introductary presentation of SLURM <https://confluence.ecmwf.int/download/attachments/73008494/intro-slurm-2017.pdf?version=1&modificationDate=1488574096323&api=v2>`_
-Troubleshooting
- `ECMWF Web API Troubleshooting <https://confluence.ecmwf.int/display/WEBAPI/Web-API+Troubleshooting>`_
+Trouble-shooting
+ `ECMWF Web API trouble-shooting <https://confluence.ecmwf.int/display/WEBAPI/Web-API+Troubleshooting>`_
diff --git a/Documentation/html/_sources/Ecmwf/hintsecmwf.rst.txt b/Documentation/html/_sources/Ecmwf/hintsecmwf.rst.txt
index e601cffa1e17f1976883f8baa2d1969ad3e579cf..00e3bc105ca142ab96012e69b38d48d3b2c7b5ee 100644
--- a/Documentation/html/_sources/Ecmwf/hintsecmwf.rst.txt
+++ b/Documentation/html/_sources/Ecmwf/hintsecmwf.rst.txt
@@ -1,5 +1,5 @@
##################################
-Hints to specify dataset retrieval
+Hints for data set selection
##################################
.. contents::
@@ -7,13 +7,13 @@ Hints to specify dataset retrieval
-How can I find out what data is available?
-==========================================
+How can I find out what data are available?
+===========================================
-Go to the `Web Interface for accessing member state datasets <http://apps.ecmwf.int/archive-catalogue/>`_
+Go to the `Web Interface for accessing member-state data sets <http://apps.ecmwf.int/archive-catalogue/>`_
and click yourself through the steps to define your set of data and see what is available to you.
-For public users there is the `Web Interface for accessing public datasets <http://apps.ecmwf.int/datasets/>`_.
+For public users there is the `Web Interface for accessing public data sets <http://apps.ecmwf.int/datasets/>`_.
diff --git a/Documentation/html/_sources/Ecmwf/msdata.rst.txt b/Documentation/html/_sources/Ecmwf/msdata.rst.txt
index da321a9807365d90f16d463601f1381c390718da..009dbc2ccea125686c1dd61d87d5bb496c0318b8 100644
--- a/Documentation/html/_sources/Ecmwf/msdata.rst.txt
+++ b/Documentation/html/_sources/Ecmwf/msdata.rst.txt
@@ -1,16 +1,16 @@
-#########################################
-Available Datasets for Member State users
-#########################################
+##########################################
+Available data sets for member-state users
+##########################################
-Model level data
+Model-level data
================
.. figure:: ../_files/ECMWF_FPparameter_ml.png
-Surface level data
+Surface data
==================
.. figure:: ../_files/ECMWF_FPparameter_sfc-0.png
diff --git a/Documentation/html/_sources/Ecmwf/pubdata.rst.txt b/Documentation/html/_sources/Ecmwf/pubdata.rst.txt
index 277b09106f662789f45d2d578b1d25390175b0d5..51a09bbcb991ebb0b8a8249f593c54f0c7447250 100644
--- a/Documentation/html/_sources/Ecmwf/pubdata.rst.txt
+++ b/Documentation/html/_sources/Ecmwf/pubdata.rst.txt
@@ -1,7 +1,7 @@
-Available Datasets for Public users
-***********************************
+Available data sets for public users
+************************************
- IN PREPARATION
+ UNDER PREPARATION
.. toctree::
diff --git a/Documentation/html/_sources/Evaluation/staticcode.rst.txt b/Documentation/html/_sources/Evaluation/staticcode.rst.txt
index 52e54138a51157463e6603d3fa443d0c7b1f580e..a90b9bfcb77af67cbb33e6d417231d064a73c5fd 100644
--- a/Documentation/html/_sources/Evaluation/staticcode.rst.txt
+++ b/Documentation/html/_sources/Evaluation/staticcode.rst.txt
@@ -1,5 +1,5 @@
********************
-Static Code Analysis
+Static code analysis
********************
UNDER CONSTRUCTION
diff --git a/Documentation/html/_sources/Evaluation/testcases.rst.txt b/Documentation/html/_sources/Evaluation/testcases.rst.txt
index 4855aa703ec7129d8ee536afc7dab6f715314152..825995612f9e9199b1c52a8a4f9c5fbcb72d9b18 100644
--- a/Documentation/html/_sources/Evaluation/testcases.rst.txt
+++ b/Documentation/html/_sources/Evaluation/testcases.rst.txt
@@ -1,5 +1,5 @@
********************
-Testcases
+Test cases
********************
@@ -10,7 +10,7 @@ Comparison of MARS requests
-Comparison of grib files
+Comparison of GRIB files
========================
UNDER CONSTRUCTION
diff --git a/Documentation/html/_sources/Installation/local.rst.txt b/Documentation/html/_sources/Installation/local.rst.txt
index cf86470b625d135acfea6f15db98b58daf924f0a..6a7cecca50ad076461827a9ffc7898e1370965d8 100644
--- a/Documentation/html/_sources/Installation/local.rst.txt
+++ b/Documentation/html/_sources/Installation/local.rst.txt
@@ -50,33 +50,34 @@ Local mode - dependencies
The installation is the same for the access modes **member** and **public**.
-The environment on your local system has to provide these software packages
+The environment on your local system has to provide the following software packages
and libraries, since the preparation of the extraction and the post-processing is done on the local machine:
-+------------------------------------------------+-----------------+
-| Python part | Fortran part |
-+------------------------------------------------+-----------------+
-| * `Python3`_ | * `gfortran`_ |
-| * `numpy`_ | * `fftw3`_ |
-| * `genshi`_ | * `eccodes`_ |
-| * `eccodes for python`_ | * `emoslib`_ |
-| * `ecmwf-api-client`_ (everything except ERA5) | |
-| * `cdsapi`_ (just for ERA5 and member user) | |
-+------------------------------------------------+-----------------+
++-------------------------------------------------+-----------------+
+| Python part | Fortran part |
++-------------------------------------------------+-----------------+
+| 1. `Python3`_ | 1. `gfortran`_ |
+| 2. `numpy`_ | 2. `fftw3`_ |
+| 3. `genshi`_ | 3. `eccodes`_ |
+| 4. `eccodes for python`_ | 4. `emoslib`_ |
+| 5. `ecmwf-api-client`_ (everything except ERA5) | |
+| 6. `cdsapi`_ (just for ERA5 and member user) | |
++-------------------------------------------------+-----------------+
.. _ref-prep-local:
-Prepare local environment
-=========================
+Preparing the local environment
+===============================
-The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights.
+The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights.
The installation was tested on a *Debian GNU/Linux buster* and an *Ubuntu 18.04 Bionic Beaver* system.
.. code-block:: sh
- # On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager):
- # (if not already available):
+ # On a Debian or Debian-derived (e. g. Ubuntu) system,
+ # you may use the following commands (or equivalent commands of your preferred package manager):
+ # (if respective packages are not already available):
apt-get install python3 (usually already available on GNU/Linux systems)
apt-get install python3-eccodes
apt-get install python3-genshi
@@ -85,46 +86,47 @@ The installation was tested on a *Debian GNU/Linux buster* and an *Ubuntu 18.04
apt-get install fftw3-dev
apt-get install libeccodes-dev
apt-get install libemos-dev
- # Some of these packages will pull in further packages as dependencies. This is fine, and some are even needed by ``flex_extract''.
-
+ # Some of these packages will pull in further packages as dependencies.
+ # This is fine, and some are even needed by ``flex_extract''.
- # As currently the CDS and ECMWF API packages are not available as Debian packages, they need to be installed outside of the Debian (Ubuntu etc.) package management system. The recommended way is:
+ # As currently the CDS and ECMWF API packages are not available as Debian packages,
+ # they need to be installed outside of the Debian (Ubuntu etc.) package management system.
+ # The recommended way is:
apt-get install pip
pip install cdsapi
pip install ecmwf-api-client
.. note::
- In case you would like to use Anaconda Python we recommend you follow the installation instructions of
- `Anaconda Python Installation for Linux <https://docs.anaconda.com/anaconda/install/linux/>`_ and then install the
- ``eccodes`` package from ``conda`` with:
+ If you are using Anaconda Python, we recommend to follow the installation instructions of
+ `Anaconda Python Installation for Linux <https://docs.anaconda.com/anaconda/install/linux/>`_
+ and then install the ``eccodes`` package from ``conda`` with:
.. code-block:: bash
conda install conda-forge::python-eccodes
-The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.
+The CDS API (``cdsapi``) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.
.. note::
- Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``.
+ Since **public users** currently don't have access to the full *ERA5* dataset, they can skip the installation of the CDS API.
-Both user groups have to provide keys with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
+Both user groups have to provide keys with their credentials for the Web APIs in their home directory, following these instructions:
ECMWF Web API:
- Go to `MARS access`_ website and log in with your credentials. Afterwards, on this site in section "Install ECMWF KEY" the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file `.ecmwfapirc` in your home directory).
+ Go to the `MARS access`_ website and log in with your credentials. Afterwards, go to the section "Install ECMWF KEY", where the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file ``.ecmwfapirc`` in your home directory).
CDS API:
- Go to `CDS API registration`_ and register there too. Log in at the `cdsapi`_ website and follow the instructions at section "Install the CDS API key" to save your credentials in a `.cdsapirc` file.
+ Go to `CDS API registration`_ and register there, too. Log in on the `cdsapi`_ website and follow the instructions in the section "Install the CDS API key" to save your credentials in file ``.cdsapirc``.
.. _ref-test-local:
-Test local environment
-======================
-
-Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment.
+Testing the local environment
+=============================
+Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell:
.. code-block:: python
# check in python3 console
@@ -134,10 +136,11 @@ Check the availability of the python packages by typing ``python3`` in a termina
import cdsapi
import ecmwfapi
+If there are no error messages, you succeeded in setting up the environment.
-Test the Web API's
-------------------
+Testing the Web APIs
+--------------------
You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using ``flex_extract`` later on.
@@ -147,7 +150,7 @@ ECMWF Web API
+----------------------------------------------------------+----------------------------------------------------------+
-|Please use this piece of Python code for **Member user**: |Please use this piece of Python code for **Public user**: |
+|Please use this Python code snippet as a **Member user**: |Please use this Python code snippet as a **Public user**: |
+----------------------------------------------------------+----------------------------------------------------------+
|.. code-block:: python |.. code-block:: python |
| | |
@@ -177,7 +180,7 @@ CDS API
Extraction of ERA5 data via CDS API might take time as currently there is a high demand for ERA5 data. Therefore, as a simple test for the API just retrieve pressure-level data (even if that is NOT what we need for FLEXPART), as they are stored on disk and don't need to be retrieved from MARS (which is the time-consuming action):
-Please use this piece of Python code to retrieve a small sample of *ERA5* pressure levels:
+Please use the following Python code snippet to retrieve a small sample of *ERA5* pressure level data:
.. code-block:: python
@@ -203,7 +206,7 @@ If you know that your CDS API works, you can try to extract some data from MARS.
.. **Member-state user**
-Please use this piece of Python code to retrieve a small *ERA5* data sample as a **member-state user**! The **Public user** do not have access to the full *ERA5* dataset!
+Please use the following Python code snippet to retrieve a small *ERA5* data sample as a **member-state user**! The **Public user** do not have access to the full *ERA5* dataset!
.. code-block:: python
@@ -267,26 +270,22 @@ Please use this piece of Python code to retrieve a small *ERA5* data sample as a
Local installation
==================
-First prepare the Fortran ``makefile`` for your environment and set it in the ``setup.sh`` script. (See section :ref:`Fortran Makefile <ref-convert>` for more information.)
-``flex_extract`` comes with two ``makefiles`` prepared for the ``gfortran`` compiler. One for the normal use ``makefile_fast`` and one for debugging ``makefile_debug`` which is usually only resonable for developers.
-
-They assume that ``eccodes`` and ``emoslib`` are installed as distribution packages and can be found at ``flex_extract_vX.X/Source/Fortran``, where ``vX.X`` should be substituted with the current version number.
+First, adapt the Fortran ``makefile`` for your environment (if necessary) and insert it into ``setup.sh`` script (see :ref:`Fortran Makefile <ref-convert>` for more information).
+They can be found at ``flex_extract_vX.X/Source/Fortran/``, where ``vX.X`` should be substituted by the current flex_extract version number.
.. caution::
It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
``makefiles`` if other than standard paths are used.
-So starting from the root directory of ``flex_extract``,
-go to the ``Fortran`` source directory and open the ``makefile`` of your
-choice to modify with an editor of your choice. We use the ``nedit`` in this case.
+Thus, go to the ``Fortran`` source directory and open the ``makefile`` of your
+choice, and check / modify with an editor of your choice:
.. code-block:: bash
cd flex_extract_vX.X/Source/Fortran
nedit makefile_fast
-Edit the paths to the ``eccodes`` library on your local machine.
-
+Set the paths to the ``eccodes`` library on your local machine, if necessary.
.. caution::
This can vary from system to system.
@@ -301,22 +300,22 @@ Edit the paths to the ``eccodes`` library on your local machine.
to find out the path to the ``eccodes`` library.
-Substitute these paths in the ``makefile`` for parameters **ECCODES_INCLUDE_DIR**
-and **ECCODES_LIB** and save it.
+Assign these paths to the parameters **ECCODES_INCLUDE_DIR**
+and **ECCODES_LIB** in the makefile, and save it.
.. code-block:: bash
- # these are the paths on a current Debian 10 Testing system (May 2019)
+ # these are the paths on Debian Buster:
ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm
The Fortran program called ``calc_etadot`` will be compiled during the
-installation process.Therefore the name of the ``makefile`` to be used needs to be given in ``setup.sh``.
+installation process. Therefore, the name of the ``makefile`` to be used needs to be given in ``setup.sh``.
In the root directory of ``flex_extract``, open the ``setup.sh`` script
-and adapt the installation parameters in the section labelled with
-"AVAILABLE COMMANDLINE ARGUMENTS TO SET" like shown below.
+with an editor and adapt the installation parameters in the section labelled with
+"AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:
.. code-block:: bash
diff --git a/Documentation/html/_sources/dev_guide.rst.txt b/Documentation/html/_sources/dev_guide.rst.txt
index 05cde2cccd2032d6d12935156d3b5259a7f58e2d..69f585e106015565edfcee0ddf105b02b00dd4ae 100644
--- a/Documentation/html/_sources/dev_guide.rst.txt
+++ b/Documentation/html/_sources/dev_guide.rst.txt
@@ -5,9 +5,9 @@ Developer Guide
.. note::
- This section still needs to be done.
+ This section still needs to be written.
-.. repository (how /who manages the code, where to get)
+.. repository (how / who manages the code, where to get)
.. toctree::
diff --git a/Documentation/html/_sources/documentation.rst.txt b/Documentation/html/_sources/documentation.rst.txt
index b6f78f596f5a67e82f85ee490e9c231e9f8e07e6..c7c8fc782cb867a7705224d60087031aeba39e2b 100644
--- a/Documentation/html/_sources/documentation.rst.txt
+++ b/Documentation/html/_sources/documentation.rst.txt
@@ -2,21 +2,21 @@
Documentation
*************
- Overview (Under construction)
+ Overview (under construction)
- Control & Input Data
+ Control & input data
- Output Data (Under construction)
+ Output data (under construction)
- Disaggregation of Flux Data (Under construction)
+ Disaggregation of flux data (under construction)
- Vertical Coordinate (Under construction)
- - Methods (GAUSS, ETA, OMEGA)
+ Vertical coordinate (under construction)
+ - methods (GAUSS, ETA, OMEGA)
- calc_etadot
- Auto Generated Documentation
+ Auto-generated documentation
- Python
- - Fortran (Under construction)
+ - Fortran (under construction)
.. toctree::
diff --git a/Documentation/html/_sources/ecmwf_data.rst.txt b/Documentation/html/_sources/ecmwf_data.rst.txt
index 35ddb57bb0566255586d1cd9088d6d48b215dd71..cfaacf79fdafa1132b08baf751dee3cecec4ee04 100644
--- a/Documentation/html/_sources/ecmwf_data.rst.txt
+++ b/Documentation/html/_sources/ecmwf_data.rst.txt
@@ -6,29 +6,29 @@ ECMWF Data
.. _Member States: https://www.ecmwf.int/en/about/who-we-are/member-states
-The European Centre for Medium-Range Weather Forecasts (`ECMWF`_), based in Reading, UK, is an independent intergovernmental organisation supported by 34 states. It is both a research institute and a full time operational service. It produces global numerical weather predictions and some other data which is fully available to the national meteorological services in the `Member States`_, Co-operating States and the broader community. Especially, the published re-analysis datasets are made available to the public with some limits in specific datasets.
+The European Centre for Medium-Range Weather Forecasts (`ECMWF`_), based in Reading, UK, is an independent intergovernmental organisation supported by 34 states. It is both a research institute and a 24 h / 7 d operational service. It produces global numerical weather predictions and some other data which are fully available to the national meteorological services in the `Member States`_, Co-operating States, and to some extend to the broader community. Specifically, re-analysis data sets are made available to the public, however, with some limitations for specific data sets.
-The amount and structure of the available data from ECMWF is very complex. The operational data changes regularly in time and spatial resolution, physics and parameter. This has to be taken into account carefully and each user has to investigate his dataset of interest carefully before selecting and retrieving it with ``flex_extract``.
-The re-analysis datasets are consistent in all the above mentioned topics over their whole period but they have each their own specialities which makes treatment with ``flex_extract`` special in some way. For example, they have different starting times for their forecasts or different parameter availability. They also have differences in time and spatial resolution and most importantly for ``flex_extract`` they are different in the way of providing the vertical coordinate.
+There is vast amount and of data with a complex structure available from ECMWF. The operational data undergo changes with respect to temporal and spatial resolution, model physics and parameters available. This has to be taken into account carefully and every user should have a clear idea of the data set intended to be used before retrieving it with ``flex_extract``.
+Each re-analysis data set is homogeneous with respect to resolution etc., but the different re-analyses alll have specific properties which requires a corresponding treatment with ``flex_extract``. For example, the starting times of the forecasts may be different, or the availability of parameters (model output variables) may vary. They also differ in their temporal and spatial resolution, and - most importantly for ``flex_extract`` - there are differences in the way how the vertical wind component may be accessed.
-There is much to learn from ECMWF and their datasets and data handling and this might be confusing at first. We therefore collected the most important information for ``flex_extract`` users. In the following sections the user can use them to get to know enough to understand how ``flex_extract`` is best used and to select the parameters of the ``CONTROL`` files.
+As there is much to learn about ECMWF and its data sets and data handling, it might be confusing at first. Therefore, we have here collected the information which is most important for ``flex_extract`` users. Study the following sections to learn how ``flex_extract`` is best used, and to select the right parameters in the ``CONTROL`` files.
:doc:`Ecmwf/access`
- Description of available access methods to the ECMWF data.
+ Description of available methods to access the ECMWF data.
:doc:`Ecmwf/msdata`
- Information about available data and parameters for member state users which can be retrieved with ``flex_extract``
+ Information about available data and parameters for member-state users which can be retrieved with ``flex_extract``
:doc:`Ecmwf/pubdata`
- Information about available data and parameters for the public datasets which can be retrieved with ``flex_extract``
+ Information about available data and parameters for the public data sets which can be retrieved with ``flex_extract``
:doc:`Ecmwf/hintsecmwf`
- Collection of hints to best find information to define the dataset for retrievement and
- to define the ``CONTROL`` files.
+ Collection of hints to best find information to define the data set for retrieval, and
+ to define the content of the ``CONTROL`` files.
:doc:`Ecmwf/ec-links`
- Link collection for additional and useful information as well as references to specific dataset publications.
+ Link collection for additional and useful information as well as references to publications on specific data sets.
.. toctree::
diff --git a/Documentation/html/_sources/evaluation.rst.txt b/Documentation/html/_sources/evaluation.rst.txt
index 65ef79934adc72117f61376f7af16e32c0486879..2987b908c7eefad56f844ae4bb4253c5c40c2400 100644
--- a/Documentation/html/_sources/evaluation.rst.txt
+++ b/Documentation/html/_sources/evaluation.rst.txt
@@ -5,8 +5,8 @@ Evaluation
.. note::
- This section in the online documentation still needs to be done.
- Currently, evaluation methods and information can be found in the `flex_extract discussion paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ of the Geoscientific Model Development journal.
+ This section still needs to be written.
+ Currently, evaluation methods can be found in the `flex_extract discussion paper <https://www.geosci-model-dev-discuss.net/gmd-2019-358/>`_ of the journal Geoscientific Model Development.
diff --git a/Documentation/html/_sources/index.rst.txt b/Documentation/html/_sources/index.rst.txt
index 9835e975aa60a61927233136b935645fea4d0126..be0f055ced67a84c805ceb789406db524a059c4c 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>
@@ -76,7 +76,7 @@ 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="Developers/gen_docu.html">Updateing the documentation</a></li>
<li><a href=""></a><Placeholder></li>
<li><a href=""></a><Placeholder></li>
</ul>
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..5b927c2c8f3477a8a1e12dc1d35850999fefeb3a 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.
@@ -262,8 +262,8 @@ The next level of differentiation would be the field type, level type and time p
CONTROL_OD.OPER.FC.eta.highres
CONTROL_OD.OPER.FC.gauss.highres
CONTROL_OD.OPER.FC.operational
- CONTROL_OD.OPER.FC.twiceaday.1hourly
- CONTROL_OD.OPER.FC.twiceaday.3hourly
+ CONTROL_OD.OPER.FC.twicedaily.1hourly
+ CONTROL_OD.OPER.FC.twicedaily.3hourly
@@ -276,21 +276,20 @@ The main differences and features in the datasets are listed in the table shown
-A common problem for beginners in retrieving ECMWF datasets is the mismatch in the definition of these parameters. For example, if you would like to retrieve operational data before ``June 25th 2013`` and set the maximum level to ``137`` you will get an error because this number of levels was first introduced at this effective day. So, be cautious in the combination of space and time resolution as well as the field types which are not available all the time.
+A common problem for beginners in retrieving ECMWF datasets is a mismatch in the choice of values for these parameters. For example, if you try to retrieve operational data for 24 June 2013 or earlier and set the maximum level to 137, you will get an error because this number of levels was introduced only on 25 June 2013. Thus, be careful in the combination of space and time resolution as well as the field types.
.. note::
- Sometimes it might not be clear how specific parameters in the control file must be set in terms of format. Please see the description of the parameters in section `CONTROL parameters <Documentation/Input/control_params.html>`_ or have a look at the ECMWF user documentation for `MARS keywords <https://confluence.ecmwf.int/display/UDOC/MARS+keywords>`_
+ Sometimes it might not be clear how specific parameters in the control file must be set in terms of format. Please consult the description of the parameters in section `CONTROL parameters <Documentation/Input/control_params.html>`_ or have a look at the ECMWF user documentation for `MARS keywords <https://confluence.ecmwf.int/display/UDOC/MARS+keywords>`_
-
-In the following we shortly discuss the main retrieval opportunities of the different datasets and categoize the ``CONTROL`` files.
+In the following, we shortly discuss the typical retrievals for the different datasets and point to the respective ``CONTROL`` files.
Public datasets
---------------
-The main difference in the definition of a ``CONRTOL`` file for a public dataset is the setting of the parameter ``DATASET``. This specification enables the selection of a public dataset in MARS. Otherwise the request would not find the dataset.
+The main characteristic in the definition of a ``CONTROL`` file for a public dataset is the parameter ``DATASET``. Its specification enables the selection of a public dataset in MARS. Without this parameter, the request would not find the dataset.
For the two public datasets *CERA-20C* and *ERA-Interim* an example file with the ending ``.public`` is provided and can be used straightaway.
.. code-block:: bash
@@ -298,50 +297,50 @@ For the two public datasets *CERA-20C* and *ERA-Interim* an example file with th
CONTROL_CERA.public
CONTROL_EI.public
-For *CERA-20C* it seems that there are no differences in the dataset against the full dataset, while the *public ERA-Interim* has only analysis fields every 6 hour without filling forecasts in between for model levels. Therefore it is only possible to retrieve 6-hourly data for *public ERA-Interim*.
+For *CERA-20C* it seems that there are no differences compared the full dataset, whereas the *public ERA-Interim* has only 6-hourly analysis fields, without forecasts to fill in between, for model levels. Therefore, it is only possible to retrieve 6-hourly data for *public ERA-Interim*.
.. note::
- In general, *ERA5* is a public dataset. However, since the model levels are not yet publicly available, it is not possible to retrieve *ERA5* data to drive the ``FLEXPART`` model. As soon as this is possible it will be announced at the community website and per newsletter.
+ In principle, *ERA5* is a public dataset. However, since the model levels are not yet publicly available, it is not possible to retrieve *ERA5* data to drive the ``FLEXPART`` model. As soon as this is possible it will be announced at the community website and on the FLEXPART user email list.
CERA
----
-For this dataset it is important to keep in mind that the dataset is available for the period 09/1901 until 12/2010 and the temporal resolution is limited to 3-hourly fields.
-It is also a pure ensemble data assimilation dataset and is stored under the ``enda`` stream. It has ``10`` ensemble members. The example ``CONTROL`` files will only select the first member (``number=0``). You may change this to another number or a list of numbers (e.g. ``NUMBER 0/to/10``).
-Another important difference to all other datasets is the forecast starting time which is 18 UTC. Which means that the forecast in *CERA-20C* for flux fields is 12 hours long. Since the forecast extends over a single day we need to extract one day in advance and one day subsequently. This is automatically done in ``flex_extract``.
+For this dataset, it is important to keep in mind that it is available for the period 09/1901 until 12/2010, and that the temporal resolution is limited to 3 h.
+It is also a pure ensemble data assimilation dataset and is stored under the ``enda`` stream.
+There are 10 ensemble members. The example ``CONTROL`` files retrieves the first member only (``number=0``). You may change this to another number or a list of numbers (e.g. ``NUMBER 0/to/10``).
+Another important difference to all other datasets is that there is one forecast per day, starting at 18 UTC. The forecast lead time is 24 hours and extends beyond the calendar day. Therefore, ``flex_extract`` needs to extract also the day before the first day for which data are desired, which is handled automatically.
ERA 5
-----
-This is the newest re-analysis dataset and has a temporal resolution of 1-hourly analysis fields. Up to date it is available until April 2019 with regular release of new months.
-The original horizontal resolution is ``0.28125°`` which needs some caution in the definition of the domain, since the length of the domain in longitude or latitude direction must be an exact multiple of the resolution. It might be easier for users to use ``0.25`` for the resolution which MARS will automatically interpolate.
-The forecast starting time is ``06/18 UTC`` which is important for the flux data. This should be set in the ``CONTROL`` file via the ``ACCTIME 06/18`` parameter in correspondence with ``ACCMAXSTEP 12`` and ``ACCTYPE FC``.
+This is the latest re-analysis dataset, and has a temporal resolution of 1-h (analysis fields). At the time of writing, it is available until April 2019 with regular release of new months.
+The original horizontal resolution is 0.28125° which needs some caution in the definition of the domain, since the length of the domain in longitude or latitude direction must be an integer multiple of the resolution. It is also possible to use ``0.25`` for the resolution; MARS will then automatically interpolate to this resolution which is still close enough to be acceptable.
+The forecast starting time is ``06/18 UTC`` which is important for the flux data. Correspondingly, one should set in the ``CONTROL`` file ``ACCTIME 06/18``, ``ACCMAXSTEP 12``, and ``ACCTYPE FC``.
.. note::
- We know that *ERA5* also has an ensemble data assimilation system but this is not yet retrievable with ``flex_extract`` since the deaccumulation of the flux fields works differently in this stream. Ensemble retrieval for *ERA5* is a future ToDo.
+ *ERA5* also includes an ensemble data assimilation system but related fields are not yet retrievable with ``flex_extract`` since the deaccumulation of the flux fields works differently in this stream. Ensemble field retrieval for *ERA5* is a *to-do* for the future.
ERA-Interim
-----------
-This re-analysis dataset will exceed its end of production at 31st August 2019!
-It is then available from 1st January 1979 to 31st August 2019. The ``etadot`` is not available in this dataset. Therefore ``flex_extract`` must select the ``GAUSS`` parameter to retrieve the divergence field in addition. The vertical velocity is the calculated with the continuity equation in the Fortran program ``calc_etadot``. Since the analysis fields are only available for every 6th hour, the dataset can be made 3 hourly by adding forecast fields in between. No ensemble members are available.
-
+The production of this re-analysis dataset has stopped on 31 August 2019!
+It is available for the period from 1 January 1979 to 31 August 2019. The ``etadot`` parameter is not available in this dataset. Therefore, one must use the ``GAUSS`` parameter, which retrieves the divergence field in addition and calculates the vertical velocity from the continuity equation in the Fortran program ``calc_etadot``. While the analysis fields are only available for every 6th hour, the dataset can be made 3-hourly by adding forecast fields in between. No ensemble members are available.
Operational data
----------------
-This is the real time atmospheric model in high resolution with a 10-day forecast. This means it underwent regular adaptations and improvements over the years. Hence, retrieving data from this dataset needs extra attention in selecting correct settings of parameter. See :ref:`ref-tab-dataset-cmp` for the most important parameters.
-Nowadays, it is available 1 hourly by filling the gaps of the 6 hourly analysis fields with 1 hourly forecast fields. Since 4th June 2008 the eta coordinate is directly available so that ``ETA`` should be set to ``1`` to save computation time. The horizontal resolution can be up to ``0.1°`` and in combination with ``137`` vertical levels can lead to troubles in retrieving this high resolution dataset in terms of job duration and quota exceedence.
-It is recommended to submit such high resolution cases for single day retrievals (see ``JOB_CHUNK`` parameter in ``run.sh`` script) to avoid job failures due to exceeding limits.
+This data set provides the output of the real-time atmospheric model runs in high resolution, including 10-day forecasts. The model undergoes frequent adaptations and improvements. Thus, retrieving data from this dataset requires extra attention in selecting correct settings of the parameters. See :ref:`[Table of datasets]<ref-tab-dataset-cmp>` for the most important parameters.
+Currently, fields can be retrieved at 1 h temporal resolution by filling the gaps between analysis fields with 1-hourly forecast fields. Since 4 June 2008, the eta coordinate vertical velocity is directly available from MARS, therefore ``ETA`` should be set to ``1`` to save computation time. The horizontal resolution can be up to ``0.1°`` and in combination with ``137`` vertical levels can lead to problems in terms of job duration and disk space quota.
+It is recommended to submit such high resolution cases as single day retrievals (see ``JOB_CHUNK`` parameter in ``run.sh`` script) to avoid job failures due to exceeding limits.
-``CONTROL`` files for normal daily retrievals with a mix of analysis and forecast fields are listed below:
+``CONTROL`` files for standard retrievals with a mix of analysis and forecast fields are listed below:
.. code-block:: bash
@@ -350,20 +349,18 @@ It is recommended to submit such high resolution cases for single day retrievals
CONTROL_OD.OPER.FC.eta.highres
CONTROL_OD.OPER.FC.gauss.highres
-These files defines the minimum number of parameters necessary to retrieve a daily subset. The setup of field types is optimal and should only be changed if the user understands what he does. The grid, domain and temporal resolution can be changed according to availability.
+These files defines the minimum number of parameters necessary to retrieve a daily subset. The given settings for the TYPE parameter are already optimised, and should only be changed if you know what you are doing. Grid, domain, and temporal resolution may be changed according to availability.
-
.. note::
- Please see `Information about MARS retrievement <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency>`_ to get to know hints about retrieval efficiency and troubleshooting.
-
+ Please see `Information about MARS retrievement <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency>`_ for hints about retrieval efficiency and troubleshooting.
Pure forecast
- It is possible to retrieve pure forecasts exceeding a day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecast of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
- The *CV* field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the *CF* type since this is available from 1992 (3-hourly) on up to today in 1-hourly temporal resolution. *CV* and *CF* field types belong to the *Ensemble prediction system (ENFO)* which contain 50 ensemble members.
- Please be aware that in this case it is necessary to set the specific type for flux fields explicitly, otherwise it could select a default value which might be different from what you expect!
+ It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
+ The *CV* field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the *CF* type since this is available from 1992 (3-hourly) on up to today (1-hourly). *CV* and *CF* field types belong to the *Ensemble prediction system (ENFO)* which currently works with 50 ensemble members.
+ Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!
.. code-block:: bash
@@ -372,62 +369,60 @@ Pure forecast
CONTROL_OD.OPER.FC.36hours
-
Half-day retrievals
- If a forecast for just half a day is wanted it can be done by substituting the analysis fields also by forecast fields as shown in files with ``twiceaday`` in it. They produce a full day retrieval with pure 12 hour forecasts twice a day. It is also possible to use the operational version which would get the time information from ECMWF's environmental variables and therefore get the newest forecast per day. This version uses a ``BASETIME`` parameter which tells MARS to extract the exact 12 hours upfront to the selected date. If the ``CONTROL`` file with ``basetime`` in the filename is used this can be done for any other date too.
+ If a forecast is wanted for half a day only, this can be done by substituting the analysis fields by forecast fields as shown in files with ``twicedaily`` in their name. They produce a full-day retrieval with pure 12 hour forecasts, twice a day. It is also possible to use the operational version which would obtain the time information from ECMWF's environment variables and therefore use the newest forecast for each day. This version uses a ``BASETIME`` parameter which tells MARS to extract the exact 12 hours up to the selected date. If the ``CONTROL`` file with ``basetime`` in the filename is used, this can be done for any other date, too.
.. code-block:: bash
CONTROL_OD.OPER.FC.eta.basetime
CONTROL_OD.OPER.FC.operational
- CONTROL_OD.OPER.FC.twiceaday.1hourly
- CONTROL_OD.OPER.FC.twiceaday.3hourly
-
-
+ CONTROL_OD.OPER.FC.twicedaily.1hourly
+ CONTROL_OD.OPER.FC.twicedaily.3hourly
Ensemble members
- The retrieval of ensemble members were already mentioned in the pure forecast section and for *CERA-20C* data.
- In this ``flex_extract`` version there is an additional possibility to retrieve the *Ensemble Long window Data Assimilation (ELDA)* stream from the real-time dataset. This model version has (up to May 2019) 25 ensemble members and a control run (``number 0``). Starting from June 2019 it has 50 ensemble members. Therefore we created the possibility to double up the 25 ensemble members (before June 2019) to 50 members by taking the original 25 members from MARS and subtracting 2 times the difference between the member value and the control value. This is done by selecting the parameter ``DOUBLEELDA`` and set it to ``1``.
-
+ The retrieval of ensemble members was already mentioned in the pure forecast section and for *CERA-20C* data.
+ This ``flex_extract`` version allows to retrieve the *Ensemble Long window Data Assimilation (ELDA)* stream from the operational dataset. Until May 2019, there were 25 ensemble members and a control run (``number 0``). Starting with June 2019, the number of ensemble members has been increased to 50. Therefore, we created the option to create 25 additional "pseudo-ensemble members" for periods before June 2019. The original 25 members from MARS are taken, and the difference between the member value and the control value is subtracted twice. This is done if the parameter ``DOUBLEELDA`` is included and set it to ``1``.
.. code-block:: bash
CONTROL_OD.ELDA.FC.eta.ens.double
CONTROL_OD.ENFO.PF.ens
-
-
Specific features
-----------------
rrint
- Decides if the precipitation flux data uses the old (``0``) or new (``1``) disaggregation scheme. See :doc:`Documentation/disagg` for explanaition.
+ Selects the disaggregation scheme for precipitation flux: old (``0``) or new (``1``). See :doc:`Documentation/disagg` for explanation.
cwc
- Decides if the total cloud water content will be retrieved (set to ``1``) in addition. This is the sum of cloud liquid and cloud ice water content.
+ If present and set to ``1``, the total cloud water content will be retrieved in addition. This is the sum of cloud liquid and cloud ice water content.
addpar
- With this parameter an additional list of 2-dimensional, non-flux parameters can be retrieved. Use format ``param1/param2/.../paramx`` to list the parameters. Please be consistent in using either the parameter IDs or the short names.
+ With this parameter. an additional list of 2-dimensional, non-flux parameters can be retrieved. Use the format ``param1/param2/.../paramx`` to list the parameters. Please be consistent in using either the parameter IDs or the short names as defined by MARS.
doubleelda
- Use this to double the ensemble member number by adding further disturbance to each member.
+ Use this to double the ensemble member number by adding further disturbance to each member (to be used with 25 members).
debug
- If set to ``1`` all temporary files were kept at the end. Otherwise everything except the final output files will be deleted.
+ If set to ``1``, all temporary files are preserved. Otherwise, everything except the final output files will be deleted.
request
- This produces an extra *csv* file ``mars_requests.csv`` where the content of each mars request of the job is stored. Useful for debugging and documentation.
+ This produces an extra *csv* file ``mars_requests.csv`` where the content of each MARS request submitted within the job is stored, which is useful for debugging and documentation. Possible values are 0 for normal data retrieval, 1 for not retrieving data and just writing out the MARS requests, and 2 to retrieve data and write out requests.
mailfail
- At default the mail is send to the mail connected with the user account. Add additional email addresses if you want. But as soon as you enter a new mail, the default will be overwritten. If you would like to keep the mail from your user account, please add ``${USER}`` to the list ( comma seperated ) or mail addresses.
-
+ As a default, e-mails are sent to the mail address defined for the ECMWF user account. It is possible to overwrite this by specifying one or more e-mail addresses (comma-separated list). In order to include the e-mail associated with the user account, add ``${USER}`` to the list.
-Hints for definition of some parameter combinations
----------------------------------------------------
+Hints for proper definition of certain parameter combinations
+-------------------------------------------------------------
+
+Field type and time
+ This combination is very important. It defines the temporal resolution and which field type is extracted on each time step.
+ The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
+ The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
+
+ .. todo::
-Field types and times
- This combination is very important. It defines the temporal resolution and which field type is extracted per time step.
- The time declaration for analysis (AN) fields uses the times of the specific analysis and (forecast time) steps have to be ``0``. The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) times and the (forecast) steps. Both of them together defines the actual time step. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general it is enough to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
+ #PS needs to be rephrased
.. code-block:: bash
- :caption: Example of a setting for the field types and temporal resolution.
+ :caption: Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.
DTIME 3
TYPE AN FC FC FC AN FC FC FC
@@ -436,10 +431,12 @@ Field types and times
Vertical velocity
- The vertical velocity for ``FLEXPART`` is not directly available from MARS. Therefore it has to be calculated. There are a couple of different options. The following parameters are responsible for the selection. See :doc:`Documentation/vertco` for a detailed explanation. The ``ETADIFF``, ``OMEGA`` and ``OMEGADIFF`` versions are only recommended for debugging and testing reasons. Usually it is a decision between ``GAUSS`` and ``ETA``, where for ``GAUSS`` spectral fields of the horizontal wind fields and the divergence are to be retrieved and used with the continuity equation to calculate the vertical velocity. For ``ETA`` the latitude/longitude fields of horizontal wind fields and eta-coordinate are to be retrieved. It is recommended to use ``ETA`` where possible due to a reduced computation time.
+ The vertical velocity for ``FLEXPART`` is not directly available from MARS and has to be calculated.
+ There are several options for this, and the following parameters are responsible for the selection. See :doc:`Documentation/vertco` for a detailed explanation. Using ``ETADIFF 1``, ``OMEGA 1`` and ``OMEGADIFF 1`` is recommended for debugging and testing only.
+ Usually, one has to decide between ``GAUSS 1`` and ``ETA 1``. ``GAUSS 1`` means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. ``ETA 1`` means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use ``ETA 1`` where possible, as there is a substantial computational overhead for solving the continuity equation.
.. code-block:: bash
- :caption: Example setting for the vertical coordinate retrieval.
+ :caption: Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).
GAUSS 0
ETA 1
@@ -450,12 +447,17 @@ Vertical velocity
Grid resolution and domain
- The grid and domain selection depends on each other. The grid can be defined in the format of normal degrees (e.g. ``1.``) or as in older versions by 1/1000. degrees (e.g. ``1000`` for ``1°``).
- After selecting the grid, the domain has to be defined in a way that the length of the domain in longitude or latitude direction must be an exact multiple of the grid.
- The horizontal resolution for spectral fields will be set by the parameter ``RESOL``. For information about how to select an appropriate value you can read the explanation of the MARS keyword `here <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and in `this table <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
+ The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
+ After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
+
+ .. todo::
+
+ #PS shouldn't we explain how to define a domain??
+
+ The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
.. code-block:: bash
- :caption: Example setting for a northern hemisphere domain with a grid of ``0.25°``.
+ :caption: Example setting for a domain covering the northern hemisphere domain with a grid resolution of ``0.25°``.
GRID 0.25
RESOL 799
@@ -467,17 +469,21 @@ Grid resolution and domain
Flux data
- The flux fields are accumulated forecast fields all the time. Since some re-analysis dataset nowadays have complete set of analysis fields in their temporal resolution it was important to define a new parameter set to define the flux fields since the information could not be taken from ``TYPE``, ``TIME`` and ``STEP`` any longer. Select a forecast field type ``ACCTYPE``, the forecast starting time ``ACCTIME`` and the maximum forecast step ``ACCMAXSTEP``. The ``DTIME`` parameter defines the temporal resolution for the whole period.
+ Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
+ .. todo::
+
+ #PS for which application would this be typical?
+
.. code-block:: bash
:caption: Example setting for the definition of flux fields.
+
DTIME 3
ACCTYPE FC
ACCTIME 00/12
ACCMAXSTEP 36
-
.. toctree::
:hidden:
diff --git a/Documentation/html/_sources/todo.rst.txt b/Documentation/html/_sources/todo.rst.txt
index 902e69e5f3b60fdd23fb121dc013416d5b0c212c..f8607af19b164a45a339d6978bdd062a7c60ac90 100644
--- a/Documentation/html/_sources/todo.rst.txt
+++ b/Documentation/html/_sources/todo.rst.txt
@@ -6,3 +6,5 @@ ToDos
.. todolist::
+
+
diff --git a/Documentation/html/dev_guide.html b/Documentation/html/dev_guide.html
index 03085d3ee5436e5b83b8ac8142f021f752ef5c0d..6332d59b50535062499419a5a562ceda99c660b7 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>
@@ -173,7 +173,7 @@
</div></blockquote>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>This section still needs to be done.</p>
+<p>This section still needs to be written.</p>
</div>
<div class="toctree-wrapper compound">
</div>
@@ -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/documentation.html b/Documentation/html/documentation.html
index 9f2a694106fedcbd5422232f90d174a5eebc6634..4fdf428dd2f6b0d7f003d17d79227ca3f241b961 100644
--- a/Documentation/html/documentation.html
+++ b/Documentation/html/documentation.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="Overview" href="Documentation/overview.html" />
- <link rel="prev" title="Link Collection for Quick finder" href="Ecmwf/ec-links.html" />
+ <link rel="prev" title="Link collection" href="Ecmwf/ec-links.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,11 +94,11 @@
<li class="toctree-l1"><a class="reference internal" href="ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Documentation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Documentation/overview.html">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Documentation/input.html">Control & Input Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Documentation/output.html">Output Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Documentation/disagg.html">Disaggregation of Flux Data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Documentation/vertco.html">Vertical Coordinate</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Documentation/api.html">Auto Generated Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Documentation/input.html">Control & input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Documentation/output.html">Output data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Documentation/disagg.html">Disaggregation of flux data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Documentation/vertco.html">Vertical wind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Documentation/api.html">Auto-generated documentation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="evaluation.html">Evaluation</a></li>
@@ -174,19 +174,19 @@
<div class="section" id="documentation">
<h1>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h1>
<blockquote>
-<div><p>Overview (Under construction)</p>
-<p>Control & Input Data</p>
-<p>Output Data (Under construction)</p>
-<p>Disaggregation of Flux Data (Under construction)</p>
+<div><p>Overview (under construction)</p>
+<p>Control & input data</p>
+<p>Output data (under construction)</p>
+<p>Disaggregation of flux data (under construction)</p>
<dl class="simple">
-<dt>Vertical Coordinate (Under construction)</dt><dd><ul class="simple">
-<li><p>Methods (GAUSS, ETA, OMEGA)</p></li>
+<dt>Vertical coordinate (under construction)</dt><dd><ul class="simple">
+<li><p>methods (GAUSS, ETA, OMEGA)</p></li>
<li><p>calc_etadot</p></li>
</ul>
</dd>
-<dt>Auto Generated Documentation</dt><dd><ul class="simple">
+<dt>Auto-generated documentation</dt><dd><ul class="simple">
<li><p>Python</p></li>
-<li><p>Fortran (Under construction)</p></li>
+<li><p>Fortran (under construction)</p></li>
</ul>
</dd>
</dl>
@@ -206,7 +206,7 @@
<a href="Documentation/overview.html" class="btn btn-neutral float-right" title="Overview" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="Ecmwf/ec-links.html" class="btn btn-neutral float-left" title="Link Collection for Quick finder" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="Ecmwf/ec-links.html" class="btn btn-neutral float-left" title="Link collection" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/ecmwf_data.html b/Documentation/html/ecmwf_data.html
index d43e95840e5388be8f07362c2ee3a2a15d528811..af8de77de3bb241da4dae9d5448ae96033a68275 100644
--- a/Documentation/html/ecmwf_data.html
+++ b/Documentation/html/ecmwf_data.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="Access Modes" href="Ecmwf/access.html" />
+ <link rel="next" title="Access modes" href="Ecmwf/access.html" />
<link rel="prev" title="Quick Start" href="quick_start.html" />
</head>
@@ -92,11 +92,11 @@
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">ECMWF Data</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Ecmwf/access.html">Access Modes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Ecmwf/msdata.html">Available Datasets for Member State users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Ecmwf/pubdata.html">Available Datasets for Public users</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Ecmwf/hintsecmwf.html">Hints to specify dataset retrieval</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Ecmwf/ec-links.html">Link Collection for Quick finder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Ecmwf/access.html">Access modes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Ecmwf/msdata.html">Available data sets for member-state users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Ecmwf/pubdata.html">Available data sets for public users</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Ecmwf/hintsecmwf.html">Hints for data set selection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Ecmwf/ec-links.html">Link collection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="documentation.html">Documentation</a></li>
@@ -172,21 +172,21 @@
<div class="section" id="ecmwf-data">
<h1>ECMWF Data<a class="headerlink" href="#ecmwf-data" title="Permalink to this headline">¶</a></h1>
-<p>The European Centre for Medium-Range Weather Forecasts (<a class="reference external" href="http://www.ecmwf.int">ECMWF</a>), based in Reading, UK, is an independent intergovernmental organisation supported by 34 states. It is both a research institute and a full time operational service. It produces global numerical weather predictions and some other data which is fully available to the national meteorological services in the <a class="reference external" href="https://www.ecmwf.int/en/about/who-we-are/member-states">Member States</a>, Co-operating States and the broader community. Especially, the published re-analysis datasets are made available to the public with some limits in specific datasets.</p>
-<p>The amount and structure of the available data from ECMWF is very complex. The operational data changes regularly in time and spatial resolution, physics and parameter. This has to be taken into account carefully and each user has to investigate his dataset of interest carefully before selecting and retrieving it with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.
-The re-analysis datasets are consistent in all the above mentioned topics over their whole period but they have each their own specialities which makes treatment with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> special in some way. For example, they have different starting times for their forecasts or different parameter availability. They also have differences in time and spatial resolution and most importantly for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> they are different in the way of providing the vertical coordinate.</p>
-<p>There is much to learn from ECMWF and their datasets and data handling and this might be confusing at first. We therefore collected the most important information for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> users. In the following sections the user can use them to get to know enough to understand how <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is best used and to select the parameters of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
+<p>The European Centre for Medium-Range Weather Forecasts (<a class="reference external" href="http://www.ecmwf.int">ECMWF</a>), based in Reading, UK, is an independent intergovernmental organisation supported by 34 states. It is both a research institute and a 24 h / 7 d operational service. It produces global numerical weather predictions and some other data which are fully available to the national meteorological services in the <a class="reference external" href="https://www.ecmwf.int/en/about/who-we-are/member-states">Member States</a>, Co-operating States, and to some extend to the broader community. Specifically, re-analysis data sets are made available to the public, however, with some limitations for specific data sets.</p>
+<p>There is vast amount and of data with a complex structure available from ECMWF. The operational data undergo changes with respect to temporal and spatial resolution, model physics and parameters available. This has to be taken into account carefully and every user should have a clear idea of the data set intended to be used before retrieving it with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.
+Each re-analysis data set is homogeneous with respect to resolution etc., but the different re-analyses alll have specific properties which requires a corresponding treatment with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. For example, the starting times of the forecasts may be different, or the availability of parameters (model output variables) may vary. They also differ in their temporal and spatial resolution, and - most importantly for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> - there are differences in the way how the vertical wind component may be accessed.</p>
+<p>As there is much to learn about ECMWF and its data sets and data handling, it might be confusing at first. Therefore, we have here collected the information which is most important for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> users. Study the following sections to learn how <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is best used, and to select the right parameters in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
<dl class="simple">
-<dt><a class="reference internal" href="Ecmwf/access.html"><span class="doc">Access Modes</span></a></dt><dd><p>Description of available access methods to the ECMWF data.</p>
+<dt><a class="reference internal" href="Ecmwf/access.html"><span class="doc">Access modes</span></a></dt><dd><p>Description of available methods to access the ECMWF data.</p>
</dd>
-<dt><a class="reference internal" href="Ecmwf/msdata.html"><span class="doc">Available Datasets for Member State users</span></a></dt><dd><p>Information about available data and parameters for member state users which can be retrieved with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></p>
+<dt><a class="reference internal" href="Ecmwf/msdata.html"><span class="doc">Available data sets for member-state users</span></a></dt><dd><p>Information about available data and parameters for member-state users which can be retrieved with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></p>
</dd>
-<dt><a class="reference internal" href="Ecmwf/pubdata.html"><span class="doc">Available Datasets for Public users</span></a></dt><dd><p>Information about available data and parameters for the public datasets which can be retrieved with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></p>
+<dt><a class="reference internal" href="Ecmwf/pubdata.html"><span class="doc">Available data sets for public users</span></a></dt><dd><p>Information about available data and parameters for the public data sets which can be retrieved with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></p>
</dd>
-<dt><a class="reference internal" href="Ecmwf/hintsecmwf.html"><span class="doc">Hints to specify dataset retrieval</span></a></dt><dd><p>Collection of hints to best find information to define the dataset for retrievement and
-to define the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
+<dt><a class="reference internal" href="Ecmwf/hintsecmwf.html"><span class="doc">Hints for data set selection</span></a></dt><dd><p>Collection of hints to best find information to define the data set for retrieval, and
+to define the content of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
</dd>
-<dt><a class="reference internal" href="Ecmwf/ec-links.html"><span class="doc">Link Collection for Quick finder</span></a></dt><dd><p>Link collection for additional and useful information as well as references to specific dataset publications.</p>
+<dt><a class="reference internal" href="Ecmwf/ec-links.html"><span class="doc">Link collection</span></a></dt><dd><p>Link collection for additional and useful information as well as references to publications on specific data sets.</p>
</dd>
</dl>
<div class="toctree-wrapper compound">
@@ -201,7 +201,7 @@ to define the <code class="docutils literal notranslate"><span class="pre">CONTR
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="Ecmwf/access.html" class="btn btn-neutral float-right" title="Access Modes" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="Ecmwf/access.html" class="btn btn-neutral float-right" title="Access modes" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="quick_start.html" class="btn btn-neutral float-left" title="Quick Start" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/Documentation/html/evaluation.html b/Documentation/html/evaluation.html
index 8f3905e41bf650ec488515e986587a82df29bf3f..9a5a54f4e2c2c10f209b4ffe1e509395bc8f271d 100644
--- a/Documentation/html/evaluation.html
+++ b/Documentation/html/evaluation.html
@@ -38,8 +38,8 @@
<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="Static Code Analysis" href="Evaluation/staticcode.html" />
- <link rel="prev" title="Fortran’s Auto Generated Documentation" href="Documentation/Api/api_fortran.html" />
+ <link rel="next" title="Static code analysis" href="Evaluation/staticcode.html" />
+ <link rel="prev" title="Auto-generated documentation for the Fortran programme" href="Documentation/Api/api_fortran.html" />
</head>
<body class="wy-body-for-nav">
@@ -94,8 +94,8 @@
<li class="toctree-l1"><a class="reference internal" href="ecmwf_data.html">ECMWF Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation.html">Documentation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Evaluation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Evaluation/staticcode.html">Static Code Analysis</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Evaluation/testcases.html">Testcases</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Evaluation/staticcode.html">Static code analysis</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Evaluation/testcases.html">Test cases</a></li>
<li class="toctree-l2"><a class="reference internal" href="Evaluation/metrics.html">Metrics</a></li>
</ul>
</li>
@@ -175,8 +175,8 @@
</div></blockquote>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>This section in the online documentation still needs to be done.
-Currently, evaluation methods and information can be found in the <a class="reference external" href="https://www.geosci-model-dev-discuss.net/gmd-2019-358/">flex_extract discussion paper</a> of the Geoscientific Model Development journal.</p>
+<p>This section still needs to be written.
+Currently, evaluation methods can be found in the <a class="reference external" href="https://www.geosci-model-dev-discuss.net/gmd-2019-358/">flex_extract discussion paper</a> of the journal Geoscientific Model Development.</p>
</div>
<div class="toctree-wrapper compound">
</div>
@@ -190,10 +190,10 @@ Currently, evaluation methods and information can be found in the <a class="refe
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="Evaluation/staticcode.html" class="btn btn-neutral float-right" title="Static Code Analysis" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="Evaluation/staticcode.html" class="btn btn-neutral float-right" title="Static code analysis" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="Documentation/Api/api_fortran.html" class="btn btn-neutral float-left" title="Fortran’s Auto Generated Documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="Documentation/Api/api_fortran.html" class="btn btn-neutral float-left" title="Auto-generated documentation for the Fortran programme" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/index.html b/Documentation/html/index.html
index 9802a9e1b867600d0ed2931fc7a3a0f68c229f23..43b187ce95db3389feacde1dd789677c4d765564 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>
@@ -230,7 +230,7 @@
</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="Developers/gen_docu.html">Updateing the documentation</a></li>
<li><a href=""></a><Placeholder></li>
<li><a href=""></a><Placeholder></li>
</ul>
@@ -284,7 +284,7 @@ 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>
@@ -309,7 +309,7 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p>
<li class="toctree-l3"><a class="reference internal" href="quick_start.html#era-interim">ERA-Interim</a></li>
<li class="toctree-l3"><a class="reference internal" href="quick_start.html#operational-data">Operational data</a></li>
<li class="toctree-l3"><a class="reference internal" href="quick_start.html#specific-features">Specific features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="quick_start.html#hints-for-definition-of-some-parameter-combinations">Hints for definition of some parameter combinations</a></li>
+<li class="toctree-l3"><a class="reference internal" href="quick_start.html#hints-for-proper-definition-of-certain-parameter-combinations">Hints for proper definition of certain parameter combinations</a></li>
</ul>
</li>
</ul>
@@ -354,7 +354,7 @@ 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..e93b2f6af7e5b2345397e4298606a080de2b0881 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>
@@ -186,21 +186,21 @@
<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>
</div>
<div class="section" id="registration-at-ecmwf">
<span id="ref-registration"></span><h2>Registration at ECMWF<a class="headerlink" href="#registration-at-ecmwf" title="Permalink to this headline">¶</a></h2>
-<p>The registration depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and in case of the local mode also on the data set you’d like to retrieve. The following table gives an overview where you need to register.</p>
+<p>The registration depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application modes</span></a> and in case of the local mode also on the data set you’d like to retrieve. The following table gives an overview where you need to register.</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 23%" />
@@ -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>
@@ -282,7 +282,7 @@
</div>
<div class="section" id="dependencies">
<span id="ref-requirements"></span><h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
-<p>The software required for running <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and therefore is described in the respective specific installation sections.</p>
+<p>The software required for running <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application modes</span></a> and therefore is described in the respective specific installation sections.</p>
<p>Generally speaking, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> requires <a class="reference external" href="https://docs.python.org/3/">Python 3</a> and Fortran together with certain modules / libraries.
We tested <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python’s own package manager <code class="docutils literal notranslate"><span class="pre">pip</span></code> (this may mess up some aspects of your python installation, especially if you use <code class="docutils literal notranslate"><span class="pre">pip</span></code> as root. Think about using virtual environments.).</p>
<p>Before installing the system packages check the availability with <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>, depending on your system. For example:</p>
@@ -295,7 +295,7 @@ $ rpm -q libeccodes-dev
<div class="section" id="installation-of-flex-extract">
<span id="ref-install-fe"></span><h2>Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#installation-of-flex-extract" title="Permalink to this headline">¶</a></h2>
<p>The actual installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by executing a shell script called <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.
-It defines some parameters and calls a Python script passing the parameters as command line arguments. For details, see <a class="reference internal" href="Documentation/Input/setup.html"><span class="doc">The Installation Script - setup.sh</span></a>.</p>
+It defines some parameters and calls a Python script passing the parameters as command line arguments. For details, see <a class="reference internal" href="Documentation/Input/setup.html"><span class="doc">The installation script - setup.sh</span></a>.</p>
<p>For each application mode installation section we describe the requirements for the explicit
environment and how it is installed, test if it works and how the actual <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>
installation has to be done. At the users local side not all software has to be present for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
diff --git a/Documentation/html/objects.inv b/Documentation/html/objects.inv
index 1e625b249615126d33701c9a23b6b3fc0b8f5acb..b61652e308e78d6f146dc827453ec7d96844023d 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..893850250b50cd53a7928f0a7360ed948cb9b4fd 100644
--- a/Documentation/html/quick_start.html
+++ b/Documentation/html/quick_start.html
@@ -103,7 +103,7 @@
<li class="toctree-l3"><a class="reference internal" href="#era-interim">ERA-Interim</a></li>
<li class="toctree-l3"><a class="reference internal" href="#operational-data">Operational data</a></li>
<li class="toctree-l3"><a class="reference internal" href="#specific-features">Specific features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#hints-for-definition-of-some-parameter-combinations">Hints for definition of some parameter combinations</a><ul class="simple">
+<li class="toctree-l3"><a class="reference internal" href="#hints-for-proper-definition-of-certain-parameter-combinations">Hints for proper definition of certain parameter combinations</a><ul class="simple">
</ul>
</li>
</ul>
@@ -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>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>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 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>
@@ -285,8 +285,8 @@ ls -rthl
</pre></div>
</div>
<p>The last command lists the most recent logs and temporary retrieval directories (usually <code class="docutils literal notranslate"><span class="pre">pythonXXXXX</span></code>, where XXXXX is the process id). Under <code class="docutils literal notranslate"><span class="pre">pythonXXXXX</span></code> a copy of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored under the name <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code>, the protocol is stored in the file <code class="docutils literal notranslate"><span class="pre">prot</span></code> and the temporary files as well as the resulting files are stored in a directory <code class="docutils literal notranslate"><span class="pre">work</span></code>. The original name of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored in this new file under parameter <code class="docutils literal notranslate"><span class="pre">controlfile</span></code>.</p>
-<div class="literal-block-wrapper docutils container" id="id3">
-<div class="code-block-caption"><span class="caption-text">“Example structure of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output directory on ECMWF servers.”</span><a class="headerlink" href="#id3" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id5">
+<div class="code-block-caption"><span class="caption-text">“Example structure of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output directory on ECMWF servers.”</span><a class="headerlink" href="#id5" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pythonXXXXX
├── CONTROL
├── prot
@@ -398,8 +398,8 @@ ls -rthl
<p>Additionally, you can find a lot of helpful links to dataset documentations, direct links to specific dataset web catalogues or further general information at the <a class="reference external" href="Ecmwf/ec-links.html">link collection</a> in the ECMWF data section.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is specialised to retrieve a limited number of datasets, namely <em>ERA-Interim</em>, <em>CERA-20C</em>, <em>ERA5</em> and <em>HRES (operational data)</em> as well as the <em>ENS (operational data, 15-day forecast)</em>. The limitation relates mainly to the dataset itself, the stream (what kind of forecast or what subset of dataset) and the experiment number. Mostly, the experiment number is equal to <code class="docutils literal notranslate"><span class="pre">1</span></code> to signal that the actual version should be used.</p>
<p>The next level of differentiation would be the field type, level type and time period. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> currently only supports the main streams for the re-analysis datasets and provides extraction of different streams for the operational dataset. The possibilities of compositions of dataset and stream selection are represented by the current list of example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files. You can see this in the naming of the example files:</p>
-<div class="literal-block-wrapper docutils container" id="id4">
-<div class="code-block-caption"><span class="caption-text">“Current example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files distributed with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. “</span><a class="headerlink" href="#id4" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id6">
+<div class="code-block-caption"><span class="caption-text">“Current example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files distributed with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. “</span><a class="headerlink" href="#id6" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_CERA
CONTROL_CERA.global
CONTROL_CERA.public
@@ -420,8 +420,8 @@ CONTROL_OD.OPER.FC.eta.global
CONTROL_OD.OPER.FC.eta.highres
CONTROL_OD.OPER.FC.gauss.highres
CONTROL_OD.OPER.FC.operational
-CONTROL_OD.OPER.FC.twiceaday.1hourly
-CONTROL_OD.OPER.FC.twiceaday.3hourly
+CONTROL_OD.OPER.FC.twicedaily.1hourly
+CONTROL_OD.OPER.FC.twicedaily.3hourly
</pre></div>
</div>
</div>
@@ -429,84 +429,85 @@ CONTROL_OD.OPER.FC.twiceaday.3hourly
<div class="figure align-default" id="ref-tab-dataset-cmp">
<img alt="_images/dataset_cmp_table.png" src="_images/dataset_cmp_table.png" />
</div>
-<p>A common problem for beginners in retrieving ECMWF datasets is the mismatch in the definition of these parameters. For example, if you would like to retrieve operational data before <code class="docutils literal notranslate"><span class="pre">June</span> <span class="pre">25th</span> <span class="pre">2013</span></code> and set the maximum level to <code class="docutils literal notranslate"><span class="pre">137</span></code> you will get an error because this number of levels was first introduced at this effective day. So, be cautious in the combination of space and time resolution as well as the field types which are not available all the time.</p>
+<p>A common problem for beginners in retrieving ECMWF datasets is a mismatch in the choice of values for these parameters. For example, if you try to retrieve operational data for 24 June 2013 or earlier and set the maximum level to 137, you will get an error because this number of levels was introduced only on 25 June 2013. Thus, be careful in the combination of space and time resolution as well as the field types.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>Sometimes it might not be clear how specific parameters in the control file must be set in terms of format. Please see the description of the parameters in section <a class="reference external" href="Documentation/Input/control_params.html">CONTROL parameters</a> or have a look at the ECMWF user documentation for <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/MARS+keywords">MARS keywords</a></p>
+<p>Sometimes it might not be clear how specific parameters in the control file must be set in terms of format. Please consult the description of the parameters in section <a class="reference external" href="Documentation/Input/control_params.html">CONTROL parameters</a> or have a look at the ECMWF user documentation for <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/MARS+keywords">MARS keywords</a></p>
</div>
-<p>In the following we shortly discuss the main retrieval opportunities of the different datasets and categoize the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
+<p>In the following, we shortly discuss the typical retrievals for the different datasets and point to the respective <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files.</p>
<div class="section" id="public-datasets">
<h3>Public datasets<a class="headerlink" href="#public-datasets" title="Permalink to this headline">¶</a></h3>
-<p>The main difference in the definition of a <code class="docutils literal notranslate"><span class="pre">CONRTOL</span></code> file for a public dataset is the setting of the parameter <code class="docutils literal notranslate"><span class="pre">DATASET</span></code>. This specification enables the selection of a public dataset in MARS. Otherwise the request would not find the dataset.
+<p>The main characteristic in the definition of a <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file for a public dataset is the parameter <code class="docutils literal notranslate"><span class="pre">DATASET</span></code>. Its specification enables the selection of a public dataset in MARS. Without this parameter, the request would not find the dataset.
For the two public datasets <em>CERA-20C</em> and <em>ERA-Interim</em> an example file with the ending <code class="docutils literal notranslate"><span class="pre">.public</span></code> is provided and can be used straightaway.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_CERA.public
CONTROL_EI.public
</pre></div>
</div>
-<p>For <em>CERA-20C</em> it seems that there are no differences in the dataset against the full dataset, while the <em>public ERA-Interim</em> has only analysis fields every 6 hour without filling forecasts in between for model levels. Therefore it is only possible to retrieve 6-hourly data for <em>public ERA-Interim</em>.</p>
+<p>For <em>CERA-20C</em> it seems that there are no differences compared the full dataset, whereas the <em>public ERA-Interim</em> has only 6-hourly analysis fields, without forecasts to fill in between, for model levels. Therefore, it is only possible to retrieve 6-hourly data for <em>public ERA-Interim</em>.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>In general, <em>ERA5</em> is a public dataset. However, since the model levels are not yet publicly available, it is not possible to retrieve <em>ERA5</em> data to drive the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> model. As soon as this is possible it will be announced at the community website and per newsletter.</p>
+<p>In principle, <em>ERA5</em> is a public dataset. However, since the model levels are not yet publicly available, it is not possible to retrieve <em>ERA5</em> data to drive the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> model. As soon as this is possible it will be announced at the community website and on the FLEXPART user email list.</p>
</div>
</div>
<div class="section" id="cera">
<h3>CERA<a class="headerlink" href="#cera" title="Permalink to this headline">¶</a></h3>
-<p>For this dataset it is important to keep in mind that the dataset is available for the period 09/1901 until 12/2010 and the temporal resolution is limited to 3-hourly fields.
-It is also a pure ensemble data assimilation dataset and is stored under the <code class="docutils literal notranslate"><span class="pre">enda</span></code> stream. It has <code class="docutils literal notranslate"><span class="pre">10</span></code> ensemble members. The example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files will only select the first member (<code class="docutils literal notranslate"><span class="pre">number=0</span></code>). You may change this to another number or a list of numbers (e.g. <code class="docutils literal notranslate"><span class="pre">NUMBER</span> <span class="pre">0/to/10</span></code>).
-Another important difference to all other datasets is the forecast starting time which is 18 UTC. Which means that the forecast in <em>CERA-20C</em> for flux fields is 12 hours long. Since the forecast extends over a single day we need to extract one day in advance and one day subsequently. This is automatically done in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
+<p>For this dataset, it is important to keep in mind that it is available for the period 09/1901 until 12/2010, and that the temporal resolution is limited to 3 h.
+It is also a pure ensemble data assimilation dataset and is stored under the <code class="docutils literal notranslate"><span class="pre">enda</span></code> stream.
+There are 10 ensemble members. The example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files retrieves the first member only (<code class="docutils literal notranslate"><span class="pre">number=0</span></code>). You may change this to another number or a list of numbers (e.g. <code class="docutils literal notranslate"><span class="pre">NUMBER</span> <span class="pre">0/to/10</span></code>).
+Another important difference to all other datasets is that there is one forecast per day, starting at 18 UTC. The forecast lead time is 24 hours and extends beyond the calendar day. Therefore, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> needs to extract also the day before the first day for which data are desired, which is handled automatically.</p>
</div>
<div class="section" id="era-5">
<h3>ERA 5<a class="headerlink" href="#era-5" title="Permalink to this headline">¶</a></h3>
-<p>This is the newest re-analysis dataset and has a temporal resolution of 1-hourly analysis fields. Up to date it is available until April 2019 with regular release of new months.
-The original horizontal resolution is <code class="docutils literal notranslate"><span class="pre">0.28125°</span></code> which needs some caution in the definition of the domain, since the length of the domain in longitude or latitude direction must be an exact multiple of the resolution. It might be easier for users to use <code class="docutils literal notranslate"><span class="pre">0.25</span></code> for the resolution which MARS will automatically interpolate.
-The forecast starting time is <code class="docutils literal notranslate"><span class="pre">06/18</span> <span class="pre">UTC</span></code> which is important for the flux data. This should be set in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file via the <code class="docutils literal notranslate"><span class="pre">ACCTIME</span> <span class="pre">06/18</span></code> parameter in correspondence with <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span> <span class="pre">12</span></code> and <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span> <span class="pre">FC</span></code>.</p>
+<p>This is the latest re-analysis dataset, and has a temporal resolution of 1-h (analysis fields). At the time of writing, it is available until April 2019 with regular release of new months.
+The original horizontal resolution is 0.28125° which needs some caution in the definition of the domain, since the length of the domain in longitude or latitude direction must be an integer multiple of the resolution. It is also possible to use <code class="docutils literal notranslate"><span class="pre">0.25</span></code> for the resolution; MARS will then automatically interpolate to this resolution which is still close enough to be acceptable.
+The forecast starting time is <code class="docutils literal notranslate"><span class="pre">06/18</span> <span class="pre">UTC</span></code> which is important for the flux data. Correspondingly, one should set in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file <code class="docutils literal notranslate"><span class="pre">ACCTIME</span> <span class="pre">06/18</span></code>, <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span> <span class="pre">12</span></code>, and <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span> <span class="pre">FC</span></code>.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>We know that <em>ERA5</em> also has an ensemble data assimilation system but this is not yet retrievable with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> since the deaccumulation of the flux fields works differently in this stream. Ensemble retrieval for <em>ERA5</em> is a future ToDo.</p>
+<p><em>ERA5</em> also includes an ensemble data assimilation system but related fields are not yet retrievable with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> since the deaccumulation of the flux fields works differently in this stream. Ensemble field retrieval for <em>ERA5</em> is a <em>to-do</em> for the future.</p>
</div>
</div>
<div class="section" id="era-interim">
<h3>ERA-Interim<a class="headerlink" href="#era-interim" title="Permalink to this headline">¶</a></h3>
-<p>This re-analysis dataset will exceed its end of production at 31st August 2019!
-It is then available from 1st January 1979 to 31st August 2019. The <code class="docutils literal notranslate"><span class="pre">etadot</span></code> is not available in this dataset. Therefore <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> must select the <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> parameter to retrieve the divergence field in addition. The vertical velocity is the calculated with the continuity equation in the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>. Since the analysis fields are only available for every 6th hour, the dataset can be made 3 hourly by adding forecast fields in between. No ensemble members are available.</p>
+<p>The production of this re-analysis dataset has stopped on 31 August 2019!
+It is available for the period from 1 January 1979 to 31 August 2019. The <code class="docutils literal notranslate"><span class="pre">etadot</span></code> parameter is not available in this dataset. Therefore, one must use the <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> parameter, which retrieves the divergence field in addition and calculates the vertical velocity from the continuity equation in the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>. While the analysis fields are only available for every 6th hour, the dataset can be made 3-hourly by adding forecast fields in between. No ensemble members are available.</p>
</div>
<div class="section" id="operational-data">
<h3>Operational data<a class="headerlink" href="#operational-data" title="Permalink to this headline">¶</a></h3>
-<p>This is the real time atmospheric model in high resolution with a 10-day forecast. This means it underwent regular adaptations and improvements over the years. Hence, retrieving data from this dataset needs extra attention in selecting correct settings of parameter. See <span class="xref std std-ref">ref-tab-dataset-cmp</span> for the most important parameters.
-Nowadays, it is available 1 hourly by filling the gaps of the 6 hourly analysis fields with 1 hourly forecast fields. Since 4th June 2008 the eta coordinate is directly available so that <code class="docutils literal notranslate"><span class="pre">ETA</span></code> should be set to <code class="docutils literal notranslate"><span class="pre">1</span></code> to save computation time. The horizontal resolution can be up to <code class="docutils literal notranslate"><span class="pre">0.1°</span></code> and in combination with <code class="docutils literal notranslate"><span class="pre">137</span></code> vertical levels can lead to troubles in retrieving this high resolution dataset in terms of job duration and quota exceedence.
-It is recommended to submit such high resolution cases for single day retrievals (see <code class="docutils literal notranslate"><span class="pre">JOB_CHUNK</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> script) to avoid job failures due to exceeding limits.</p>
-<p><code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files for normal daily retrievals with a mix of analysis and forecast fields are listed below:</p>
+<p>This data set provides the output of the real-time atmospheric model runs in high resolution, including 10-day forecasts. The model undergoes frequent adaptations and improvements. Thus, retrieving data from this dataset requires extra attention in selecting correct settings of the parameters. See <a class="reference internal" href="#ref-tab-dataset-cmp"><span class="std std-ref">[Table of datasets]</span></a> for the most important parameters.
+Currently, fields can be retrieved at 1 h temporal resolution by filling the gaps between analysis fields with 1-hourly forecast fields. Since 4 June 2008, the eta coordinate vertical velocity is directly available from MARS, therefore <code class="docutils literal notranslate"><span class="pre">ETA</span></code> should be set to <code class="docutils literal notranslate"><span class="pre">1</span></code> to save computation time. The horizontal resolution can be up to <code class="docutils literal notranslate"><span class="pre">0.1°</span></code> and in combination with <code class="docutils literal notranslate"><span class="pre">137</span></code> vertical levels can lead to problems in terms of job duration and disk space quota.
+It is recommended to submit such high resolution cases as single day retrievals (see <code class="docutils literal notranslate"><span class="pre">JOB_CHUNK</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">run.sh</span></code> script) to avoid job failures due to exceeding limits.</p>
+<p><code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files for standard retrievals with a mix of analysis and forecast fields are listed below:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_OD.OPER.4V.eta.global
CONTROL_OD.OPER.FC.eta.global
CONTROL_OD.OPER.FC.eta.highres
CONTROL_OD.OPER.FC.gauss.highres
</pre></div>
</div>
-<p>These files defines the minimum number of parameters necessary to retrieve a daily subset. The setup of field types is optimal and should only be changed if the user understands what he does. The grid, domain and temporal resolution can be changed according to availability.</p>
+<p>These files defines the minimum number of parameters necessary to retrieve a daily subset. The given settings for the TYPE parameter are already optimised, and should only be changed if you know what you are doing. Grid, domain, and temporal resolution may be changed according to availability.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
-<p>Please see <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency">Information about MARS retrievement</a> to get to know hints about retrieval efficiency and troubleshooting.</p>
+<p>Please see <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency">Information about MARS retrievement</a> for hints about retrieval efficiency and troubleshooting.</p>
</div>
<dl>
-<dt>Pure forecast</dt><dd><p>It is possible to retrieve pure forecasts exceeding a day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecast of <em>Forecast (FC)</em>, <em>Control forecast (CF)</em> and <em>Calibration/Validation forecast (CV)</em>.
-The <em>CV</em> field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the <em>CF</em> type since this is available from 1992 (3-hourly) on up to today in 1-hourly temporal resolution. <em>CV</em> and <em>CF</em> field types belong to the <em>Ensemble prediction system (ENFO)</em> which contain 50 ensemble members.
-Please be aware that in this case it is necessary to set the specific type for flux fields explicitly, otherwise it could select a default value which might be different from what you expect!</p>
+<dt>Pure forecast</dt><dd><p>It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of <em>Forecast (FC)</em>, <em>Control forecast (CF)</em> and <em>Calibration/Validation forecast (CV)</em>.
+The <em>CV</em> field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the <em>CF</em> type since this is available from 1992 (3-hourly) on up to today (1-hourly). <em>CV</em> and <em>CF</em> field types belong to the <em>Ensemble prediction system (ENFO)</em> which currently works with 50 ensemble members.
+Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_OD.ENFO.CF.36hours
CONTROL_OD.ENFO.CV.36hours
CONTROL_OD.OPER.FC.36hours
</pre></div>
</div>
</dd>
-<dt>Half-day retrievals</dt><dd><p>If a forecast for just half a day is wanted it can be done by substituting the analysis fields also by forecast fields as shown in files with <code class="docutils literal notranslate"><span class="pre">twiceaday</span></code> in it. They produce a full day retrieval with pure 12 hour forecasts twice a day. It is also possible to use the operational version which would get the time information from ECMWF’s environmental variables and therefore get the newest forecast per day. This version uses a <code class="docutils literal notranslate"><span class="pre">BASETIME</span></code> parameter which tells MARS to extract the exact 12 hours upfront to the selected date. If the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file with <code class="docutils literal notranslate"><span class="pre">basetime</span></code> in the filename is used this can be done for any other date too.</p>
+<dt>Half-day retrievals</dt><dd><p>If a forecast is wanted for half a day only, this can be done by substituting the analysis fields by forecast fields as shown in files with <code class="docutils literal notranslate"><span class="pre">twicedaily</span></code> in their name. They produce a full-day retrieval with pure 12 hour forecasts, twice a day. It is also possible to use the operational version which would obtain the time information from ECMWF’s environment variables and therefore use the newest forecast for each day. This version uses a <code class="docutils literal notranslate"><span class="pre">BASETIME</span></code> parameter which tells MARS to extract the exact 12 hours up to the selected date. If the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file with <code class="docutils literal notranslate"><span class="pre">basetime</span></code> in the filename is used, this can be done for any other date, too.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_OD.OPER.FC.eta.basetime
CONTROL_OD.OPER.FC.operational
-CONTROL_OD.OPER.FC.twiceaday.1hourly
-CONTROL_OD.OPER.FC.twiceaday.3hourly
+CONTROL_OD.OPER.FC.twicedaily.1hourly
+CONTROL_OD.OPER.FC.twicedaily.3hourly
</pre></div>
</div>
</dd>
-<dt>Ensemble members</dt><dd><p>The retrieval of ensemble members were already mentioned in the pure forecast section and for <em>CERA-20C</em> data.
-In this <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version there is an additional possibility to retrieve the <em>Ensemble Long window Data Assimilation (ELDA)</em> stream from the real-time dataset. This model version has (up to May 2019) 25 ensemble members and a control run (<code class="docutils literal notranslate"><span class="pre">number</span> <span class="pre">0</span></code>). Starting from June 2019 it has 50 ensemble members. Therefore we created the possibility to double up the 25 ensemble members (before June 2019) to 50 members by taking the original 25 members from MARS and subtracting 2 times the difference between the member value and the control value. This is done by selecting the parameter <code class="docutils literal notranslate"><span class="pre">DOUBLEELDA</span></code> and set it to <code class="docutils literal notranslate"><span class="pre">1</span></code>.</p>
+<dt>Ensemble members</dt><dd><p>The retrieval of ensemble members was already mentioned in the pure forecast section and for <em>CERA-20C</em> data.
+This <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version allows to retrieve the <em>Ensemble Long window Data Assimilation (ELDA)</em> stream from the operational dataset. Until May 2019, there were 25 ensemble members and a control run (<code class="docutils literal notranslate"><span class="pre">number</span> <span class="pre">0</span></code>). Starting with June 2019, the number of ensemble members has been increased to 50. Therefore, we created the option to create 25 additional “pseudo-ensemble members” for periods before June 2019. The original 25 members from MARS are taken, and the difference between the member value and the control value is subtracted twice. This is done if the parameter <code class="docutils literal notranslate"><span class="pre">DOUBLEELDA</span></code> is included and set it to <code class="docutils literal notranslate"><span class="pre">1</span></code>.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_OD.ELDA.FC.eta.ens.double
CONTROL_OD.ENFO.PF.ens
</pre></div>
@@ -517,29 +518,34 @@ CONTROL_OD.ENFO.PF.ens
<div class="section" id="specific-features">
<h3>Specific features<a class="headerlink" href="#specific-features" title="Permalink to this headline">¶</a></h3>
<dl class="simple">
-<dt>rrint</dt><dd><p>Decides if the precipitation flux data uses the old (<code class="docutils literal notranslate"><span class="pre">0</span></code>) or new (<code class="docutils literal notranslate"><span class="pre">1</span></code>) disaggregation scheme. See <a class="reference internal" href="Documentation/disagg.html"><span class="doc">Disaggregation of Flux Data</span></a> for explanaition.</p>
+<dt>rrint</dt><dd><p>Selects the disaggregation scheme for precipitation flux: old (<code class="docutils literal notranslate"><span class="pre">0</span></code>) or new (<code class="docutils literal notranslate"><span class="pre">1</span></code>). See <a class="reference internal" href="Documentation/disagg.html"><span class="doc">Disaggregation of flux data</span></a> for explanation.</p>
</dd>
-<dt>cwc</dt><dd><p>Decides if the total cloud water content will be retrieved (set to <code class="docutils literal notranslate"><span class="pre">1</span></code>) in addition. This is the sum of cloud liquid and cloud ice water content.</p>
+<dt>cwc</dt><dd><p>If present and set to <code class="docutils literal notranslate"><span class="pre">1</span></code>, the total cloud water content will be retrieved in addition. This is the sum of cloud liquid and cloud ice water content.</p>
</dd>
-<dt>addpar</dt><dd><p>With this parameter an additional list of 2-dimensional, non-flux parameters can be retrieved. Use format <code class="docutils literal notranslate"><span class="pre">param1/param2/.../paramx</span></code> to list the parameters. Please be consistent in using either the parameter IDs or the short names.</p>
+<dt>addpar</dt><dd><p>With this parameter. an additional list of 2-dimensional, non-flux parameters can be retrieved. Use the format <code class="docutils literal notranslate"><span class="pre">param1/param2/.../paramx</span></code> to list the parameters. Please be consistent in using either the parameter IDs or the short names as defined by MARS.</p>
</dd>
-<dt>doubleelda</dt><dd><p>Use this to double the ensemble member number by adding further disturbance to each member.</p>
+<dt>doubleelda</dt><dd><p>Use this to double the ensemble member number by adding further disturbance to each member (to be used with 25 members).</p>
</dd>
-<dt>debug</dt><dd><p>If set to <code class="docutils literal notranslate"><span class="pre">1</span></code> all temporary files were kept at the end. Otherwise everything except the final output files will be deleted.</p>
+<dt>debug</dt><dd><p>If set to <code class="docutils literal notranslate"><span class="pre">1</span></code>, all temporary files are preserved. Otherwise, everything except the final output files will be deleted.</p>
</dd>
-<dt>request</dt><dd><p>This produces an extra <em>csv</em> file <code class="docutils literal notranslate"><span class="pre">mars_requests.csv</span></code> where the content of each mars request of the job is stored. Useful for debugging and documentation.</p>
+<dt>request</dt><dd><p>This produces an extra <em>csv</em> file <code class="docutils literal notranslate"><span class="pre">mars_requests.csv</span></code> where the content of each MARS request submitted within the job is stored, which is useful for debugging and documentation. Possible values are 0 for normal data retrieval, 1 for not retrieving data and just writing out the MARS requests, and 2 to retrieve data and write out requests.</p>
</dd>
-<dt>mailfail</dt><dd><p>At default the mail is send to the mail connected with the user account. Add additional email addresses if you want. But as soon as you enter a new mail, the default will be overwritten. If you would like to keep the mail from your user account, please add <code class="docutils literal notranslate"><span class="pre">${USER}</span></code> to the list ( comma seperated ) or mail addresses.</p>
+<dt>mailfail</dt><dd><p>As a default, e-mails are sent to the mail address defined for the ECMWF user account. It is possible to overwrite this by specifying one or more e-mail addresses (comma-separated list). In order to include the e-mail associated with the user account, add <code class="docutils literal notranslate"><span class="pre">${USER}</span></code> to the list.</p>
</dd>
</dl>
</div>
-<div class="section" id="hints-for-definition-of-some-parameter-combinations">
-<h3>Hints for definition of some parameter combinations<a class="headerlink" href="#hints-for-definition-of-some-parameter-combinations" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="hints-for-proper-definition-of-certain-parameter-combinations">
+<h3>Hints for proper definition of certain parameter combinations<a class="headerlink" href="#hints-for-proper-definition-of-certain-parameter-combinations" title="Permalink to this headline">¶</a></h3>
<dl>
-<dt>Field types and times</dt><dd><p>This combination is very important. It defines the temporal resolution and which field type is extracted per time step.
-The time declaration for analysis (AN) fields uses the times of the specific analysis and (forecast time) steps have to be <code class="docutils literal notranslate"><span class="pre">0</span></code>. The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) times and the (forecast) steps. Both of them together defines the actual time step. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general it is enough to give information for the exact time steps, but it is also possible to have more time step combinations of <code class="docutils literal notranslate"><span class="pre">TYPE</span></code>, <code class="docutils literal notranslate"><span class="pre">TIME</span></code> and <code class="docutils literal notranslate"><span class="pre">STEP</span></code> because the temporal (hourly) resolution with the <code class="docutils literal notranslate"><span class="pre">DTIME</span></code> parameter will select the correct combinations.</p>
-<div class="literal-block-wrapper docutils container" id="id5">
-<div class="code-block-caption"><span class="caption-text">Example of a setting for the field types and temporal resolution.</span><a class="headerlink" href="#id5" title="Permalink to this code">¶</a></div>
+<dt>Field type and time</dt><dd><p>This combination is very important. It defines the temporal resolution and which field type is extracted on each time step.
+The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be <code class="docutils literal notranslate"><span class="pre">0</span></code>.
+The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of <code class="docutils literal notranslate"><span class="pre">TYPE</span></code>, <code class="docutils literal notranslate"><span class="pre">TIME</span></code> and <code class="docutils literal notranslate"><span class="pre">STEP</span></code> because the temporal (hourly) resolution with the <code class="docutils literal notranslate"><span class="pre">DTIME</span></code> parameter will select the correct combinations.</p>
+<div class="admonition-todo admonition" id="id2">
+<p class="admonition-title">Todo</p>
+<p>#PS needs to be rephrased</p>
+</div>
+<div class="literal-block-wrapper docutils container" id="id7">
+<div class="code-block-caption"><span class="caption-text">Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.</span><a class="headerlink" href="#id7" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> DTIME <span class="m">3</span>
TYPE AN FC FC FC AN FC FC FC
TIME <span class="m">00</span> <span class="m">00</span> <span class="m">00</span> <span class="m">00</span> <span class="m">12</span> <span class="m">12</span> <span class="m">12</span> <span class="m">12</span>
@@ -548,9 +554,11 @@ The time declaration for analysis (AN) fields uses the times of the specific ana
</div>
</div>
</dd>
-<dt>Vertical velocity</dt><dd><p>The vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> is not directly available from MARS. Therefore it has to be calculated. There are a couple of different options. The following parameters are responsible for the selection. See <a class="reference internal" href="Documentation/vertco.html"><span class="doc">Vertical Coordinate</span></a> for a detailed explanation. The <code class="docutils literal notranslate"><span class="pre">ETADIFF</span></code>, <code class="docutils literal notranslate"><span class="pre">OMEGA</span></code> and <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span></code> versions are only recommended for debugging and testing reasons. Usually it is a decision between <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> and <code class="docutils literal notranslate"><span class="pre">ETA</span></code>, where for <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> spectral fields of the horizontal wind fields and the divergence are to be retrieved and used with the continuity equation to calculate the vertical velocity. For <code class="docutils literal notranslate"><span class="pre">ETA</span></code> the latitude/longitude fields of horizontal wind fields and eta-coordinate are to be retrieved. It is recommended to use <code class="docutils literal notranslate"><span class="pre">ETA</span></code> where possible due to a reduced computation time.</p>
-<div class="literal-block-wrapper docutils container" id="id6">
-<div class="code-block-caption"><span class="caption-text">Example setting for the vertical coordinate retrieval.</span><a class="headerlink" href="#id6" title="Permalink to this code">¶</a></div>
+<dt>Vertical velocity</dt><dd><p>The vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> is not directly available from MARS and has to be calculated.
+There are several options for this, and the following parameters are responsible for the selection. See <a class="reference internal" href="Documentation/vertco.html"><span class="doc">Vertical wind</span></a> for a detailed explanation. Using <code class="docutils literal notranslate"><span class="pre">ETADIFF</span> <span class="pre">1</span></code>, <code class="docutils literal notranslate"><span class="pre">OMEGA</span> <span class="pre">1</span></code> and <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span> <span class="pre">1</span></code> is recommended for debugging and testing only.
+Usually, one has to decide between <code class="docutils literal notranslate"><span class="pre">GAUSS</span> <span class="pre">1</span></code> and <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code>. <code class="docutils literal notranslate"><span class="pre">GAUSS</span> <span class="pre">1</span></code> means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code> means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code> where possible, as there is a substantial computational overhead for solving the continuity equation.</p>
+<div class="literal-block-wrapper docutils container" id="id8">
+<div class="code-block-caption"><span class="caption-text">Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).</span><a class="headerlink" href="#id8" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>GAUSS <span class="m">0</span>
ETA <span class="m">1</span>
ETADIFF <span class="m">0</span>
@@ -561,11 +569,17 @@ OMEGADIFF <span class="m">0</span>
</div>
</div>
</dd>
-<dt>Grid resolution and domain</dt><dd><p>The grid and domain selection depends on each other. The grid can be defined in the format of normal degrees (e.g. <code class="docutils literal notranslate"><span class="pre">1.</span></code>) or as in older versions by 1/1000. degrees (e.g. <code class="docutils literal notranslate"><span class="pre">1000</span></code> for <code class="docutils literal notranslate"><span class="pre">1°</span></code>).
-After selecting the grid, the domain has to be defined in a way that the length of the domain in longitude or latitude direction must be an exact multiple of the grid.
-The horizontal resolution for spectral fields will be set by the parameter <code class="docutils literal notranslate"><span class="pre">RESOL</span></code>. For information about how to select an appropriate value you can read the explanation of the MARS keyword <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol">here</a> and in <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation">this table</a>.</p>
-<div class="literal-block-wrapper docutils container" id="id7">
-<div class="code-block-caption"><span class="caption-text">Example setting for a northern hemisphere domain with a grid of <code class="docutils literal notranslate"><span class="pre">0.25°</span></code>.</span><a class="headerlink" href="#id7" title="Permalink to this code">¶</a></div>
+<dt>Grid resolution and domain</dt><dd><p>The grid and domain parameters depends on each other. <code class="docutils literal notranslate"><span class="pre">grid</span></code> refers to the grid resolution. It can be given as decimal values (e.g., <code class="docutils literal notranslate"><span class="pre">1.</span></code> meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., <code class="docutils literal notranslate"><span class="pre">1000</span></code> means also 1°). The code applies common sense to determine what format is to be assumed.
+After selecting grid, the <code class="docutils literal notranslate"><span class="pre">domain</span></code> has to be defined. The extension in longitude or latitude direction must be an integer multiple of <code class="docutils literal notranslate"><span class="pre">grid</span></code>.</p>
+<blockquote>
+<div><div class="admonition-todo admonition" id="id3">
+<p class="admonition-title">Todo</p>
+<p>#PS shouldn’t we explain how to define a domain??</p>
+</div>
+</div></blockquote>
+<p>The horizontal resolution for spectral fields is set by the parameter <code class="docutils literal notranslate"><span class="pre">RESOL</span></code>. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol">in this entry of the ECMWF on-line documentation</a> and <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation">this table (also ECMWF documentation)</a>.</p>
+<div class="literal-block-wrapper docutils container" id="id9">
+<div class="code-block-caption"><span class="caption-text">Example setting for a domain covering the northern hemisphere domain with a grid resolution of <code class="docutils literal notranslate"><span class="pre">0.25°</span></code>.</span><a class="headerlink" href="#id9" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>GRID <span class="m">0</span>.25
RESOL <span class="m">799</span>
SMOOTH <span class="m">0</span>
@@ -577,9 +591,15 @@ RIGHT <span class="m">180</span>.
</div>
</div>
</dd>
-<dt>Flux data</dt><dd><p>The flux fields are accumulated forecast fields all the time. Since some re-analysis dataset nowadays have complete set of analysis fields in their temporal resolution it was important to define a new parameter set to define the flux fields since the information could not be taken from <code class="docutils literal notranslate"><span class="pre">TYPE</span></code>, <code class="docutils literal notranslate"><span class="pre">TIME</span></code> and <code class="docutils literal notranslate"><span class="pre">STEP</span></code> any longer. Select a forecast field type <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span></code>, the forecast starting time <code class="docutils literal notranslate"><span class="pre">ACCTIME</span></code> and the maximum forecast step <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span></code>. The <code class="docutils literal notranslate"><span class="pre">DTIME</span></code> parameter defines the temporal resolution for the whole period.</p>
-<div class="literal-block-wrapper docutils container" id="id8">
-<div class="code-block-caption"><span class="caption-text">Example setting for the definition of flux fields.</span><a class="headerlink" href="#id8" title="Permalink to this code">¶</a></div>
+<dt>Flux data</dt><dd><p>Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span></code> is the field type (must be a type of forecast), <code class="docutils literal notranslate"><span class="pre">ACCTIME</span></code> the forecast starting time, and <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span></code> the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.</p>
+<blockquote>
+<div><div class="admonition-todo admonition" id="id4">
+<p class="admonition-title">Todo</p>
+<p>#PS for which application would this be typical?</p>
+</div>
+</div></blockquote>
+<div class="literal-block-wrapper docutils container" id="id10">
+<div class="code-block-caption"><span class="caption-text">Example setting for the definition of flux fields.</span><a class="headerlink" href="#id10" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> DTIME <span class="m">3</span>
ACCTYPE FC
ACCTIME <span class="m">00</span>/12
diff --git a/Documentation/html/searchindex.js b/Documentation/html/searchindex.js
index aa859fce5489e0a6903ac805637ab796f6104a35..f00b92b7cb647e9e7d0c37a820fdf4bb29757995 100644
--- a/Documentation/html/searchindex.js
+++ b/Documentation/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["Developers/gen_docu","Documentation/Api/api_fortran","Documentation/Api/api_python","Documentation/Input/changes","Documentation/Input/compilejob","Documentation/Input/control","Documentation/Input/control_params","Documentation/Input/ecmwf_env","Documentation/Input/examples","Documentation/Input/fortran_makefile","Documentation/Input/jobscript","Documentation/Input/run","Documentation/Input/setup","Documentation/Input/templates","Documentation/Overview/app_modes","Documentation/Overview/prog_flow","Documentation/api","Documentation/disagg","Documentation/input","Documentation/output","Documentation/overview","Documentation/vertco","Ecmwf/access","Ecmwf/ec-links","Ecmwf/hintsecmwf","Ecmwf/msdata","Ecmwf/pubdata","Evaluation/metrics","Evaluation/staticcode","Evaluation/testcases","Installation/gateway","Installation/local","Installation/remote","Support/faq","Support/known_bugs_issues","authors","changelog","dev_guide","documentation","ecmwf_data","evaluation","index","installation","quick_start","support","todo"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.index":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":2,"sphinx.ext.viewcode":1,sphinx:56},filenames:["Developers/gen_docu.rst","Documentation/Api/api_fortran.rst","Documentation/Api/api_python.rst","Documentation/Input/changes.rst","Documentation/Input/compilejob.rst","Documentation/Input/control.rst","Documentation/Input/control_params.rst","Documentation/Input/ecmwf_env.rst","Documentation/Input/examples.rst","Documentation/Input/fortran_makefile.rst","Documentation/Input/jobscript.rst","Documentation/Input/run.rst","Documentation/Input/setup.rst","Documentation/Input/templates.rst","Documentation/Overview/app_modes.rst","Documentation/Overview/prog_flow.rst","Documentation/api.rst","Documentation/disagg.rst","Documentation/input.rst","Documentation/output.rst","Documentation/overview.rst","Documentation/vertco.rst","Ecmwf/access.rst","Ecmwf/ec-links.rst","Ecmwf/hintsecmwf.rst","Ecmwf/msdata.rst","Ecmwf/pubdata.rst","Evaluation/metrics.rst","Evaluation/staticcode.rst","Evaluation/testcases.rst","Installation/gateway.rst","Installation/local.rst","Installation/remote.rst","Support/faq.rst","Support/known_bugs_issues.rst","authors.rst","changelog.rst","dev_guide.rst","documentation.rst","ecmwf_data.rst","evaluation.rst","index.rst","installation.rst","quick_start.rst","support.rst","todo.rst"],objects:{"":{ControlFile:[2,0,0,"-"],EcFlexpart:[2,0,0,"-"],GribUtil:[2,0,0,"-"],MarsRetrieval:[2,0,0,"-"],UioFiles:[2,0,0,"-"],checks:[2,0,0,"-"],disaggregation:[2,0,0,"-"],get_mars_data:[2,0,0,"-"],install:[2,0,0,"-"],prepare_flexpart:[2,0,0,"-"],submit:[2,0,0,"-"],tools:[2,0,0,"-"]},"ControlFile.ControlFile":{"public":[2,2,1,""],accmaxstep:[2,2,1,""],acctime:[2,2,1,""],acctype:[2,2,1,""],accuracy:[2,2,1,""],addpar:[2,2,1,""],area:[2,2,1,""],assign_args_to_control:[2,3,1,""],assign_envs_to_control:[2,3,1,""],basetime:[2,2,1,""],cds_api:[2,2,1,""],check_conditions:[2,3,1,""],controlfile:[2,2,1,""],cwc:[2,2,1,""],dataset:[2,2,1,""],date_chunk:[2,2,1,""],debug:[2,2,1,""],destination:[2,2,1,""],doubleelda:[2,2,1,""],dpdeta:[2,2,1,""],dtime:[2,2,1,""],ec_api:[2,2,1,""],ecfsdir:[2,2,1,""],ecgid:[2,2,1,""],ecstorage:[2,2,1,""],ectrans:[2,2,1,""],ecuid:[2,2,1,""],end_date:[2,2,1,""],eta:[2,2,1,""],etadiff:[2,2,1,""],etapar:[2,2,1,""],exedir:[2,2,1,""],expver:[2,2,1,""],flexextractdir:[2,2,1,""],format:[2,2,1,""],gateway:[2,2,1,""],gauss:[2,2,1,""],gaussian:[2,2,1,""],grid:[2,2,1,""],inputdir:[2,2,1,""],install_target:[2,2,1,""],installdir:[2,2,1,""],left:[2,2,1,""],level:[2,2,1,""],levelist:[2,2,1,""],logicals:[2,2,1,""],lower:[2,2,1,""],mailfail:[2,2,1,""],mailops:[2,2,1,""],makefile:[2,2,1,""],marsclass:[2,2,1,""],maxstep:[2,2,1,""],number:[2,2,1,""],omega:[2,2,1,""],omegadiff:[2,2,1,""],oper:[2,2,1,""],outputdir:[2,2,1,""],prefix:[2,2,1,""],purefc:[2,2,1,""],request:[2,2,1,""],resol:[2,2,1,""],right:[2,2,1,""],rrint:[2,2,1,""],smooth:[2,2,1,""],start_date:[2,2,1,""],step:[2,2,1,""],stream:[2,2,1,""],time:[2,2,1,""],to_list:[2,3,1,""],type:[2,2,1,""],upper:[2,2,1,""],wrf:[2,2,1,""]},"EcFlexpart.EcFlexpart":{"public":[2,2,1,""],accmaxstep:[2,2,1,""],acctime:[2,2,1,""],acctype:[2,2,1,""],accuracy:[2,2,1,""],addpar:[2,2,1,""],area:[2,2,1,""],basetime:[2,2,1,""],calc_extra_elda:[2,3,1,""],create:[2,3,1,""],dataset:[2,2,1,""],dates:[2,2,1,""],deacc_fluxes:[2,3,1,""],dtime:[2,2,1,""],expver:[2,2,1,""],gaussian:[2,2,1,""],glevelist:[2,2,1,""],grid:[2,2,1,""],inputdir:[2,2,1,""],level:[2,2,1,""],levelist:[2,2,1,""],marsclass:[2,2,1,""],mreq_count:[2,2,1,""],number:[2,2,1,""],outputfilelist:[2,2,1,""],params:[2,2,1,""],process_output:[2,3,1,""],purefc:[2,2,1,""],resol:[2,2,1,""],retrieve:[2,3,1,""],server:[2,2,1,""],stream:[2,2,1,""],types:[2,2,1,""],write_namelist:[2,3,1,""]},"GribUtil.GribUtil":{copy_dummy_msg:[2,3,1,""],get_keys:[2,3,1,""],index:[2,3,1,""],set_keys:[2,3,1,""]},"MarsRetrieval.MarsRetrieval":{"public":[2,2,1,""],accuracy:[2,2,1,""],area:[2,2,1,""],data_retrieve:[2,3,1,""],dataset:[2,2,1,""],date:[2,2,1,""],display_info:[2,3,1,""],expver:[2,2,1,""],gaussian:[2,2,1,""],grid:[2,2,1,""],levelist:[2,2,1,""],levtype:[2,2,1,""],marsclass:[2,2,1,""],number:[2,2,1,""],param:[2,2,1,""],print_infodata_csv:[2,3,1,""],repres:[2,2,1,""],resol:[2,2,1,""],server:[2,2,1,""],step:[2,2,1,""],stream:[2,2,1,""],target:[2,2,1,""],time:[2,2,1,""],type:[2,2,1,""]},"UioFiles.UioFiles":{delete_files:[2,3,1,""],files:[2,2,1,""],path:[2,2,1,""],pattern:[2,2,1,""]},ControlFile:{ControlFile:[2,1,1,""]},EcFlexpart:{EcFlexpart:[2,1,1,""]},GribUtil:{GribUtil:[2,1,1,""]},MarsRetrieval:{MarsRetrieval:[2,1,1,""]},UioFiles:{UioFiles:[2,1,1,""]},checks:{check_accmaxstep:[2,4,1,""],check_acctime:[2,4,1,""],check_acctype:[2,4,1,""],check_addpar:[2,4,1,""],check_area:[2,4,1,""],check_basetime:[2,4,1,""],check_dates:[2,4,1,""],check_grid:[2,4,1,""],check_job_chunk:[2,4,1,""],check_len_type_time_step:[2,4,1,""],check_levels:[2,4,1,""],check_logicals_type:[2,4,1,""],check_mail:[2,4,1,""],check_maxstep:[2,4,1,""],check_number:[2,4,1,""],check_pathes:[2,4,1,""],check_ppid:[2,4,1,""],check_public:[2,4,1,""],check_purefc:[2,4,1,""],check_queue:[2,4,1,""],check_request:[2,4,1,""],check_step:[2,4,1,""],check_time:[2,4,1,""],check_type:[2,4,1,""]},disaggregation:{IA3:[2,4,1,""],dapoly:[2,4,1,""],darain:[2,4,1,""]},get_mars_data:{check_dates_for_nonflux_fc_times:[2,4,1,""],do_retrievement:[2,4,1,""],get_mars_data:[2,4,1,""],main:[2,4,1,""],mk_dates:[2,4,1,""],mk_server:[2,4,1,""],remove_old:[2,4,1,""],write_reqheader:[2,4,1,""]},install:{check_install_conditions:[2,4,1,""],del_convert_build:[2,4,1,""],get_install_cmdline_args:[2,4,1,""],install_local:[2,4,1,""],install_via_gateway:[2,4,1,""],main:[2,4,1,""],mk_compilejob:[2,4,1,""],mk_convert_build:[2,4,1,""],mk_env_vars:[2,4,1,""],mk_job_template:[2,4,1,""],mk_tarball:[2,4,1,""],un_tarball:[2,4,1,""]},prepare_flexpart:{main:[2,4,1,""],prepare_flexpart:[2,4,1,""]},submit:{main:[2,4,1,""],mk_jobscript:[2,4,1,""],submit:[2,4,1,""]},tools:{clean_up:[2,4,1,""],execute_subprocess:[2,4,1,""],generate_retrieval_period_boundary:[2,4,1,""],get_cmdline_args:[2,4,1,""],get_dimensions:[2,4,1,""],get_informations:[2,4,1,""],get_list_as_string:[2,4,1,""],init128:[2,4,1,""],make_dir:[2,4,1,""],my_error:[2,4,1,""],none_or_int:[2,4,1,""],none_or_str:[2,4,1,""],normal_exit:[2,4,1,""],product:[2,4,1,""],put_file_to_ecserver:[2,4,1,""],read_ecenv:[2,4,1,""],send_mail:[2,4,1,""],setup_controldata:[2,4,1,""],silent_remove:[2,4,1,""],submit_job_to_ecserver:[2,4,1,""],to_param_id:[2,4,1,""],to_param_id_with_tablenumber:[2,4,1,""]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","attribute","Python attribute"],"3":["py","method","Python method"],"4":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:class","2":"py:attribute","3":"py:method","4":"py:function"},terms:{"00h":[6,11],"10u":19,"10v":19,"12h":[6,11],"180w":6,"18utc":2,"1hourli":[8,43],"1st":43,"20c":[5,6,19,21,22,23,34,36,42,43],"20gb":43,"24h":[2,6],"25th":43,"31st":43,"32000mb":[10,13],"3200mb":[4,13],"36hour":[8,43],"3hourli":[8,43],"4th":43,"6th":43,"althanstra\u00df":35,"boolean":2,"break":17,"case":[0,2,4,6,10,13,14,17,19,21,22,31,32,33,42,43],"class":[0,5,6,31],"default":[2,3,5,6,8,10,11,12,18,19,43],"export":[4,10,13],"f\u00fcr":13,"final":[0,2,11,15,17,19,21,43],"float":[2,11],"function":[2,17,41],"import":[2,6,11,30,31,33,34,39,43],"int":[2,6,30,32,43],"long":43,"m\u00e4r":31,"new":[2,6,10,11,17,18,41,43,44],"public":[2,5,6,8,10,11,12,14,22,23,24,31,36,39,41],"return":[2,4,10,34],"short":[2,5,6,17,30,43],"switch":[2,4,6,10,13,19],"true":[0,2],"try":[31,42],"while":[22,43],ARE:5,But:43,C3S:23,CDS:[2,22,23,33,36,42],Dps:[2,6],ENS:[23,43],FOR:[11,12],For:[0,2,3,5,6,9,11,12,13,14,18,19,21,22,24,30,32,33,34,39,42,43],HAS:[11,12,30,31,32,43],Has:[6,11],IDs:[6,15,43],Its:2,NOT:[11,12,31],Not:12,One:31,PBS:[4,10,13],THE:[11,12,30,31,32,43],THESE:[11,12,30,31,32,43],The:[0,2,7,13,14,15,17,18,19,20,21,22,30,31,32,34,39,42,43,44],Then:[2,11,14,42],There:[2,18,19,22,39,42,43],These:[2,4,10,13,17,42,43],Use:[0,6,30,32,43],Used:[2,12],Useful:43,Uses:2,Using:31,WITH:[11,12],With:[6,11,12,43],_acc:19,_config:2,_expand:2,_file:0,_local:44,_orolsm:19,_templat:2,a_0:17,a_1:17,a_2:17,a_3:17,abcd:2,abl:[2,13,17,18,22,30,43],about:[2,5,11,14,19,33,39,42,43],abov:[2,39,43],accept:[6,14,21,22,42],access:[2,5,6,12,14,19,23,24,30,31,32,39,41,42,43],accmaxstep:[2,5,6,10,43],accomplish:15,accord:[6,12,43],account:[30,32,39,42,43],acctim:[2,5,6,10,43],acctyp:[2,5,6,10,43],accumlu:2,accumul:[2,6,17,19,43],accur:43,accuraci:[2,5,6,10,19,21],achiev:21,action:[23,31,32],activid:32,actual:[2,6,12,13,18,19,42,43],adapt:[0,2,5,6,9,11,12,13,18,30,31,32,33,36,43],add:[2,43],added:[17,19],adding:[2,43],addit:[2,5,11,14,15,17,30,39,43],addition:[2,5,6,14,18,20,30,43,44],addpar:[2,5,6,10,43],address:[2,6,19,30,32,43],adjac:17,adjust:41,admin:[30,31,33],adress:12,advanc:[2,43],aerosol:35,affect:17,after:[2,5,6,11,12,15,17,18,19,43],afterward:[2,13,17,30,31,32],again:[11,12],against:43,aggreg:19,agreement:[14,22,41],algorithm:[2,17,36],alist:2,all:[2,5,6,8,11,12,13,15,17,19,30,31,32,33,39,42,43,44],allow:[2,6,11,22],alpabet:2,alreadi:[2,11,22,30,31,32,42,43],also:[2,5,6,10,11,12,15,17,18,19,21,22,32,39,42,43],altern:42,alwai:[6,11],amount:[2,6,11,17,39],anaconda:[31,42],analys:21,analysi:[2,5,6,11,19,22,39,43],ani:[2,3,5,6,11,12,14,17,21,32,33,42,43,44],ann:[2,5,10,11,12,19,35],annep:10,announc:[43,44],anog__ml:19,anog__sl:19,anoth:[2,6,22,43],ansh__sl:19,anymor:[3,36],anyon:44,anyth:[6,11,12,13],api:[2,6,11,14,22,23,33,36,42,43],app:[30,32],appear:[21,43],append:2,appli:[2,11,17,21,36,42,43],applic:[2,4,6,7,9,10,11,12,13,20,21,42,43,44],approach:17,appropri:[6,43],approri:6,april:43,apt:[30,31],arbitrari:2,archiv:[2,5,11,18,20,22,30,41,42],area:[2,5,6,10,11,12,17,19,31,43],arg:2,argument:[2,11,12,18,22,30,31,32,42,43,44],aris:14,around:[17,20],arrai:[2,34],arrang:2,array_t1:2,array_t2:2,array_t3:2,array_t4:2,articl:[2,6],ascrib:17,ask:[19,32,41,42,44],aspect:42,assign:2,assign_args_to_control:2,assign_envs_to_control:2,assimil:43,assoc_nam:30,associ:[2,12,30],assum:[21,31],atm:21,atmospher:[17,20,23,34,41,43],attent:[6,43],attribut:[2,11,12,41],august:43,austria:35,author:[2,5,11,12,32],auto:38,automat:[6,11,14,17,22,30,32,43,44],autoprogram:1,avail:[2,3,5,6,11,12,15,17,19,21,22,23,30,31,32,33,34,39,42,43],averag:17,avoid:[19,21,36,43],awar:43,awk:[4,13],back:[6,11,42],bahaviour:5,ball:[2,4,12,42],base:[2,7,10,11,17,36,39],basetim:[2,5,6,10,11,17,36,43],bash:[11,12],basic:[2,17],batch:[4,10,11,12,13,18,20,30,43],bdynam:31,beaver:[30,31],becaus:[21,43],beck:2,been:[15,30,31,32,42],befor:[0,2,6,10,17,32,34,39,42,43],begin:[2,13,17],beginn:[18,43],behaviour:18,being:[12,13,19],belong:[42,43],below:[9,17,19,21,31,43],best:[6,17,39,43],better:[6,43],between:[2,4,6,7,10,17,19,21,30,43],bicub:17,big:[30,31,32],bilinear:17,bin:[4,10,11,12,13],bionic:[30,31],bit:[2,6],blank:2,block:[19,43],blockdiag:0,blockdiag_fontpath:0,blog:33,blue:[12,17],border:17,both:[2,21,31,39,43],boundari:[2,11,17],box:[2,11,12,41],bracket:43,branch:42,broader:39,bstatic:31,bug:41,build:[2,23],built:32,bunch:2,buster:[30,31],button:42,bypass:22,calc_etadot:[4,12,13,15,18,21,30,31,32,36,38,42,43],calc_etadot_fast:[30,31,32],calc_extra_elda:2,calcul:[2,5,6,15,17,19,20,43],calibr:[6,43],call:[2,4,10,11,12,13,15,18,19,30,31,42,43],can:[2,3,5,6,9,11,12,13,14,15,18,19,20,21,22,30,31,32,34,39,40,41,42,43,44],cancel:22,cannot:[21,43],care:[6,11],carefulli:39,carri:[2,6,17],cat:[10,13],catalogu:[6,43],catego:43,caution:43,cautiou:43,cautious:43,caveat:43,cca:[2,4,9,10,11,12,13,14,30,32,43],ccb:[4,9,10,11,13,14,30,32,43],cdot:17,cds_api:[2,10],cdsapi:31,cdsapirc:31,ce00010800:19,ce000908:43,cell:17,centr:[19,20,39,41],central:[2,17],cera20c:[6,31],cera:[5,6,19,21,22,23,34,36,41,42],cera_exampl:43,cera_testgrid_local_cd:19,cerapubl:43,certain:42,certif:30,chang:[5,6,11,12,13,15,17,18,19,23,32,39,41,42,43],changelog:41,charact:2,character:2,characteris:2,check:[4,6,10,11,12,15,18,30,31,33,36,42,43],check_accmaxstep:2,check_acctim:2,check_acctyp:2,check_addpar:2,check_area:2,check_basetim:2,check_condit:2,check_dat:2,check_dates_for_nonflux_fc_tim:2,check_grid:2,check_install_condit:2,check_job_chunk:2,check_len_type_time_step:2,check_level:2,check_logicals_typ:2,check_mail:2,check_maxstep:2,check_numb:2,check_path:2,check_ppid:2,check_publ:2,check_purefc:2,check_queu:2,check_request:2,check_step:2,check_tim:2,check_typ:2,checkerboard:17,choic:[21,31,43],choos:21,chosen:[2,21],chunk:[2,11],circl:17,classif:[2,6],clean:2,clean_up:2,clear:43,click:[24,42],client:[2,31],climat:[22,23,42],clist:2,clone:42,cloud:[2,6,19,43],cmd_list:2,cmp:43,coarser:[3,6],code:[0,2,6,13,31,32,36,41,42],collect:[2,39,41,43,44],collis:19,colour:17,column:2,combin:[2,11,41],come:31,comma:[2,6,43],command:[2,4,5,10,11,12,15,18,22,30,31,32,34,42,43],commandlin:[2,11,12,30,31,32,43,44],comment:[3,5,13],common:[2,11,12,41,43],commonli:2,commun:[15,17,39,42,43,44],compar:17,compat:[3,6,18,21],compil:[2,9,12,13,18,30,31,32,33,42],compilejob:[18,43],complet:[2,14,17,23,31,36,43],complex:39,compon:[0,2,17,19,42],composit:[5,19,43],comprehens:5,comput:[13,17,21,22,23,30,42,43],concaten:2,concatenate_sign:2,concern:2,conda:31,condit:[2,6,11,17],conduct:12,configur:[2,12,42],confluenc:2,confus:39,congratul:42,connect:[2,22,30,32,43],conrtol:43,conserv:[2,6,17],consider:17,consist:[2,3,11,17,18,19,20,21,39,43],consol:[30,31],constel:8,constitut:11,construct:[0,27,28,29,37,38,40],consum:31,contact:23,contain:[0,2,5,7,11,13,17,19,21,33,34,42,43,44],content:[2,6,13,23,30,32,41,43],context:2,continu:[2,6,17,43],control:[2,10,11,12,13,15,19,21,22,34,38,39,41,42,44],control_:[5,43],control_cera:[8,10,43],control_cont:13,control_ea5:[8,11,12,30,31,32,43],control_ei:[8,43],control_od:[8,43],controlfil:[10,11,12,13,30,31,32,43],controlparamet:5,convect:[2,11,17,19],conveni:43,convent:[2,5],convers:[2,20],convert2:[2,36],convert:[2,15,17,42,43],coordin:[5,19,38,39,43],copernicu:42,copi:[2,11,12,41,43],copy_dummy_msg:2,copyright:[2,11,12],corner:6,correct:[2,6,36,43],correctli:[2,6],correspon:18,correspond:[2,6,11,13,19,34,43],cost:21,could:[17,43],count:[6,11],counter:2,coupl:[2,8,9,12,13,43],cours:34,crai:[4,10,13],creat:[0,2,4,6,7,10,11,12,13,15,18,20,21,30,32,43,44],creativ:[2,11,12,41],creativecommon:[2,11,12,41],credenti:[12,13,15,18,31,42,43,44],cross:6,csv:[2,6,15,19,43],cubic:2,current:[0,2,6,9,12,14,21,31,40,42,43],cvh:19,cvl:19,cwc:[2,5,6,10,43],cycl:43,cyclic:[6,21],d64:[30,32],dai:[2,6,11,17,19,23,30,31,43],daili:[6,43],damp:17,dapoli:2,darain:2,dark:17,dat:11,data:[2,5,8,11,12,15,20,21,22,23,31,36,38,41,42],data_retriev:2,databas:23,dataset:[2,5,6,10,11,14,17,18,19,21,22,23,31,39,41],datatyp:[11,19],date:[2,5,6,11,12,17,19,31,34,43],date_chunk:[2,5,6,10,11,43],date_time_steprang:19,datechunk:2,datelin:6,datetim:2,deacc_flux:2,deaccumul:[2,43],debian:[30,31],debug:[2,5,6,9,10,11,19,21,31,36,43],decid:[2,5,18,42,43],decis:[2,43],declar:43,declin:22,decompos:2,defin:[2,5,6,10,11,12,19,21,24,34,39,42,43],definit:[2,5,18,34,41],degre:[6,21,43],degress:3,dejavu:0,dejavuserif:0,del_convert_build:2,delai:44,delet:[2,6,19,32,43],delete_fil:2,delta:17,delta_t:2,demand:[17,21,31,43],demonstr:19,denot:[2,17],depart:35,depend:[2,6,11,12,13,14,15,17,19,20,21,34,41,43],deposit:17,deprec:2,depthbelowlandlay:19,deriv:[2,30,31],describ:[12,14,18,20,22,32,42,43],descript:[2,5,6,8,11,12,13,18,19,21,34,39,42,43,44],design:43,desir:[2,6,17,21],destin:[2,5,6,7,10,12,13,15,30,31,32,36,43],destination_nam:[7,13],deta:21,detail:[2,5,15,19,20,21,42,43],detect:[6,44],determin:[2,11,12,17],dev:[17,31,42],develop:[0,2,6,17,31,40,41,44],diagnost:[2,6],diagram:[0,12,15],diamond:17,dict:2,dictionari:2,differ:[2,6,8,14,21,22,34,39,43],differenti:[4,10,43],difficulti:15,digit:19,dimens:[2,17],dimension:[2,17,43],direct:[2,13,14,21,22,34,43],directli:[2,4,10,11,12,13,14,22,42,43],directoi:42,directori:[0,2,4,5,6,7,8,9,10,11,12,13,14,18,31,32,36,42,43],dis:19,disabl:[6,21],disaggegr:2,disaggreg:[5,6,15,36,38,43],discard:6,discret:[17,19],discuss:[22,40,43],disk:31,dispers:[2,6,17],displai:[2,6,32],display_info:2,disregard:2,distinct:2,distinguish:[6,11],distribut:[30,31,41,42,43],disturb:43,diverg:[19,43],divers:[2,36],divid:[2,11,17,22],do_retriev:2,document:[5,8,11,19,21,23,30,32,36,40,43],doe:[2,11,12,14,33,43],doesn:[6,11,12],doi:[6,17],doing:2,domain:[5,43],don:[31,33,42],done:[2,4,6,10,11,12,13,14,15,17,20,22,31,37,40,42,43],dot:0,doubl:[2,4,6,8,10,11,13,43],doubleelda:[2,5,6,10,43],down:[17,42],download:[23,32,36,41],download_cdsapi:31,download_cera20c_ecmwfapi:31,download_era5_cdsapi:31,download_erainterim_ecmwfapi:31,downward:[3,6,18],dpdeta:[2,5,6,10,43],dpkg:[31,42],drive:[2,19,20,43],dry:17,dtime:[2,3,5,6,10,43],due:[6,11,12,17,43],durat:43,dure:[2,4,9,12,13,15,18,31,42],each:[2,5,6,10,11,13,14,17,19,39,42,43],easi:[17,18,20,43],easier:[18,22,43],easiest:[30,31],easili:[2,11],east:[2,11],eastern:2,eastward:[17,19],ec_api:[2,10],ec_memory_per_task:[4,10,13],ec_threads_per_task:[4,10,13],ecac:32,ecaccess:[2,4,10,12,13,14,15,22,23,30,32,43],ecaccess_do_not_remov:[4,10,13,43],ecc:2,eccod:[4,10,12,13,23,30,31,32,33,36],eccodes_include_dir:[9,31],eccodes_lib:[9,31],ecd:2,ecf:[2,6,32],ecfsdir:[2,5,6,10],ecg:[4,10,13],ecgat:[2,4,6,9,10,11,12,13,14,21,30,32,43],ecgb11:[32,43],ecgb:[4,10,13],ecgid:[2,5,6,7,10,12,13,30,31,32,43],echo:[4,12,13],echom:32,ecmf:19,ecmwf:[2,4,5,6,9,10,11,12,13,14,15,17,18,19,20,21,22,23,30,32,33,36,41,43],ecmwf_env:[2,11,12,18,43],ecmwfapi:[31,33],ecmwfapirc:31,ecmwfdataserv:[2,31],ecmwfservic:[2,31],ecnam:12,econdemand:[2,5,6,10],ecscratch:32,ecstorag:[2,5,6,10],ectmp:[2,5,6,10],ectran:[2,5,6,10,15,30,32,43],ecuid:[2,5,6,7,10,12,13,30,31,32,43],ecwmf:42,edg:12,edit:[19,31],editor:[30,31,32],effect:[13,21,43],effici:[13,17,19,43],egat:12,either:[2,6,11,14,15,43],elda:[2,6,8,36,43],element:[2,3],els:[4,10,12,13],email:[2,4,6,10,13,30,32,43,44],emo:[4,10,13],emoslib:[21,23,31,32,33],empti:[2,11,12],enabl:[22,30,43],encount:42,end:[2,4,6,10,11,13,17,19,43],end_dat:[2,5,6,10,11,17,43],end_period:2,enda:[10,19,31,43],endian:[30,31,32],endif:17,endo:6,enfo:[6,8,36,43],enough:[6,39,43],ens:[8,43],ensembl:[2,6,23,36,43],ensemble_memb:19,ensur:21,enter:[30,43],entri:[2,11],env:[2,4,13],environ:[2,4,6,10,11,12,13,14,20,33,41,42,43,44],environment:[2,35,43],eof:[10,13],equal:[2,6,11,21,43],equat:[2,6,17,43],equidistantli:17,equival:[30,31],era5:[2,5,6,21,22,23,31,42,43],era:[5,6,11,19,21,22,23,34,36,41,42],error:[2,4,10,12,13,21,30,31,43],error_msg:2,esac:[4,10,13],escap:13,especi:[21,39,42,43],establish:[14,30],eta:[2,5,6,8,10,19,21,38,43],etadiff:[2,5,6,10,21,43],etadot:[2,6,19,43],etapar:[2,5,6,10],etayymmddhh:[6,21],etc:[31,44],europ:43,european:[20,39,41],evalu:41,even:[17,21,31,32,43],event:17,eventu:[11,15],everi:[22,30,43],everyon:6,everyth:[0,2,14,31,43],everytim:34,ewss:[17,19],exact:[2,17,43],exampl:[2,3,6,7,11,17,18,19,22,23,31,34,39,42,43],exce:43,exceed:43,excelt:0,except:[2,6,21,31,43],execut:[2,9,10,12,13,14,15,18,19,32,36,42],execute_subprocess:2,exedir:2,exist:[2,6,11,43],exit:[2,11,12,34],expect:[2,43],expens:[6,21],experi:[6,43,44],experienc:43,explain:43,explan:43,explanait:43,explic:20,explicit:[22,42],explicitli:[6,20,22,43],express:2,expver:[2,5,6,10,19,31],extend:43,extens:[0,2,6,17],extra:[2,5,6,14,19,36,42,43],extract:[2,5,6,19,21,22,31,34,43],f90:[30,31,32,36],f_i:17,facil:[22,30],fail:[2,4,6,10,13,34,43],failur:43,fals:2,familiar:43,faq:41,far:6,fast:20,faster:[18,22,44],fcog_acc_sl:19,fconvert:[30,31,32],fdefault:[30,31,32],feasibl:21,featur:[2,6,20,41,44],februari:5,fedir:2,feel:42,few:[6,30,32,43],fewer:43,fftw3:[31,32],fftw:[23,30,32,33],field:[2,5,11,15,20,21,23,36,41,43],field_typ:19,fig:17,figur:[14,17,43],file1:2,file2:2,file:[0,2,4,9,10,11,12,13,15,17,18,20,22,23,30,31,32,34,36,39,41,42,44],filemod:2,filenam:[2,17,19,43],filename_in:2,filepath:2,fill:[6,42,43],filter:[2,17],find:[5,31,39,42,43],finder:39,fine:[21,31],finer:[3,21],finish:[42,43],first:[2,5,6,11,17,31,32,36,39,42,43],fit:2,fix:[4,10,17,41],flex:[10,13,43],flex_ecmwf:[4,10,13],flex_extract:[0,2,4,5,6,8,9,10,11,12,13,14,15,17,18,19,20,21,22,30,31,32,33,34,39,40,43,44],flex_extract_v7:[10,13,19,31,34],flex_extract_v:[4,13],flex_extract_vx:[5,7,8,9,11,12,13,18,30,31,32,42,43],flexcompil:[4,13,30,32],flexextract:[10,19],flexextractdir:2,flexpart:[2,6,11,15,17,20,21,22,31,34,41,43,44],flexpart_root:[4,13],flexpart_root_script:[4,13],flexpartdir:12,flextra:[2,20,21,41],flow:[2,11,12,20],flux:[2,5,15,21,38,43],fluxyyyymmddhh:17,flxacc2:17,follow:[2,5,7,12,13,15,17,18,19,21,30,31,32,33,34,39,42,43],font:0,fontpath:0,fopenmp:[30,31,32],for_develop:0,forecast:[2,5,6,11,17,20,21,22,23,39,41,43],forecast_step:19,forescast:43,forg:31,forget:33,form:[6,42],format:[2,6,10,12,15,17,19,20,31,43],formul:17,fort:[2,13],fortran90:[12,21],fortran:[2,4,12,13,15,16,17,18,20,30,31,32,36,38,41,43],fortran_program:13,found:[2,5,6,9,13,19,20,21,30,31,40,43,44],four:[2,42],fp_root:2,fp_root_path:13,fp_root_script:13,fpdir:2,frac32:17,frac:17,framework:[13,30],free:42,frequent:[41,44],from:[2,3,4,5,6,10,11,12,13,14,15,17,18,19,20,22,23,30,31,32,34,36,39,41,42,43,44],fromfil:2,fsr:19,ftime:2,ftp:32,ftrafo:[30,31,32],ftype:2,fulfil:17,full:[2,6,11,12,21,22,31,39,41,43],fulli:39,further:[2,31,32,43],futur:[6,21,43],g_i:17,g_ig_:17,gain:17,gap:43,gate:2,gatewai:[2,4,5,6,7,9,10,12,13,14,15,18,20,22,31,32,36,41,42],gateway_nam:[7,13],gatewaynam:[12,30,32],gatewayserv:43,gauss:[2,5,6,8,10,21,38,43],gaussian:[2,6,10,19,21,23],gen_docu:0,gener:[0,4,5,10,13,17,19,21,23,30,38,42,43],general:2,generate_retrieval_period_boundari:2,genericsftp:[2,10,12,30,32],genshi:[4,10,13,30,31,32,36],geometr:2,geophys:35,geosci:17,geoscientif:[2,6,17,40],get:[2,6,9,15,30,31,32,34,36,39,42,43],get_cmdline_arg:2,get_dimens:2,get_inform:2,get_install_cmdline_arg:2,get_kei:2,get_list_as_str:2,gfortran:[2,9,10,12,23,30,31,32,33],gid:32,git:42,gitmob:42,give:[2,6,21,34,42,43],given:[2,5,10,14,17,21,31],glevelist:2,global:[5,6,8,21,39,43],gmd:[6,17],gnu:[30,31,32,42],goe:2,going:[2,6,11],good:21,grant:42,graphviz:0,grb:[2,19],greater:[6,11],green:[12,17],grep:[10,13,31,42],grib1:[2,5,6,10,15],grib2:[2,6,15],grib2flexpart:10,grib:[2,6,11,15,23,31],grib_api:[4,10,13,33,36],grib_l:19,gribmessag:11,grid:[2,3,5,6,10,17,19,20,21,23,31,43],grid_simpl:19,grid_typ:19,gridtyp:19,group:[2,4,5,12,13,14,22,31,42],groupid:[12,30,32],groupnam:12,grphreal:[30,31,32],guarante:[2,11,12,17,43],guid:[23,36,41,43],guidanc:21,haimberg:[2,35],half:[2,6,11,17,21,43],handl:[2,5,39,41],happen:0,hard:2,harmon:19,has:[0,2,4,6,8,9,10,11,12,13,14,17,20,21,22,30,31,32,39,42,43],hast:6,have:[2,3,5,6,11,12,14,15,18,22,30,31,32,33,34,39,42,43],hcc:19,header:2,heat:[2,17,19],heavili:21,height:[17,19],help:[2,11,12,17,18,43,44],hemispher:43,henc:[17,43],here:[2,6,8,11,15,19,31,43,44],high:[6,11,13,21,31,43],higher:[2,21],highest:21,highli:21,highlight:43,highr:[8,43],hint:[5,33,39,41,44],his:[12,39],histor:21,hittmeir:[2,6,17],home:[4,10,12,13,14,23,30,31,32,42,43],horizont:[2,5,6,17,43],hoskin:6,host:[4,10,13,43],hostnam:[32,43],hour:[2,6,11,17,19,22,43],hourli:[6,22,43],how:[2,5,6,9,15,18,22,23,39,42,43],howev:[6,15,17,19,21,22,43],hpc:[21,43],hre:[23,43],http:[2,6,11,12,17,30,32,41,42,44],humid:19,hybrid:19,i32:[30,32],i_i:17,ia3:2,ice:[2,6,43],identif:2,identifi:[2,6,11,12,17,19],identificationkeyword:2,idir:2,idirectionincrementindegre:2,ids:[2,19],idx:[2,19],ifort:12,iid:2,img:10,implement:[17,43],impli:17,importantli:39,improv:[2,43],inbetween:6,includ:[6,11,12,13,30,31,32,42,44],incorpor:42,increas:34,incur:21,independ:39,index:2,index_fil:2,index_kei:2,index_v:2,indic:[2,5,17,19],individu:[2,4,6,10],ineffici:43,info:2,inform:[2,5,6,11,14,18,19,20,22,23,31,32,34,39,40,42,43,44],informt:2,init128:2,init:2,initi:[2,11,12,18,36],initialis:[2,36],input:[2,5,6,10,11,12,15,17,20,38,41,43],inputdir:[2,10,11,13,43],inputfil:[2,11],instal:[0,4,5,6,7,9,10,13,14,15,18,20,22,36,41,43],install_loc:2,install_target:[2,10,12],install_via_gatewai:2,installdir:[2,12,30,31,32,42],instanc:2,instantan:19,instead:[2,11,12,22],institut:39,instruct:[2,6,9,14,30,31,33,42,43],intact:11,integ:[2,6,11],integr:[2,17],intel:[4,10,13],intend:[6,8,11,14],interact:30,interest:[39,42],interfac:[2,5,23,24,36,43],intergovernment:39,interim:[5,6,11,19,21,22,23,31,34,41,42],intermedi:2,intern:[2,11,12,41],internet:43,interpol:[2,6,10,11,17,19,43],interpret:18,interv:[2,3,6,12,17,19],introduc:[17,19,36,43],introducst:34,introduct:23,introdut:[],investig:39,involv:12,ipar:2,ipnam:32,isol:17,issu:41,iter:2,its:[2,10,11,13,17,18,19,21,42,43],itself:[2,10,43],jame:[2,17],januari:43,jasper:[30,32],jdirectionincrementindegre:2,job:[2,4,6,11,12,14,15,18,19,20,30,31,32,41],job_chunk:[2,10,11,43],job_fil:2,job_id:[2,4,13],job_templ:[2,10,11,12,30,31,32,43],jobfil:2,jobnam:[2,4,13],jobop:43,jobscript:[11,18,43],journal:[17,40],jtemplat:2,june:[2,43],just:[2,3,6,12,19,31,43,44],k_i:17,keep:[2,13,17,42,43],kei:[2,31,42],kept:[6,43],keynam:2,keyvalu:2,keyword:[2,6,11,19,22,23,43],kind:[2,6,19,43],km4a:[4,10,13],know:[31,39,43],known:[5,41],korn:[2,4,10,12,18,20,36,43],kornshel:13,ksh:[13,18,43],kwd:2,label:[12,31],lagrangian:[2,6,17],larg:[2,6,11,17,19,36,43],larger:[6,11,21],last:[2,6,11,17,30,32,34,43],lat:[2,6,11,19,21],later:[2,31,34],latest:[22,42],latitu:2,latitud:[2,6,20,43],latitudeoffirstgridpointindegre:2,latitudeoflastgridpointindegre:2,latter:12,lcc:19,ld_library_path:33,lead:[6,11,13,17,32,43],learn:39,least:[2,12],leav:11,leccod:[30,31,32],leccodes_f90:[30,31,32],left:[2,5,6,10,17,21,42,43],lemo:[30,32],lemosr64:31,length:[2,17,43],leopold:[2,35],less:21,let:11,letter:[2,11,12,19,41],level:[2,5,6,10,11,12,15,18,19,21,22,31,34,43],level_typ:19,levelist:[2,5,6,10,11,19,31,43],levellist:34,levtyp:[2,19,31],lfftw3:[30,32],lib:[30,31,32,33],libeccod:[31,42],libemo:[30,31,32],librari:[4,10,12,14,20,23,31,32,41,42,44],licenc:[11,12,22,23,41],licens:[2,6,11,12,14,22,41],lies:2,light:12,like:[2,5,11,17,30,31,32,34,42,43],limit:[6,11,19,22,34,39,43],line:[2,5,11,12,13,15,17,18,19,22,30,32,42,43],linear:[2,6,17],linearli:17,link:[0,1,39,41,42,43],linux:[14,15,22,30,31,42,44],liquid:[2,6,43],list:[2,5,6,8,9,11,12,15,17,19,23,31,34,41,43],list_obj:2,littl:17,ljasper:[30,31,32],load:[2,4,10,13,30,32,43],local:[2,5,6,7,9,11,12,14,22,30,32,33,36,41,42],localmachin:32,localus:32,locat:[2,7,11,12,43],lock:34,log:[2,4,6,10,13,31,32,42,43,44],logarithm:19,logic:[2,10],login:[32,43],lon:[2,6,11,19,21],longer:[2,6,19,36,43],longitud:[2,6,20,43],longitudeoffirstgridpointindegre:2,longitudeoflastgridpointindegre:2,longiud:2,look:[2,30,32,43],lot:[21,43,44],lower:[2,5,6,10,17,21,43],lowest:19,lp64:[30,32],lpthread:[30,32],lrwxrwxrwx:[30,31,32],lsm:19,lsp:[17,19],machin:[2,4,10,12,13,14,15,31,32,42,43],made:[2,39,43],magnitud:2,mai:[6,11,15,17,30,31,42,43],mail:[2,4,6,10,13,35,41,43],mailfail:[2,5,10,13,43],mailop:[2,5,6,10,13],main:[2,5,18,20,22,43],mainli:[19,43,44],maintain:17,make:[0,4,13,18,30,33,39],make_dir:2,makefil:[2,4,10,12,13,18,30,31,32,33,36],makefile_crai:[9,30,32],makefile_debug:[9,31],makefile_ecg:[4,9,12,30,32],makefile_fast:[9,31],manag:[13,30,31,42],mani:[17,43],manipul:2,mar:[2,6,11,15,18,20,22,23,30,31,32,33,36,41,42,43],march:[2,22,30,31,32],mark:[4,5,10,13,17,19,43],mars_request:[2,6,11,15,19,43],marsclass:[2,10,19],marsfil:2,maschin:11,mask:43,mass:21,master:42,match:2,mathrm:17,matter:[2,12],max:[6,11],max_level_list:2,maxb:[2,13,19],maxim:2,maxima:17,maximum:[2,5,6,11,34,43],maxl:[2,13,19],maxstep:[2,5,6,10],mcc:19,mdpdeta:[2,13,19],mean:[2,4,12,13,17,19,43],measur:21,medium:[20,39,41],member:[2,6,12,14,19,22,23,24,30,31,39,42,43],memberst:[2,6],memori:[6,11],mention:[2,13,14,39,43],merg:15,mess:42,messag:[2,11,12,19,21,30,31,34],meta:[2,13,19],metadiff:[2,13,19],metapar:[2,13,19],meteorolog:[2,17,19,20,35,39,41],meter:19,method:[2,5,6,11,17,19,22,38,39,40,43],mgauss:[2,13,19],might:[0,2,6,11,15,18,22,31,39,42,43],migrat:[2,23],min:17,mind:[6,43],minim:[20,42],minima:17,minimis:31,minimum:43,minut:[2,30,32],mismatch:43,missingvalu:2,mix:[19,43],mk_compilejob:2,mk_convert_build:2,mk_date:2,mk_env_var:2,mk_job_templ:2,mk_jobscript:2,mk_server:2,mk_tarbal:2,mkdir:[4,10,13],mlevel:[2,13,19],mlevelist:[2,13,19],mnauf:[2,13,19],mnt:19,mock:0,mod:[2,4,13,31],mode:[2,4,6,7,9,10,11,12,13,18,19,20,39,41,42,44],model:[2,6,15,17,19,20,21,22,23,34,40,41,43],modif:2,modifi:[2,17,22,31,43],modul:[4,10,13,14,30,32,42,43],modular:36,momega:[2,13,19],momegadiff:[2,13,19],moment:6,mon:17,monitor:43,monoton:[2,17],month:[11,31,43],monthli:6,more:[2,3,5,6,11,12,14,15,17,19,31,43],most:[2,6,13,39,43],mostli:[2,6,43],motiv:17,mountain:[2,11,12,41],move:[0,2,22],mreq_count:2,msgatwai:30,msl:19,msmooth:[2,13,19],much:[39,44],multipl:[2,43],multipli:[6,21],muser:[10,13],must:[5,6,11,14,32,43],my_error:2,myuser:12,name:[2,4,5,6,9,10,11,12,13,17,19,22,30,31,32,36,42,43],name_of_this_fil:[4,10,13],namelist:[2,13,19],namespac:2,namgen:[13,19],nano:[30,32],nas:[10,19],nation:39,nativ:[30,31,32],natur:17,necessari:[0,2,3,4,5,6,9,10,11,12,13,14,18,20,30,31,32,33,43,44],nedit:31,need:[0,2,3,5,6,11,12,13,14,18,19,20,21,31,32,37,40,42,43],neg:[2,17],neglect:6,net:[17,19],nevertheless:2,newer:19,newest:43,newslett:43,next:[30,32,43],nfield:2,night:43,non:[2,6,17,34,43],noncycl:6,none:[2,5,6,10,11,12,17,19,30,31,32,43],none_or_int:2,none_or_str:2,normal:[4,6,10,13,21,31,43],normal_exit:2,north:[2,11],northern:[2,43],northward:[17,19],notabl:43,notat:17,note:[6,15,17,32,42,43],notif:[2,5],notifi:2,novemb:[2,21],now:42,nowadai:43,nsss:[17,19],number:[2,3,4,5,6,8,9,10,11,13,17,18,19,20,21,31,34,36,43],numer:39,numpi:[2,30,31,32],object:2,observ:2,obtain:[17,42],obvious:17,occur:[2,17],octahedr:23,octob:11,odir:2,off:[2,5,6,19],often:21,og_orolsm__sl:19,old:[0,2,6,11,17,36,43],older:[6,15,43],omega:[2,5,6,10,21,38,43],omegadiff:[2,5,6,10,21,43],omegayymmddhh:[6,21],onc:[11,43],one:[2,5,6,11,12,17,18,19,31,32,33,34,42,43],ones:[17,32],onli:[2,3,5,6,11,12,17,19,21,22,31,32,42,43,44],onlin:[36,40,43],onward:6,open:[2,20,30,31,32,41,43],opend:12,oper:[2,5,6,8,10,11,12,17,21,23,31,34,39,41,42],operation:6,oportun:22,opportun:43,opt:19,optim:[9,12,21,43],optimis:15,option:[2,5,6,15,17,19,21,33,36,42,43],optionalind:5,orang:12,order:[2,5,17],org:[2,6,11,12,17,41],organis:39,origin:[2,6,11,17,19,43],orographi:19,other:[1,2,5,6,11,17,31,39,42,43],otherwis:[2,43],our:[23,42],out:[2,4,6,10,13,17,30,31,32,42,43],output:[2,4,5,6,10,11,12,13,17,30,31,32,36,38,41,42,43,44],outputdir:[2,10,11,13,43],outputfilelist:2,outsid:31,over:[2,17,39,43],overal:[2,19],overlap:6,overrid:[3,11],overrul:5,overview:[8,14,15,17,23,34,38,41,42],overwrit:[0,2,43],overwritten:[2,18,43],own:[32,39,42],p_a:17,p_b:17,p_c:17,p_d:17,packag:[0,4,10,13,20,30,31,41,42],package_nam:42,packingtyp:19,page:[30,42],panel:42,paper:[34,40],par:2,parallel:19,param1:43,param2:43,param:[2,19,31],paramat:2,paramet:[2,3,4,5,8,10,13,15,17,18,19,20,23,30,31,32,36,39,41,42],parameteris:43,parameterlist:[11,12],parameternam:2,paramx:43,parent:[2,11,19],part:[2,17,19,20,31,32],parti:[14,20,23,41],particl:[2,6,17],pass:[2,34,42],passcod:30,password:[30,32],path:[0,2,4,6,8,10,11,12,13,14,31,32,33,34,42,43],path_flexextract_dir:2,path_fortran_src:2,path_input_dir:2,pattern:[2,43],paul:17,pbs_jobid:[10,13],pdf:21,pep8:36,per:[2,5,6,11,15,19,43],perform:[2,13,15,19,21],period:[2,5,6,11,17,30,39,43],person:12,perturb:[6,19],petra:2,phgrreal:[30,31,32],philipp:[2,5,6,11,12,17,35],physic:[35,39],pid:[19,43],piec:[17,19,31],piecewis:17,pip:[0,31,42],place:[2,12,13,14,30,43,44],placehold:[13,32],plan:[6,21],platform:42,pleas:[5,9,14,15,21,30,31,32,42,43,44],plot:23,plu:17,png:0,point:[2,11,17,19,43],polynomi:[2,17],posit:[2,6,13,17],posnam:[30,31,32],possibl:[2,5,6,8,11,12,17,21,22,31,33,42,43,44],post:[2,6,15,31],postprocess:2,pp_id:[11,43],ppid:[2,11,19],pre:17,precalcul:6,precip:19,precipit:[2,5,6,11,23,36,43],precis:33,preconvert:1,predict:[39,43],prefar:42,prefer:[6,30,31,32],prefix:[2,5,6,10,19,21],prepar:[0,2,4,6,9,10,11,12,13,14,15,20,26,41,42],prepare_flexpart:11,preprocessor:44,present:[7,12,23,30,32,42,43],preserv:17,pressur:[2,19,21,22,31],pressure_level:31,previou:[18,21],prgenv:[4,10,13],print:[2,4,13,43],print_infodata_csv:2,prior:[17,21],problem:[2,17,36,42,43,44],procedur:17,process:[2,4,6,7,9,10,11,12,13,14,15,17,18,19,22,31,36,42,43,44],process_output:2,prod:2,produc:[17,19,21,39,43],product:[2,42,43],product_typ:31,progam:42,program:[0,4,9,11,12,13,17,18,20,21,30,31,36,41,43],progress:[15,43],prompt:30,proper:18,properli:[2,12,15,34,42,44],properti:[2,19],propos:17,proposit:44,prot:[10,13,43],protocol:43,provid:[2,14,18,20,22,31,32,39,42,43,44],publicli:43,publish:[17,39],pull:31,pure:[2,6,11,15,43],purefc:[2,10],purpos:[2,6],put:[2,6,12,13,19],put_file_to_ecserv:2,pycallgraph:0,pylint:0,pyrevers:0,pyscript:11,pytest:0,python3:[4,10,13,18,30,31,32,36,42,43],python:[0,4,10,11,12,13,15,16,17,18,19,20,23,30,31,32,33,36,38,42,43],pythonxxxxx:43,qos:[4,10,13],quad:17,quantiti:[2,6,17],question:[41,44],queue:[2,4,10,11,12,13,15,30,43],queuenam:[4,10,13],queues_list:2,quick:[8,18,39,41,42],quickli:[13,43],quota:43,r64:[4,10,13,30,32],radiat:[2,17,19],raid60:10,rainfal:2,rais:[2,17],rang:[2,6,12,20,31,39,41,43],rare:43,rate:17,rather:21,raw:[2,15],reach:18,read:[2,6,12,13,15,20,21,32,33,39,43],read_ecenv:2,readi:[2,6,11],real:[23,30,31,32,43],real_tim:23,realis:17,realiti:17,realli:[21,43],reanalysi:[6,11,21,23,31,42],reason:[2,6,11,17,19,43],receiv:[15,30,43,44],recent:[10,43],recommend:[6,13,17,19,21,31,43],reconstruct:[2,17],record:42,rectangular:12,red:17,reduc:[19,21,23,43],ref:43,refactor:36,refer:[2,39],regard:[5,18,44],regardless:42,region:21,regist:[22,31,33,42],registr:[6,14,22,23,31,33,41,44],regress:[36,41],regular:[2,20,43],regular_l:19,regularli:39,rel:[17,43],relat:43,releas:[2,41,42,43,44],relev:[2,5],reli:42,remain:[2,17],rememb:[34,42],remot:[2,4,6,7,9,10,12,13,14,15,18,20,30,41,42],remota:12,remov:[2,3,17],remove_old:2,renam:0,renew:30,repeat:2,repo:42,report:[2,41],repositori:42,repr:[2,19],repres:[2,17,19,22,23,42,43],represent:2,request:[2,4,5,6,10,11,13,15,17,22,36,43],request_numb:[2,19],requir:[2,13,14,17,21,30,31,32,41,42,43],rerun:11,research:39,resol:[2,5,6,10,19,21,43],resolut:[3,5,6,11,21,22,39,43],resolv:21,reson:31,respect:[2,17,19,42],respectivlei:18,respons:43,rest:[2,6],restrict:21,restructur:36,result:[2,15,19,21,43],retriev:[2,5,6,11,14,15,17,18,19,20,21,22,31,33,34,36,39,41,42,43],return_list:2,review:6,revis:36,revtriev:2,right:[2,5,6,10,17,21,22,30,31,33,42,43,44],rla0:[2,13,19],rla1:[2,13,19],rlo0:[2,13,19],rlo1:[2,13,19],root:[2,4,12,13,18,31,32,42,43],round:12,rpath:[30,32],rpm:42,rrint:[2,5,6,10,11,43],rthl:43,rudimentari:12,run:[2,5,6,7,8,10,13,15,18,19,30,31,42,43,44],run_loc:[15,43],runtim:10,rwgrib2:[30,31,32,36],sabin:2,same:[2,6,11,22,30,31,33,43],sampl:[2,31],sardeshmukh:6,save:[11,19,21,31,43],sbatch:[4,10,13],scale:[2,11,17,19],scaveng:17,scenario:[14,17,43],schemat:17,scheme:[2,6,17,19,43],scientif:[23,34],scope:6,scp:32,scratch:[4,10,13,43],scriot:0,script:[2,5,6,10,13,14,15,17,18,19,20,21,23,30,31,32,36,42,43,44],scroll:42,sdor:19,second:[6,11],section:[5,12,18,22,31,36,37,39,40,42,43],see:[2,5,6,9,11,12,14,15,18,19,20,21,22,24,30,31,32,34,42,43],seem:43,seen:18,seibert:[2,6,17],select:[2,3,5,6,11,12,14,19,22,30,32,34,39,41,42],selectwher:2,send:[2,4,10,11,12,13,15,18,21,30,41,43,44],send_mail:2,sensibl:[2,17,19],sent:2,separ:[5,19],sepeart:2,seper:[2,6,43],septemb:[6,12,21],seqdiag:0,seqdiag_fontpath:0,sequenc:15,seri:[2,17],serv:[18,19,20,23,41,43],server:[2,4,5,6,7,9,10,11,12,13,14,15,18,20,22,30,31,32,36,42,43],servic:[30,39],session:[4,10],set:[0,2,4,5,6,8,10,11,12,13,17,18,19,20,21,24,30,31,32,33,34,36,42,43,44],set_kei:2,setup:[14,15,18,30,31,32,42,43],setup_controldata:2,sever:[19,42],sfc:[19,31],sgn:17,shade:17,share:[0,44],she:14,shell:[2,4,10,11,12,15,18,20,30,31,36,42,43],shift:17,shorten:43,shortli:43,shortnam:19,should:[0,2,6,9,12,13,17,19,21,30,31,32,33,36,42,43],shouldn:6,show:[7,11,12,15,17,43],shown:[9,17,31,43],side:42,sign:[4,5,10,13,42],signal:43,silent_remov:2,similar:14,simpl:[6,17,31],simplest:17,simplifi:36,simul:2,sinc:[2,12,15,19,21,31,43,44],singl:[2,4,10,11,13,15,19,33,42,43],site:[30,31],size:[34,43],sketch:[12,14,15],skip:[2,31],skt:19,slope:17,slurm:[13,23],small:[31,34,43],smaller:[2,6,11,19],smooth:[2,5,6,10,17,21,43],softwar:[2,6,12,13,14,20,21,23,30,31,32,41,42],solar:[2,17,19],sole:[6,19],solut:[2,44],some:[0,2,4,5,6,10,11,12,13,14,15,18,19,20,22,31,32,39,41,42,44],someth:43,sometim:[6,43],soon:[6,43],sort:[2,5],sourc:[0,2,4,9,10,11,12,13,18,20,31,33,34,36,41,42,43],south:[2,11],souther:2,southern:2,space:[2,5,11,17,43],spar:2,spatial:[5,6,39],spdx:[11,12],speak:42,speci:17,special:39,specialis:43,specif:[2,4,5,6,10,11,13,14,15,17,19,21,36,39,41,42],specifc:[2,11],specifi:[2,6,11,12,17,30,31,32,39,43],spectral:[2,6,20,21,43],speed:43,sphere:6,spheric:19,sphinx:36,sphinxcontrib:0,split:[15,17,19],sqrt:17,src_path:2,srvx8:10,ssh:[32,43],sshf:[17,19],ssr:[17,19],sss:6,stamp:19,standard:[2,30,31,32,42,43],start:[2,4,5,6,10,11,12,13,18,19,30,31,32,33,34,39,41,42],start_dat:[2,5,6,10,11,17,43],start_period:2,state:[2,12,14,22,23,24,30,31,39,42,43],statement:[2,30,32],statist:42,statu:[15,34,42],steer:2,step:[2,3,5,6,10,11,13,15,17,19,24,30,31,33,43],steprang:[2,11,19],still:[3,15,21,37,40,43],stl1:19,stop:[2,34,42],storag:[2,5],store:[2,6,10,11,12,15,19,21,22,23,31,42,43],str:2,str_of_list:2,straightawai:43,straightforeward:43,stream:[2,5,6,10,19,31,36,43],stress:[2,17,19],string:[2,5,6,11,12],structur:[10,36,39,43],studi:21,style:36,sub:[2,17,19],subgrid:[2,11],subinterv:17,subject:[2,30,32,43],submiss:[2,4,10,12,20,43],submit:[4,5,10,12,13,14,15,18,19,30,32,43,44],submit_job_to_ecserv:2,subprocess:2,subsect:21,subsequ:[6,43],subset:[6,11,43],substitut:[2,4,9,10,13,31,32,36,43],subtract:[6,43],succeed:[30,31],success:[4,13,19,30,32],success_mod:2,successful:42,successfulli:[18,42],suggest:31,suit:[6,43],sum:[2,6,18,43],supplement:19,support:[2,17,23,39,41,42,43],suppos:2,sure:31,surfac:[2,6,15,17,19,21,22,34],swvl1:19,symmetri:17,syntax:[2,6],synthes:[6,36],system:[2,4,6,10,11,13,20,21,30,31,32,34,41,42,43],sytem:[30,31],t1279:[21,43],t799:21,tab:[42,43],tabl:[2,5,17,19,34,41,42,43],table128:2,take:[2,31,43],taken:[2,6,18,19,39,43],tar:[2,4,12,13,32,42],tarbal:[2,30,32],tarball_path:2,tarfil:32,target:[2,12,19,30,31,32],task:[2,18,20,43],tcc:19,team:41,technic:23,tell:[2,43],temp:[2,4,10,11,43],temperatur:[19,31],templat:[2,4,5,7,10,11,12,18,30,31,32,36,43],tempor:[5,6,17,19,22,43],temporal_properti:19,temporari:[2,6,11,43],tendenc:21,tenth:6,term:[42,43],termin:[30,31],test:[0,2,5,6,12,13,19,22,33,36,41,43],textbf:17,textrm:17,than:[2,6,11,19,21,31,34,44],thei:[0,2,5,6,9,11,12,15,17,18,19,31,39,43],them:[0,2,6,11,12,15,17,18,19,39,43],therebi:[17,21],therefor:[0,2,6,17,18,19,31,34,39,42,43],thi:[0,2,4,5,6,7,8,10,11,12,13,14,17,18,19,21,22,30,31,32,33,34,37,39,40,41,42,43,44],thick:17,thing:5,think:[2,42],third:[14,20,23,41],those:[5,43],thousandth:6,three:[2,11,17],through:[2,5,22,24,30,42,43],throughout:17,thu:[17,43],ticket:[34,41],time:[2,3,4,5,10,11,13,15,17,19,21,23,31,33,39,43,44],timeseri:[2,17],timespan:[2,17],timestamp:2,tld:32,tmc:[10,31],tmpdir:[10,13],to_list:2,to_param_id:2,to_param_id_with_tablenumb:2,todai:43,todo:43,togeth:[2,12,15,19,42,43],token:30,too:[6,11,17,31,34,43],tool:[4,10,14,15,43],toolkit:22,top:[11,12,18,34],topic:39,total:[19,43],touch:43,trace:17,train:23,transfer:[2,5,6,7,12,13,15,19,30,32,43],transform:2,transport:[20,41],trapezoid:12,treatment:39,tree:43,tri:2,triangular:[2,6],trigger:[2,21],troubl:43,troubleshoot:[23,43],truetyp:0,truncat:[2,6],ttf:0,tupl:2,turbul:[17,19],twice:43,twiceadai:[8,43],two:[2,6,11,12,14,17,18,19,21,22,31,42,43],type:[0,2,3,4,5,6,10,11,13,17,18,19,30,31,32,42,43],typeoflevel:19,typic:[15,19,23,43],ubuntu:[30,31],udoc:2,uid:32,un_tarbal:2,unavail:44,unchang:17,under:[0,2,11,12,13,14,17,27,28,29,30,31,37,38,40,41,43],understand:[5,13,18,20,39,43],underw:43,undesir:17,unfortun:[17,22],uniqu:[2,19],unit:[0,17,21,36],univers:[2,35],univi:[10,35,44],unix:44,unless:6,unload:[4,10,13],unrealist:17,unreason:36,untar:[2,4,12,32,42],until:[6,11,17,22,43],updat:41,upfront:[2,6,43],upgrad:36,upper:[2,5,6,10,21,43],upstream:43,upto:2,usa:[2,11,12,41],usag:2,use:[0,2,6,9,12,13,18,20,21,22,30,31,32,33,34,36,39,42,43],used:[2,5,6,8,9,11,12,13,14,17,19,20,31,32,36,39,42,43,44],useful:[5,6,11,39,43],user:[2,4,5,10,11,12,13,14,18,20,22,23,24,30,31,32,33,36,39,42,43,44],user_group:[7,13],user_nam:[7,13],usergroup:13,usernam:[12,13,30,31,32],uses:[0,4,10,17,22,30,32,34,43],using:[2,6,11,12,17,30,31,32,42,43],usr:[0,4,10,13,30,31,32],usual:[5,6,11,13,15,19,31,43],utc:[6,11,43],util:[2,15],uza:35,v10:19,v20_update_protocol:21,v30_update_protocol:21,v40_update_protocol:21,v60_update_protocol:21,valid:[2,6,12,19,32,43],valu:[2,3,5,6,8,10,11,12,13,17,18,21,30,32,34,43],valuer:2,vanish:17,vari:[6,31,43],variabel:[4,10],variabl:[2,6,10,11,13,17,31,33,36,43],varianc:5,variat:[6,19],veloc:[15,19,20,43],veri:[2,6,11,17,21,31,39,43],version:[2,3,4,6,9,10,12,13,15,18,21,31,33,36,42,43,44],version_numb:13,vertic:[5,11,15,20,38,39,43],via:[2,4,10,11,13,14,15,22,23,30,31,32,36,43],vienna:[2,35],view:[2,11,12,13,41,44],virtual:42,visit:[2,11,12,30,41],vol:6,wai:[13,15,17,21,22,30,31,39,42,43],wait:22,want:[6,17,20,43],warn:[2,12,31],water:[2,6,19,43],wave:21,weather:[6,20,39,41],web:[2,6,11,14,22,23,24,33,36,42,43],webapi:[2,6],webserv:22,websit:[2,30,31,42,43,44],wedg:17,well:[2,6,15,21,34,39,42,43],were:[2,6,11,12,19,36,43],west:[2,11],western:2,wet:17,wether:[2,12],what:[5,23,31,41,43],whatev:43,when:[2,4,6,10,17],whenev:21,where:[2,6,9,11,12,13,17,19,20,21,31,42,43],wherea:[6,15],wherebi:11,wherekei:2,wherekeynam:2,wherekeyvalu:2,whether:42,which:[0,2,3,4,5,6,7,9,10,11,12,13,14,15,17,18,19,20,21,22,30,31,36,39,42,43,44],whith:10,who:20,whole:[2,17,39,43,44],whose:19,why:17,wiki:[2,6,32],wil:2,wildcard:43,wind:[5,19,43],window:[30,31,43],wish:42,within:[2,4,6,10,11,17,30,32,43],without:[2,13,22,33,42,43],word:2,work:[0,2,7,10,11,12,13,14,15,19,20,22,31,41,42,43],workdir:[4,10,13],workload:13,workspac:[10,19,43],workstep:20,would:[6,11,22,30,31,34,43],wrap:[11,12,18,20],wrf:[2,5,10],write:[2,6,44],write_namelist:2,write_reqhead:2,written:[2,6,21],wrong:34,www:42,x86_64:31,xvf:[4,13,32,42],xxx:19,xxxx:6,xxxxx:43,xxyymmddhh:2,year:[31,43],yet:43,yield:[2,21],you:[0,3,5,6,21,24,30,31,32,33,34,42,43,44],your:[24,30,31,32,42,43,44],yourself:24,yymmdd:[6,19],yymmddhh:[6,19,21],yyyymmdd:[2,6,11],yyyymmddhh:[17,19],zamg:[36,44],zero:[2,17,21,34],zonal:21},titles:["Update Documentation","Fortran\u2019s Auto Generated Documentation","Python\u2019s Auto Generated Documentation","CONTROL file changes","The Compilation Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF User Credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran Makefile - <code class=\"docutils literal notranslate\"><span class=\"pre\">calc_etadot</span></code>","The Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The Installation Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application Modes","Program Flow","Auto Generated Documentation","Disaggregation of Flux 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 Start","Support","ToDos"],titleterms:{"class":2,"new":[19,36],"public":[26,42,43],"static":28,CDS:[31,34],The:[4,5,6,9,10,11,12],access:22,addit:[0,6,19],adjust:43,agreement:42,analysi:28,api:[31,34],applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calc_etadot:[9,19,34],calcul:21,can:[24,33],cera:43,chang:[3,36],changelog:36,check:2,code:[28,34],collect:23,combin:[42,43],comparison:29,compil:4,compilejob:[4,13],content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert:13,coordin:21,credenti:7,data:[6,17,18,19,24,25,34,39,43],dataset:[24,25,26,42,43],definit:43,depend:[30,31,32,42],destin:34,develop:[35,37],diagramm:0,differ:15,disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,download:42,eccod:34,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era5:34,era:43,error:34,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:23,fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,34,42],frequent:33,from:[21,33],full:42,gatewai:[30,34,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,hint:[24,43],horizont:21,how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,34,42],interim:43,issu:[34,44],job:[10,13,43],jobscript:[4,10],known:[34,44],ksh:[4,10],level:25,librari:33,licenc:42,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],metric:27,mode:[14,15,22,30,31,32,43],model:25,modul:2,older:17,onlin:0,oper:43,option:[11,12],out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,34,43],parti:33,pre:21,precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,problem:34,program:[2,15,19,34,42],pure:19,python:2,question:33,quick:[23,43],registr:42,releas:[34,36],remot:[32,43],report:44,request:[19,29],rest:17,retriev:24,run:11,script:[4,11,12],section:6,select:43,sequenc:0,set:15,setup:12,softwar:0,some:43,specif:43,specifi:24,sphinx:0,standard:19,start:43,state:25,submiss:11,submit:[2,11],support:44,surfac:25,system:44,team:35,temp:13,templat:13,temporari:19,test:[30,31,42],testcas:29,third:33,ticket:44,time:6,todo:45,tool:2,uiofil:2,updat:0,usag:[11,12],user:[6,7,15,25,26,41],using:21,veloc:21,version:17,vertic:[6,19,21],web:31,welcom:41,what:[4,10,24,33],wind:[6,21],workflow:15}})
\ No newline at end of file
+Search.setIndex({docnames:["Developers/gen_docu","Documentation/Api/api_fortran","Documentation/Api/api_python","Documentation/Input/changes","Documentation/Input/compilejob","Documentation/Input/control","Documentation/Input/control_params","Documentation/Input/ecmwf_env","Documentation/Input/examples","Documentation/Input/fortran_makefile","Documentation/Input/jobscript","Documentation/Input/run","Documentation/Input/setup","Documentation/Input/templates","Documentation/Overview/app_modes","Documentation/Overview/prog_flow","Documentation/api","Documentation/disagg","Documentation/input","Documentation/output","Documentation/overview","Documentation/vertco","Ecmwf/access","Ecmwf/ec-links","Ecmwf/hintsecmwf","Ecmwf/msdata","Ecmwf/pubdata","Evaluation/metrics","Evaluation/staticcode","Evaluation/testcases","Installation/gateway","Installation/local","Installation/remote","Support/faq","Support/known_bugs_issues","authors","changelog","dev_guide","documentation","ecmwf_data","evaluation","index","installation","quick_start","support","todo"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.index":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":2,"sphinx.ext.viewcode":1,sphinx:56},filenames:["Developers/gen_docu.rst","Documentation/Api/api_fortran.rst","Documentation/Api/api_python.rst","Documentation/Input/changes.rst","Documentation/Input/compilejob.rst","Documentation/Input/control.rst","Documentation/Input/control_params.rst","Documentation/Input/ecmwf_env.rst","Documentation/Input/examples.rst","Documentation/Input/fortran_makefile.rst","Documentation/Input/jobscript.rst","Documentation/Input/run.rst","Documentation/Input/setup.rst","Documentation/Input/templates.rst","Documentation/Overview/app_modes.rst","Documentation/Overview/prog_flow.rst","Documentation/api.rst","Documentation/disagg.rst","Documentation/input.rst","Documentation/output.rst","Documentation/overview.rst","Documentation/vertco.rst","Ecmwf/access.rst","Ecmwf/ec-links.rst","Ecmwf/hintsecmwf.rst","Ecmwf/msdata.rst","Ecmwf/pubdata.rst","Evaluation/metrics.rst","Evaluation/staticcode.rst","Evaluation/testcases.rst","Installation/gateway.rst","Installation/local.rst","Installation/remote.rst","Support/faq.rst","Support/known_bugs_issues.rst","authors.rst","changelog.rst","dev_guide.rst","documentation.rst","ecmwf_data.rst","evaluation.rst","index.rst","installation.rst","quick_start.rst","support.rst","todo.rst"],objects:{"":{ControlFile:[2,0,0,"-"],EcFlexpart:[2,0,0,"-"],GribUtil:[2,0,0,"-"],MarsRetrieval:[2,0,0,"-"],UioFiles:[2,0,0,"-"],checks:[2,0,0,"-"],disaggregation:[2,0,0,"-"],get_mars_data:[2,0,0,"-"],install:[2,0,0,"-"],prepare_flexpart:[2,0,0,"-"],submit:[2,0,0,"-"],tools:[2,0,0,"-"]},"ControlFile.ControlFile":{"public":[2,2,1,""],accmaxstep:[2,2,1,""],acctime:[2,2,1,""],acctype:[2,2,1,""],accuracy:[2,2,1,""],addpar:[2,2,1,""],area:[2,2,1,""],assign_args_to_control:[2,3,1,""],assign_envs_to_control:[2,3,1,""],basetime:[2,2,1,""],cds_api:[2,2,1,""],check_conditions:[2,3,1,""],controlfile:[2,2,1,""],cwc:[2,2,1,""],dataset:[2,2,1,""],date_chunk:[2,2,1,""],debug:[2,2,1,""],destination:[2,2,1,""],doubleelda:[2,2,1,""],dpdeta:[2,2,1,""],dtime:[2,2,1,""],ec_api:[2,2,1,""],ecfsdir:[2,2,1,""],ecgid:[2,2,1,""],ecstorage:[2,2,1,""],ectrans:[2,2,1,""],ecuid:[2,2,1,""],end_date:[2,2,1,""],eta:[2,2,1,""],etadiff:[2,2,1,""],etapar:[2,2,1,""],exedir:[2,2,1,""],expver:[2,2,1,""],flexextractdir:[2,2,1,""],format:[2,2,1,""],gateway:[2,2,1,""],gauss:[2,2,1,""],gaussian:[2,2,1,""],grid:[2,2,1,""],inputdir:[2,2,1,""],install_target:[2,2,1,""],installdir:[2,2,1,""],left:[2,2,1,""],level:[2,2,1,""],levelist:[2,2,1,""],logicals:[2,2,1,""],lower:[2,2,1,""],mailfail:[2,2,1,""],mailops:[2,2,1,""],makefile:[2,2,1,""],marsclass:[2,2,1,""],maxstep:[2,2,1,""],number:[2,2,1,""],omega:[2,2,1,""],omegadiff:[2,2,1,""],oper:[2,2,1,""],outputdir:[2,2,1,""],prefix:[2,2,1,""],purefc:[2,2,1,""],request:[2,2,1,""],resol:[2,2,1,""],right:[2,2,1,""],rrint:[2,2,1,""],smooth:[2,2,1,""],start_date:[2,2,1,""],step:[2,2,1,""],stream:[2,2,1,""],time:[2,2,1,""],to_list:[2,3,1,""],type:[2,2,1,""],upper:[2,2,1,""],wrf:[2,2,1,""]},"EcFlexpart.EcFlexpart":{"public":[2,2,1,""],accmaxstep:[2,2,1,""],acctime:[2,2,1,""],acctype:[2,2,1,""],accuracy:[2,2,1,""],addpar:[2,2,1,""],area:[2,2,1,""],basetime:[2,2,1,""],calc_extra_elda:[2,3,1,""],create:[2,3,1,""],dataset:[2,2,1,""],dates:[2,2,1,""],deacc_fluxes:[2,3,1,""],dtime:[2,2,1,""],expver:[2,2,1,""],gaussian:[2,2,1,""],glevelist:[2,2,1,""],grid:[2,2,1,""],inputdir:[2,2,1,""],level:[2,2,1,""],levelist:[2,2,1,""],marsclass:[2,2,1,""],mreq_count:[2,2,1,""],number:[2,2,1,""],outputfilelist:[2,2,1,""],params:[2,2,1,""],process_output:[2,3,1,""],purefc:[2,2,1,""],resol:[2,2,1,""],retrieve:[2,3,1,""],server:[2,2,1,""],stream:[2,2,1,""],types:[2,2,1,""],write_namelist:[2,3,1,""]},"GribUtil.GribUtil":{copy_dummy_msg:[2,3,1,""],get_keys:[2,3,1,""],index:[2,3,1,""],set_keys:[2,3,1,""]},"MarsRetrieval.MarsRetrieval":{"public":[2,2,1,""],accuracy:[2,2,1,""],area:[2,2,1,""],data_retrieve:[2,3,1,""],dataset:[2,2,1,""],date:[2,2,1,""],display_info:[2,3,1,""],expver:[2,2,1,""],gaussian:[2,2,1,""],grid:[2,2,1,""],levelist:[2,2,1,""],levtype:[2,2,1,""],marsclass:[2,2,1,""],number:[2,2,1,""],param:[2,2,1,""],print_infodata_csv:[2,3,1,""],repres:[2,2,1,""],resol:[2,2,1,""],server:[2,2,1,""],step:[2,2,1,""],stream:[2,2,1,""],target:[2,2,1,""],time:[2,2,1,""],type:[2,2,1,""]},"UioFiles.UioFiles":{delete_files:[2,3,1,""],files:[2,2,1,""],path:[2,2,1,""],pattern:[2,2,1,""]},ControlFile:{ControlFile:[2,1,1,""]},EcFlexpart:{EcFlexpart:[2,1,1,""]},GribUtil:{GribUtil:[2,1,1,""]},MarsRetrieval:{MarsRetrieval:[2,1,1,""]},UioFiles:{UioFiles:[2,1,1,""]},checks:{check_accmaxstep:[2,4,1,""],check_acctime:[2,4,1,""],check_acctype:[2,4,1,""],check_addpar:[2,4,1,""],check_area:[2,4,1,""],check_basetime:[2,4,1,""],check_dates:[2,4,1,""],check_grid:[2,4,1,""],check_job_chunk:[2,4,1,""],check_len_type_time_step:[2,4,1,""],check_levels:[2,4,1,""],check_logicals_type:[2,4,1,""],check_mail:[2,4,1,""],check_maxstep:[2,4,1,""],check_number:[2,4,1,""],check_pathes:[2,4,1,""],check_ppid:[2,4,1,""],check_public:[2,4,1,""],check_purefc:[2,4,1,""],check_queue:[2,4,1,""],check_request:[2,4,1,""],check_step:[2,4,1,""],check_time:[2,4,1,""],check_type:[2,4,1,""]},disaggregation:{IA3:[2,4,1,""],dapoly:[2,4,1,""],darain:[2,4,1,""]},get_mars_data:{check_dates_for_nonflux_fc_times:[2,4,1,""],do_retrievement:[2,4,1,""],get_mars_data:[2,4,1,""],main:[2,4,1,""],mk_dates:[2,4,1,""],mk_server:[2,4,1,""],remove_old:[2,4,1,""],write_reqheader:[2,4,1,""]},install:{check_install_conditions:[2,4,1,""],del_convert_build:[2,4,1,""],get_install_cmdline_args:[2,4,1,""],install_local:[2,4,1,""],install_via_gateway:[2,4,1,""],main:[2,4,1,""],mk_compilejob:[2,4,1,""],mk_convert_build:[2,4,1,""],mk_env_vars:[2,4,1,""],mk_job_template:[2,4,1,""],mk_tarball:[2,4,1,""],un_tarball:[2,4,1,""]},prepare_flexpart:{main:[2,4,1,""],prepare_flexpart:[2,4,1,""]},submit:{main:[2,4,1,""],mk_jobscript:[2,4,1,""],submit:[2,4,1,""]},tools:{clean_up:[2,4,1,""],execute_subprocess:[2,4,1,""],generate_retrieval_period_boundary:[2,4,1,""],get_cmdline_args:[2,4,1,""],get_dimensions:[2,4,1,""],get_informations:[2,4,1,""],get_list_as_string:[2,4,1,""],init128:[2,4,1,""],make_dir:[2,4,1,""],my_error:[2,4,1,""],none_or_int:[2,4,1,""],none_or_str:[2,4,1,""],normal_exit:[2,4,1,""],product:[2,4,1,""],put_file_to_ecserver:[2,4,1,""],read_ecenv:[2,4,1,""],send_mail:[2,4,1,""],setup_controldata:[2,4,1,""],silent_remove:[2,4,1,""],submit_job_to_ecserver:[2,4,1,""],to_param_id:[2,4,1,""],to_param_id_with_tablenumber:[2,4,1,""]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","attribute","Python attribute"],"3":["py","method","Python method"],"4":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:class","2":"py:attribute","3":"py:method","4":"py:function"},terms:{"00h":[6,11],"10u":19,"10v":19,"12h":[6,11],"150px":[],"180w":6,"18utc":2,"1hourli":[8,43],"1st":[],"20c":[5,6,19,21,22,23,34,36,42,43],"20gb":43,"24h":6,"25th":[],"31st":[],"32000mb":[10,13],"3200mb":[4,13],"36hour":[8,43],"3hourli":[8,43],"4th":[],"60px":[],"6th":43,"althanstra\u00df":35,"boolean":2,"break":[],"case":[0,2,4,6,10,13,14,17,19,21,22,32,33,42,43],"class":[0,5,6,31],"default":[2,3,5,6,8,10,11,12,18,19,43],"export":[4,10,13],"f\u00fcr":13,"final":[0,2,11,15,17,19,21,43],"float":[2,11],"function":[2,17,41],"import":[2,6,11,30,31,33,34,39,43],"int":[2,6,30,32,43],"long":43,"m\u00e4r":31,"new":[2,6,10,11,17,41,43,44],"public":[2,5,6,8,10,11,12,14,22,23,24,31,36,39,41],"return":[2,4,10,34],"short":[2,5,6,17,30,43],"switch":[2,4,6,10,13,19],"true":[0,2],"try":[31,42,43],"while":[22,43],ARE:5,But:[],C3S:23,CDS:[2,22,23,33,36,42],Dps:[2,6],ENS:[23,43],FOR:[11,12],For:[0,2,5,6,9,11,13,14,18,19,21,22,24,30,32,33,34,39,42,43],HAS:[11,12,30,31,32,43],Has:[6,11],IDs:[2,6,15,43],Its:[2,43],NOT:[11,12,31],Not:12,One:43,PBS:[4,10,13],THE:[11,12,30,31,32,43],THESE:[11,12,30,31,32,43],The:[0,2,13,14,15,17,18,19,20,21,22,30,31,32,34,39,42,43,44,45],Then:[2,11,14,42],There:[2,5,18,19,22,39,42,43],These:[4,10,13,17,42,43],Use:[0,6,30,32,43],Used:[2,12],Useful:[],Uses:2,Using:[31,43],WITH:[11,12],With:[6,11,12,18,43],_acc:19,_config:2,_expand:2,_file:0,_local:44,_orolsm:19,_static:[],_templat:2,a_0:17,a_1:17,a_2:17,a_3:17,abcd:2,abl:[2,13,18,19,22,30,43],about:[2,5,11,14,19,33,39,42,43],abov:[2,17,43],absolut:[],accept:[6,14,21,22,41,43],access:[2,5,6,12,14,23,24,30,31,32,39,41,42,43],accmaxstep:[2,5,6,10,43],accomplish:15,accord:[6,12,43],account:[30,32,39,42,43],acctim:[2,5,6,10,43],acctyp:[2,5,6,10,43],accumlu:2,accumul:[2,6,17,19,43],accur:43,accuraci:[2,5,6,10,19,21],achiev:21,action:[23,31,32],activ:42,activid:32,actual:[2,6,12,13,18,19,42,43],adapt:[0,2,5,6,9,11,12,13,18,30,31,32,33,36,43],add:[2,43],added:[8,17,19,45],adding:[2,43],addit:[2,5,11,15,17,20,30,39,43],addition:[2,6,14,30,43,44],addpar:[2,5,6,10,43],address:[2,6,12,19,30,32,43],adjac:17,adjust:41,admin:[30,31,33],adress:12,advanc:2,aerosol:35,affect:17,after:[2,5,6,11,12,15,17,18,43],afterward:[2,13,17,30,31,32],again:[11,12],against:[],aggreg:19,agre:22,agreement:14,algorithm:[2,17,36],align:[],alist:2,all:[2,5,6,8,11,12,13,15,17,19,30,31,32,33,42,43,44],alll:39,allow:[2,6,11,19,22,43],alpabet:2,alreadi:[2,11,12,22,30,31,32,42,43],also:[2,5,6,10,11,12,17,18,19,21,22,32,39,42,43],alter:19,altern:42,alwai:[6,11,43],amount:[2,6,11,17,39],anaconda:[31,42],analys:[21,39,43],analysi:[2,5,6,11,19,22,39,43],ani:[2,5,6,11,12,14,17,21,32,33,42,43,44],ann:[2,5,10,11,12,19,35,45],annep:10,announc:[43,44],anog__ml:19,anog__sl:19,anoth:[2,6,9,43],ansh__sl:19,anymor:[3,36],anyon:44,anyth:[6,11,12,13],api:[1,2,6,11,14,22,23,33,36,42,43],app:[30,32],appear:21,append:2,appli:[2,11,17,21,36,42,43],applic:[2,4,6,7,9,10,11,12,13,20,21,42,43,44,45],approach:17,appropri:[6,43],approri:6,april:43,apt:[30,31],arbitrari:2,archiv:[2,5,11,18,20,22,30,41,42],area:[2,5,6,10,11,12,17,19,31,43],arg:2,argument:[2,11,12,18,22,30,31,32,42,43,44],aris:14,around:[17,20],arrai:[2,34],arrang:2,array_t1:2,array_t2:2,array_t3:2,array_t4:2,articl:[2,6],ascrib:17,ask:[19,32,41,42,44],aspect:42,assign:[2,31],assign_args_to_control:2,assign_envs_to_control:2,assimil:43,assoc_nam:30,associ:[2,12,30,43],assum:[21,43],atm:[],atmospher:[17,20,23,34,41,43],attempt:2,attent:[6,43],attribut:[2,11,12,41],august:43,austria:35,author:[2,5,11,12,32],auto:38,automat:[6,11,14,17,22,30,32,43,44],autoprogram:[],avail:[2,3,5,6,11,12,17,19,21,22,23,30,31,32,33,34,39,42,43],averag:17,avoid:[19,21,36,43],awar:43,awk:[4,13],back:[6,11,42],bahaviour:[],ball:[2,42],base:[2,7,10,11,17,36,39],basetim:[2,5,6,10,11,17,36,43],bash:[11,12,43],basic:[2,17],batch:[4,10,11,12,13,18,20,30,43],bdynam:31,beaver:[30,31],becaus:[12,21,43],beck:2,been:[5,15,30,31,32,42,43],befor:[0,2,6,10,17,19,32,34,39,42,43],begin:[2,13,17],beginn:[18,43],behaviour:[5,18],being:[12,19],belong:[42,43],below:[7,9,17,19,21,31,43],best:[6,17,39,43],better:[6,43],between:[2,4,6,7,10,17,19,21,30,43],beyond:43,bicub:17,big:[30,31,32],bilinear:17,bin:[4,10,11,12,13],bionic:[30,31],bit:[2,6],blank:2,block:[19,31,43],blockdiag:0,blockdiag_fontpath:0,blog:33,blue:[12,17],border:17,both:[2,21,31,39,43],bottom:[],boundari:[2,11,17],box:[2,11,12,41],bracket:43,branch:42,broader:39,bstatic:31,bug:41,build:[2,23],built:32,bunch:2,buster:[30,31],button:42,bypass:[],calc_etadot:[4,12,13,15,18,21,30,31,32,36,38,42,43],calc_etadot_fast:[30,31,32],calc_extra_elda:2,calcul:[2,5,6,15,17,19,20,43],calendar:43,calibr:[6,43],call:[2,4,9,10,11,12,13,15,18,19,22,30,31,42,43],can:[2,3,5,6,9,11,12,13,14,15,18,19,21,22,30,31,32,34,39,40,41,42,43,44],cancel:22,cannot:[21,43],care:[6,11,43],carefulli:39,carri:[2,6],cat:[10,13],catalogu:[6,43],catego:[],caution:43,cautiou:[],cautious:43,caveat:43,cca:[2,4,9,10,11,12,13,14,30,32,43],ccb:[4,9,10,11,13,14,30,32,43],cdot:17,cds_api:[2,10],cdsapi:31,cdsapirc:31,ce00010800:19,ce000908:43,cell:17,centr:[19,20,39,41],central:[2,17],cera20c:[6,31],cera:[5,6,19,21,22,23,34,36,41,42],cera_exampl:43,cera_testgrid_local_cd:19,cerapubl:43,certain:[2,18,41,42],certif:30,chang:[6,11,12,13,15,17,18,23,32,39,41,42,43],change_icon:[],changelog:41,charact:2,character:2,characteris:2,characterist:43,check:[4,6,10,11,12,15,18,30,31,33,36,42,43],check_accmaxstep:2,check_acctim:2,check_acctyp:2,check_addpar:2,check_area:2,check_basetim:2,check_condit:2,check_dat:2,check_dates_for_nonflux_fc_tim:2,check_grid:2,check_install_condit:2,check_job_chunk:2,check_len_type_time_step:2,check_level:2,check_logicals_typ:2,check_mail:2,check_maxstep:2,check_numb:2,check_path:2,check_ppid:2,check_publ:2,check_purefc:2,check_queu:2,check_request:2,check_step:2,check_tim:2,check_typ:2,checkerboard:17,choic:[21,31,43],choos:21,chosen:[2,21],chunk:[2,11],circl:17,classif:[2,6],clean:2,clean_up:2,clear:[39,43],click:[24,42],client:[2,31],climat:[22,23,42],clist:2,clone:42,close:43,cloud:[2,6,19,43],cmd_list:2,cmp:[],coarser:[3,6],code:[0,2,6,13,19,31,32,36,41,42,43],collect:[2,39,41,43,44],collis:19,colour:17,column:2,combin:[2,11,41],come:8,comma:[2,6,43],command:[2,4,5,10,11,12,15,18,22,30,31,32,34,42,43],commandlin:[2,11,12,30,31,32,43,44],comment:[3,5,13],common:[2,11,12,41,43],commonli:2,commun:[39,42,43,44],compar:[17,43],compat:[3,6,18,21],compil:[2,9,12,13,18,30,31,32,33,42],compilejob:[18,43],complet:[2,14,17,23,31,36],complex:39,compon:[0,2,17,19,39,42],compos:19,composit:[5,19,43],comprehens:5,comput:[13,17,21,22,23,30,42,43],concaten:2,concatenate_sign:2,concern:2,conda:31,condit:[2,6,11,17],conduct:12,configur:[2,42],confluenc:2,confus:39,congratul:42,connect:[2,22,30,32,43],conrtol:[],conserv:[2,6,17],consider:17,consist:[2,3,11,17,18,19,20,21,43],consol:[30,31],constel:8,constitut:11,construct:[0,27,28,29,37,38,40],consult:43,consum:31,contact:23,contain:[0,2,5,7,8,11,12,13,15,17,19,21,33,34,42,43,44],content:[2,6,13,23,30,32,39,41,43],context:2,continu:[2,6,17,43],control:[2,10,11,12,13,15,19,21,22,34,38,39,41,42,44],control_:[5,43],control_cera:[8,10,43],control_cont:13,control_ea5:[8,11,12,30,31,32,43],control_ei:[8,43],control_od:[8,43],controlfil:[10,11,12,13,30,31,32,43],controlparamet:5,convect:[2,11,17,19],conveni:43,convent:[2,5,19],convers:2,convert2:[2,36],convert:[2,15,17,20,42,43],coordin:[19,21,38,43],copernicu:42,copi:[2,11,12,41,43],copy_dummy_msg:2,copyright:[2,11,12],corner:6,correct:[2,6,36,43],correctli:[2,6],correspon:18,correspond:[2,6,9,11,13,17,19,34,39,43],correspondingli:43,cost:21,could:[17,43],count:[6,11],counter:2,coupl:2,cours:34,cover:43,crai:[4,10,13],creat:[0,2,4,6,7,10,11,12,13,15,18,19,20,21,30,32,43,44],creation:2,creativ:[2,11,12,41],creativecommon:[2,11,12,41],credenti:[12,13,15,18,31,42,43,44],cross:6,csv:[2,6,15,19,43],cubic:2,current:[0,2,6,9,12,14,17,21,31,40,42,43],cvh:19,cvl:19,cwc:[2,5,6,10,43],cycl:43,cyclic:[6,21],d64:[30,32],dai:[2,6,11,17,19,23,30,31,43],daili:[6,43],damp:17,dapoli:2,darain:2,dark:17,dat:11,data:[2,5,8,11,12,15,20,21,22,23,31,36,38,41,42],data_retriev:2,databas:23,dataset:[2,5,6,10,11,14,19,21,22,23,31,41],datatyp:[11,19],date:[2,5,6,11,12,17,19,31,34,43],date_chunk:[2,5,6,10,11,43],date_time_steprang:19,datechunk:2,datelin:6,datetim:2,deacc_flux:2,deaccumul:[2,43],debian:[30,31],debug:[2,5,6,9,10,11,19,21,36,43],decid:[2,5,18,43],decim:43,decis:2,declar:43,declin:[],decompos:2,dedic:22,defin:[2,5,6,10,11,12,19,21,24,34,39,42,43,45],definit:[2,5,18,34,41],degre:[6,21,43],degress:3,dejavu:0,dejavuserif:0,del_convert_build:2,delai:44,delet:[2,6,19,32,43],delete_fil:2,delta:17,delta_t:2,demand:[17,21,31,43],demonstr:19,denot:[2,17],depart:35,depend:[2,6,11,12,13,14,15,17,19,20,21,34,41,43],deposit:17,deprec:2,depthbelowlandlay:19,deriv:[2,30,31],describ:[12,14,18,19,20,22,32,42,43],descript:[2,5,6,11,12,13,19,21,34,39,43,44,45],design:[],desir:[2,6,17,21,43],destin:[2,5,6,7,10,12,13,15,30,31,32,36,43],destination_nam:[7,13],deta:21,detail:[2,5,13,19,20,21,42,43],detect:[6,44],determin:[2,11,12,17,43],dev:[17,31,42],develop:[0,2,6,9,17,40,41,44],deviat:5,diagnost:[2,6],diagram:[0,12,15],diamond:17,dict:2,dictionari:2,differ:[2,6,8,14,21,22,34,39,43],differenti:[4,10,43],difficulti:15,digit:19,dimens:[2,17],dimension:[2,17,43],direct:[2,13,14,21,22,34,43],directli:[2,4,10,11,12,13,14,21,22,42,43],directoi:42,directori:[0,2,4,5,6,7,8,9,10,11,12,13,14,18,31,32,36,42,43],dis:19,disabl:[6,21],disaggegr:2,disaggreg:[5,6,15,36,38,43],discard:6,discret:17,discretis:19,discuss:[40,43],disk:[31,43],dispers:[2,6,17],displai:[2,6,32],display_info:2,disregard:2,distinct:2,distinguish:[6,11],distribut:[30,31,41,42,43],disturb:43,div:[],diverg:[19,43],divers:[2,36],divid:[2,11,17,19,22],do_retriev:2,document:[5,8,11,19,21,23,30,32,36,43,45],doe:[2,3,11,12,14,33],doesn:[6,11,12],doi:[6,17],doing:[2,43],domain:[5,43,45],don:[9,31,33,42],done:[2,4,6,10,11,12,13,14,17,22,31,42,43],dot:0,doubl:[2,4,6,8,11,13,43],doubleelda:[2,5,6,10,43],down:42,download:[23,32,36,41],download_cdsapi:31,download_cera20c_ecmwfapi:31,download_era5_cdsapi:31,download_erainterim_ecmwfapi:31,downward:[3,6,18],dpdeta:[2,5,6,10,43],dpkg:[31,42],drive:[2,20,43],dry:17,dtime:[2,3,5,6,10,43],due:[6,11,12,17,43],durat:43,dure:[2,4,9,12,13,15,18,31,42,43],each:[2,5,6,10,11,13,14,17,19,39,42,43],earlier:43,easi:[17,18,20,43],easier:[18,22],easiest:[30,31],easili:[2,11],east:[2,11,19],eastern:2,easternmost:2,eastward:17,ec_api:[2,10],ec_memory_per_task:[4,10,13],ec_threads_per_task:[4,10,13],ecac:32,ecaccess:[2,4,10,12,13,14,15,22,23,30,32,43],ecaccess_do_not_remov:[4,10,13,43],ecc:2,eccod:[4,10,13,23,30,31,32,33,36],eccodes_include_dir:[9,31],eccodes_lib:[9,31],ecd:2,ecf:[2,6,32],ecfsdir:[2,5,6,10],ecg:[4,10,13],ecgat:[2,4,6,9,10,11,12,13,14,21,30,32,43],ecgb11:[32,43],ecgb:[4,10,13],ecgid:[2,5,6,7,10,12,13,30,31,32,43],echo:[4,12,13],echom:32,ecmf:19,ecmwf:[2,4,5,6,9,10,11,12,13,14,15,17,18,19,20,21,22,23,30,32,33,36,41,43],ecmwf_env:[2,11,12,18,43],ecmwfapi:[31,33],ecmwfapirc:31,ecmwfdataserv:[2,31],ecmwfservic:[2,31],ecnam:[],econdemand:[2,5,6,10],ecscratch:32,ecstorag:[2,5,6,10],ectmp:[2,5,6,10],ectran:[2,5,6,10,15,30,32,43],ecuid:[2,5,6,7,10,12,13,30,31,32,43],ecwmf:[22,42],edg:12,edit:19,editor:[30,31,32],effect:[13,21],effici:[13,17,19,43],egat:12,either:[2,6,11,14,15,43],elda:[2,6,8,36,43],element:[2,3],els:[4,10,12,13],email:[2,4,6,10,13,30,32,43,44],emo:[4,10,13],emoslib:[21,23,31,32,33],empti:[2,11,12],enabl:[22,30,43],encount:42,end:[2,4,6,10,11,13,17,19,43],end_dat:[2,5,6,10,11,17,43],end_period:2,enda:[10,19,31,43],endian:[30,31,32],endif:17,endo:6,enfo:[6,8,36,43],enough:[6,22,43],ens:[8,43],ensembl:[2,6,23,36,43],ensemble_memb:19,ensur:21,enter:30,entri:[11,43,45],env:[2,4,13],environ:[2,4,6,10,11,12,13,14,20,33,41,42,43,44],environment:[2,35],eof:[10,13],equal:[2,6,11,21,43],equat:[2,6,17,43],equidistantli:17,equival:[30,31],era5:[2,5,6,21,22,23,31,42,43],era:[5,6,11,19,21,22,23,34,36,41,42],eror:2,error:[2,4,10,12,13,21,30,31,43],error_msg:2,esac:[4,10,13],escap:13,especi:[21,42,43],establish:[14,30],eta:[2,5,6,8,10,19,21,38,43],etadiff:[2,5,6,10,21,43],etadot:[2,6,19,43],etapar:[2,5,6,10],etayymmddhh:[6,21],etc:[31,39,44],europ:43,european:[20,39,41],evalu:41,even:[17,21,31,32,43],event:17,eventu:[],everi:[22,30,39,43],everyon:6,everyth:[0,2,9,14,31,43],everytim:34,ewss:[17,19],exact:[2,17,43],exampl:[2,3,6,7,11,17,18,19,22,23,31,34,39,42,43,45],exce:[],exceed:43,excelt:0,except:[2,6,21,31,43],execut:[2,9,10,12,13,14,15,18,19,32,36,42],execute_subprocess:2,exedir:2,exist:[2,6,11,43],exit:[2,11,12,34],expect:[2,43],expens:[6,21],experi:[6,43,44],experienc:43,explain:[19,43,45],explan:43,explanait:[],explic:[],explicit:42,explicitli:[6,20,22,43],express:2,expver:[2,5,6,10,19,31],extend:[39,43],extens:[0,2,6,17,43],extra:[2,5,6,14,36,42,43],extract:[2,5,6,19,21,22,31,34,43],f90:[30,31,32,36],f_i:17,facil:[22,30],fail:[2,4,6,10,13,34,43],failur:43,fals:2,familiar:43,faq:41,far:6,fast:20,faster:[18,22,44],fcog_acc_sl:19,fconvert:[30,31,32],fdefault:[30,31,32],feasibl:21,featur:[2,6,20,41,44],februari:5,fedir:2,feel:42,few:[6,30,32,43],fewer:43,fftw3:[31,32],fftw:[23,30,32,33],field:[2,5,11,15,20,21,23,36,41,43],field_typ:19,fig:17,figur:[14,17,43],file1:2,file2:2,file:[0,2,4,9,10,11,12,13,15,17,18,20,22,23,30,31,32,34,36,39,41,42,44],filemod:2,filenam:[2,17,19,43],filename_in:2,filepath:2,fill:[6,42,43],filter:[2,17],find:[5,31,39,42,43],finder:[],fine:[21,31],finer:[3,21],finish:[42,43],first:[2,5,6,11,17,31,32,36,39,42,43],fit:2,fix:[4,10,17,41],flex:[10,13,43],flex_ecmwf:[4,10,13],flex_extract:[0,2,4,5,6,8,9,10,11,12,13,14,15,17,18,19,20,21,22,30,31,32,33,34,39,40,43,44,45],flex_extract_repo:45,flex_extract_v7:[10,13,19,31,34],flex_extract_v:[4,13],flex_extract_vx:[5,7,8,9,11,12,13,18,30,31,32,42,43],flexcompil:[4,13,30,32],flexextract:[10,19],flexextractdir:2,flexpart:[2,6,11,15,17,20,21,22,31,34,41,43,44],flexpart_root:[4,13],flexpart_root_script:[4,13],flexpartdir:12,flextra:[2,20,21,41],flow:[2,11,12,20],flux:[2,5,15,21,38,43],fluxyyyymmddhh:17,flxacc2:17,follow:[2,5,12,13,15,17,18,19,21,30,31,32,33,34,39,42,43],font:0,fontpath:0,fopenmp:[30,31,32],for_develop:[0,45],forecast:[2,5,6,11,17,20,21,22,23,39,41,43],forecast_step:19,forescast:43,forg:31,forget:33,form:[6,19,42],format:[2,6,10,12,15,17,19,20,31,43],formul:17,fort:[2,13],fortran90:[],fortran:[2,4,12,13,15,16,17,18,20,21,30,31,32,36,38,41,43],fortran_program:13,found:[2,5,6,9,13,19,21,30,31,40,42,43,44],four:[2,14,17,42],fp_root:2,fp_root_path:13,fp_root_script:13,fpdir:2,frac32:17,frac:17,framework:[13,30],free:42,frequent:[41,43,44],from:[2,3,4,5,6,10,11,12,13,14,15,17,18,19,20,22,23,30,31,32,34,36,39,41,42,43,44],fromfil:2,fsr:19,ftime:2,ftp:32,ftrafo:[30,31,32],ftype:2,fulfil:17,full:[2,6,11,12,21,22,31,41,43],fulli:39,further:[2,5,31,32,43],furthermor:18,futur:[6,21,43],g_i:17,g_ig_:17,gain:[],gap:43,gate:[],gatewai:[2,4,5,6,7,9,10,12,13,14,15,18,20,22,31,32,36,41,42],gateway_nam:[7,13],gatewaynam:[12,30,32],gatewayserv:43,gauss:[2,5,6,8,10,21,38,43],gaussian:[2,6,10,19,21,23],gen_docu:0,gener:[0,4,5,10,13,17,19,21,23,30,38,42,43],general:2,generate_retrieval_period_boundari:2,genericsftp:[2,10,12,30,32],genshi:[4,10,13,30,31,32,36],geometr:2,geophys:35,geosci:17,geoscientif:[2,6,17,40],get:[2,6,30,31,32,34,36,42,43],get_cmdline_arg:2,get_dimens:2,get_inform:2,get_install_cmdline_arg:2,get_kei:2,get_list_as_str:2,gfortran:[2,9,10,23,30,31,32,33],gid:[12,32],git:42,gitmob:42,give:[6,21,34,42,43],given:[2,5,14,17,21,31,43],glevelist:2,global:[5,6,8,21,39,43],gmd:[6,17],gnu:[30,31,32,42],goe:2,going:[2,6,11],good:21,grant:42,graphviz:0,grb:[2,19],greater:[6,11],green:[12,17],grep:[10,13,31,42],grib1:[2,5,6,10,15],grib2:[2,6,15],grib2flexpart:10,grib:[2,6,11,15,23,31],grib_api:[4,10,13,33,36],grib_l:19,gribmessag:11,grid:[2,3,5,6,10,17,19,20,21,23,31,43],grid_simpl:19,grid_typ:19,gridtyp:19,group:[2,4,5,12,13,14,22,31,42],groupid:[12,30,32],groupnam:[],grphreal:[30,31,32],guarante:[2,11,12,17,43],guid:[23,36,41,43],guidanc:21,haimberg:[2,35],half:[2,6,11,17,21,43],handl:[2,5,39,41,43],happen:0,hard:2,harmon:19,has:[0,2,4,6,10,11,12,13,14,17,21,22,30,31,32,39,42,43],hast:6,have:[2,3,5,6,11,12,14,15,22,30,31,32,33,34,39,42,43],hcc:19,header:2,heat:[2,17,19],heavili:21,height:17,help:[2,11,12,18,43,44],help_icon:[],hemispher:43,henc:17,her:12,here:[2,6,8,11,12,15,19,31,39,43,44],high:[6,11,13,21,31,43],higher:[2,21],highest:21,highli:21,highlight:43,highr:[8,43],hint:[5,33,39,41,44],his:12,histor:21,hittmeir:[2,6,17],home:[4,10,12,13,14,23,30,31,32,42,43],homogen:39,horizont:[2,5,6,17,43],hoskin:6,host:[4,10,13,43],hostnam:[32,43],hour:[2,6,11,17,19,22,43],hourli:[6,22,43],how:[2,5,6,9,15,18,22,23,39,42,43,45],howev:[6,15,17,21,22,39,43],hpc:[12,21,43],hre:[23,43],href:[],html:[],http:[2,6,11,12,17,30,32,41,42,44],humid:19,hybrid:19,i32:[30,32],i_i:17,ia3:2,ice:[2,6,43],idea:39,identif:2,identifi:[2,6,11,12,17,19],identificationkeyword:2,idir:2,idirectionincrementindegre:2,ids:2,idx:[2,19],ifort:[],iid:2,img:10,implement:[17,19,43],impli:17,importantli:39,improv:[2,17,43],inbetween:[6,43],includ:[6,9,11,12,13,30,31,32,42,43,44],incorpor:42,increas:[34,43],incur:21,independ:39,index:2,index_fil:2,index_kei:2,index_v:2,indic:[2,5,17,19,43],individu:[2,4,6,10],ineffici:43,info:2,inform:[2,5,6,8,11,14,18,19,20,22,23,31,32,34,39,42,43,44,45],informt:2,init128:2,init:2,initi:[2,11,12,36],initialis:[2,18,36],input:[2,5,6,10,11,12,15,17,20,38,41,43,45],inputdir:[2,10,11,13,43],inputfil:[2,11],insert:31,instal:[0,4,5,6,7,9,10,13,14,15,18,20,22,36,41,43],install_loc:2,install_target:[2,10,12],install_via_gatewai:2,installdir:[2,12,30,31,32,42],instanc:2,instantan:19,instead:[2,11,12,15,22],institut:39,instruct:[2,6,9,14,30,31,33,42,43],intact:11,integ:[2,6,11,43],integr:[2,17],intel:[4,10,13],intend:[6,8,11,14,39],interact:30,interest:42,interfac:[2,5,23,24,36,43],intergovernment:39,interim:[5,6,11,19,21,22,23,31,34,41,42],intermedi:2,intern:[2,11,12,41],internet:43,interpol:[2,6,10,11,17,19,43],interpret:18,interv:[2,3,6,12,17,19],introduc:[17,19,36,43],introducst:34,introduct:[],introductari:23,introdut:[],investig:[],involv:12,ipar:2,ipnam:32,isol:17,issu:41,iter:2,its:[2,11,13,17,19,21,39,42],itself:[2,43],jame:[2,17],januari:43,jasper:[30,32],jdirectionincrementindegre:2,job:[2,6,11,12,14,15,18,19,20,30,31,32,41],job_chunk:[2,10,11,43],job_fil:2,job_id:[2,4,13],job_templ:[2,10,11,12,30,31,32,43],jobfil:2,jobnam:[2,4,13],jobop:43,jobscript:43,journal:[17,40],jtemplat:2,june:[2,43],just:[2,3,6,8,12,31,43,44],k_i:17,keep:[2,13,17,42,43],kei:[2,31,42],kept:6,keynam:2,keyvalu:2,keyword:[2,6,11,19,22,23,43],kind:[2,6,19,43],km4a:[4,10,13],know:[31,43],known:[5,41],known_bugs_issu:[],korn:[2,4,10,12,18,20,36,43],kornshel:13,ksh:[13,18,43],kwd:2,label:[12,19,31],lagrangian:[2,6,17],larg:[2,6,11,17,19,36,43],larger:[6,11,21],last:[2,6,11,17,19,30,32,34,43],lat:[2,6,11,19,21,43],late:17,later:[2,31,34],latest:[22,42,43],latitu:2,latitud:[2,6,20,43],latitudeoffirstgridpointindegre:2,latitudeoflastgridpointindegre:2,latter:12,lcc:19,ld_library_path:33,lead:[6,11,13,17,19,32,43],learn:39,least:[2,12],leav:11,leccod:[30,31,32],leccodes_f90:[30,31,32],left:[2,5,6,10,17,21,42,43],lemo:[30,32],lemosr64:31,length:[2,17,43],leopold:[2,35],less:21,let:11,letter:[2,11,12,19,41],level:[2,5,6,10,11,12,15,18,19,21,22,31,34,43],level_typ:19,levelist:[2,5,6,10,11,19,31,43],levellist:34,levtyp:[2,19,31],lfftw3:[30,32],lib:[30,31,32,33],libeccod:[31,42],libemo:[30,31,32],librari:[4,10,14,20,23,31,32,41,42,44],licenc:[11,12,22,23,41],licens:[2,6,11,12,14,22,41],lies:2,light:12,like:[2,11,17,30,31,32,34,42,43],limit:[6,11,19,22,34,39,43],line:[2,5,11,12,13,15,17,18,19,22,30,32,42,43,45],linear:[2,6,17],linearli:17,link:[0,39,41,42,43],linux:[12,14,15,22,30,31,42,44],liquid:[2,6,43],list:[2,5,6,8,9,11,12,15,17,19,20,23,31,34,41,43],list_obj:2,littl:17,ljasper:[30,31,32],load:[2,4,10,13,30,32,43],local:[2,5,6,7,9,11,12,14,22,30,32,33,36,41,42],localmachin:32,localus:32,locat:[2,7,11,12,43,45],lock:34,log:[2,4,6,10,13,31,32,42,43,44],logarithm:19,logic:[2,10],login:[32,43],lon:[2,6,11,19,21,43],longer:[2,6,36],longitud:[2,6,20,43],longitudeoffirstgridpointindegre:2,longitudeoflastgridpointindegre:2,longiud:[],look:[2,30,32,43],lot:[21,43,44],lower:[2,5,6,10,21,43],lowest:19,lp64:[30,32],lpthread:[30,32],lrwxrwxrwx:[30,31,32],lsm:19,lsp:[17,19],machin:[2,4,10,12,13,14,15,31,32,42,43],made:[2,22,39,43],magnitud:2,mai:[6,11,12,15,17,30,31,39,42,43],mail:[2,4,6,10,13,35,41,43],mailfail:[2,5,10,13,43],mailop:[2,5,6,10,13],main:[2,5,18,20,22,43],mainli:[43,44],maintain:17,make:[0,4,13,18,30,33],make_dir:2,makefil:[2,4,10,12,13,18,30,31,32,33,36],makefile_crai:[9,30,32],makefile_debug:9,makefile_ecg:[4,9,12,30,32],makefile_fast:[9,31],manag:[13,30,31,42],mani:[17,43],manipul:2,mar:[2,6,11,15,18,20,22,23,30,31,32,33,36,41,42,43],march:[2,22,30,31,32],margin:[],mark:[4,5,10,13,17,19,43],mars_request:[2,6,11,15,19,43],marsclass:[2,10,19],marsfil:2,maschin:11,mask:43,mass:21,master:42,match:2,mathrm:17,matter:[2,12],max:[6,11],max_level_list:2,maxb:[2,13,19],maxim:[],maxima:17,maximum:[2,5,6,11,34,43],maxl:[2,13,19],maxstep:[2,5,6,10],mcc:19,mdpdeta:[2,13,19],mean:[2,4,12,13,17,19,43],measur:21,medium:[20,39,41],member:[2,6,12,14,19,22,23,24,30,31,39,42,43],memberst:[2,6],memori:[6,11],mention:[13,14,17,43],merg:15,mess:42,messag:[2,11,12,19,21,30,31,34],meta:[2,13,19],metadiff:[2,13,19],metapar:[2,13,19],meteorolog:[2,17,19,20,35,39,41],meter:[],method:[2,5,6,11,17,19,21,22,38,39,40,43],mgauss:[2,13,19],might:[0,2,6,11,15,18,22,31,39,42,43],migrat:[2,23],min:17,mind:[6,43],minim:42,minima:17,minimis:31,minimum:[20,43],minut:[2,30,32],mismatch:43,missingvalu:2,mix:43,mk_compilejob:2,mk_convert_build:2,mk_date:2,mk_env_var:2,mk_job_templ:2,mk_jobscript:2,mk_server:2,mk_tarbal:2,mkdir:[4,10,13],mlevel:[2,13,19],mlevelist:[2,13,19],mnauf:[2,13,19],mnt:19,mock:0,mod:[2,4,13,31],mode:[2,4,6,7,9,10,11,12,13,18,19,20,39,41,42,44],model:[2,6,15,17,19,20,21,22,23,34,39,40,41,43],modif:2,modifi:[2,17,22,31,43],modul:[4,10,13,14,30,32,42,43],modular:36,momega:[2,13,19],momegadiff:[2,13,19],moment:6,mon:17,monitor:43,monoton:[2,17],month:[11,19,31,43],monthli:6,more:[2,5,6,11,12,14,17,19,31,42,43,45],most:[2,6,13,39,43],mostli:[2,6,19,43],motiv:17,mountain:[2,11,12,41],move:[0,2],mreq_count:2,msgatwai:30,msl:19,msmooth:[2,13,19],much:[39,44],multipl:[2,43],multipli:[6,21],muser:[10,13],must:[6,11,14,32,43],my_error:2,myecnam:12,mygroupnam:12,myuser:12,name:[2,4,5,6,10,11,12,13,17,19,30,31,32,36,42,43],name_of_this_fil:[4,10,13],namelist:[2,13,19],namespac:2,namgen:[13,19],nano:[30,32],nas:[10,19,45],nation:[22,39],nativ:[30,31,32],natur:17,necessari:[0,2,3,4,6,9,10,11,12,13,14,18,20,30,31,32,33,43,44],necessarili:5,nedit:31,need:[0,2,3,5,6,11,12,13,14,18,19,20,21,22,31,32,37,40,42,43,45],neg:[2,17],neglect:6,net:[17,19],nevertheless:2,newer:19,newest:43,newslett:[],next:[30,32,43],nfield:2,night:[],non:[2,6,17,34,43],noncycl:6,none:[2,5,6,10,11,12,17,19,30,31,32,43],none_or_int:2,none_or_str:2,nonzero:2,normal:[4,6,10,13,43],normal_exit:2,north:[2,11],northern:[2,43],northernmost:2,northward:[17,19],notabl:43,notat:17,note:[6,15,17,32,42,43],notif:[2,5],notifi:2,novemb:[2,21],now:[22,42],nowadai:[],nsss:[17,19],number:[2,3,4,5,6,8,9,10,11,13,17,18,19,20,21,31,34,36,43],numer:39,numpi:[2,30,31,32],object:2,observ:2,obtain:[2,17,42,43],obvious:17,occur:[2,17],octahedr:23,octob:11,odir:2,off:[2,5,6,19],often:21,og_orolsm__sl:19,old:[0,2,6,11,17,36,43],older:[6,15,43],omega:[2,5,6,10,19,21,38,43],omegadiff:[2,5,6,10,21,43],omegayymmddhh:[6,21],onc:[11,43],one:[2,5,6,11,12,17,18,19,32,33,34,42,43],ones:[17,32],onli:[2,3,5,6,9,11,12,17,19,21,22,32,42,43,44],onlin:[36,43],onward:6,open:[2,20,30,31,32,41,43],opend:12,oper:[2,5,6,8,10,11,12,17,21,23,31,34,39,41,42],operation:6,oportun:[],opportun:[],opt:[],optim:21,optimis:[9,12,15,43],option:[2,5,6,15,17,19,21,33,36,42,43],optionalind:5,orang:12,order:[2,5,19,43],org:[2,6,11,12,17,41],organis:39,origin:[2,6,11,17,19,43,45],orographi:19,other:[2,5,6,11,31,39,42,43],otherwis:[2,43],our:42,out:[2,4,6,10,13,30,31,32,42,43],output:[2,4,5,6,10,11,12,13,17,30,31,32,36,38,39,41,42,43,44,45],outputdir:[2,10,11,13,43],outputfilelist:2,outsid:31,over:[2,17,43],overal:[2,19],overhead:43,overlap:[6,17],overrid:[3,11],overrul:5,overview:[8,14,15,17,23,34,38,41,42],overwrit:[0,2,43],overwritten:[2,18],own:[19,32,42],p_a:17,p_b:17,p_c:17,p_d:17,packag:[0,4,10,13,20,30,31,41,42],package_nam:42,packingtyp:19,page:[30,42],panel:42,paper:[34,40],par:2,parallel:[],param1:43,param2:43,param:[2,19,31],paramat:2,paramet:[2,3,4,5,8,10,13,15,17,18,19,20,23,30,31,32,36,39,41,42],parameteris:43,parameterlist:[11,12],parameternam:2,paramx:43,parent:[2,11,19],part:[2,17,20,31,32],parti:[14,20,23,41],particl:[2,6,17],pass:[2,10,22,34,42],passcod:30,password:[30,32],path:[0,2,4,6,8,9,10,11,12,13,14,31,32,33,34,42,43],path_flexextract_dir:2,path_fortran_src:2,path_input_dir:2,pattern:[2,43],paul:17,pbs_jobid:[10,13],pdf:21,pep8:36,per:[2,5,6,11,15,19,43],perform:[2,13,15,21],period:[2,5,6,11,17,30,43],person:12,perturb:[6,19],petra:2,phgrreal:[30,31,32],philipp:[2,5,6,11,12,17,35],physic:[35,39],pid:[19,43],piec:[17,19],piecewis:17,pip:[0,31,42],place:[2,12,13,14,30,44],placehold:[13,32],plan:[6,21],platform:42,pleas:[5,9,14,15,21,30,31,32,43,44],plot:23,plu:17,png:0,point:[2,11,17,19,43],polynomi:[2,17],posit:[2,6,13,17],posnam:[30,31,32],possibl:[2,5,6,8,11,12,17,21,22,31,33,42,43,44],post:[2,6,15,31],postprocess:2,pp_id:[11,43],ppid:[2,11,19],pre:[9,17],precalcul:6,precip:19,precipit:[2,5,6,11,23,36,43],precis:33,preconvert:[],predict:[39,43],prefar:42,prefer:[6,30,31,32],prefix:[2,5,6,10,19,21],prepar:[0,2,4,6,10,11,12,13,14,15,20,26,41,42],prepare_flexpart:11,preprocessor:44,present:[2,7,12,23,30,32,42,43],preserv:[17,19,43],pressur:[2,19,21,22,31],pressure_level:31,previou:[18,21,43],prgenv:[4,10,13],primarili:9,principl:43,print:[2,4,13,43],print_infodata_csv:2,prior:[17,21],problem:[2,17,36,42,43,44],procedur:[5,17],process:[2,4,6,7,9,10,11,12,13,14,15,17,18,19,22,31,36,42,43,44],process_output:2,prod:2,produc:[9,17,19,21,39,43],product:[2,42,43],product_typ:31,progam:42,program:[0,4,9,11,12,13,17,18,20,21,30,31,36,41,43],programm:16,progress:[15,43],prompt:30,proper:[18,41],properli:[2,12,15,34,42,44],properti:[2,19,39],propos:17,proposit:44,prot:[10,13,43],protocol:43,provid:[2,3,14,18,20,21,22,31,32,42,43,44],pseudo:43,publicli:43,publish:17,pull:31,pure:[2,6,11,43],purefc:[2,10],purpos:[2,6,19],put:[2,6,12,13],put_file_to_ecserv:2,pycallgraph:0,pylint:0,pyrevers:0,pyscript:11,pytest:0,python3:[4,10,13,18,30,31,32,36,42,43],python:[0,4,10,11,12,13,15,16,17,18,19,20,23,30,31,32,33,36,38,42,43],pythonxxxxx:43,qos:[4,10,13],quad:17,quantiti:[2,6,17],question:[41,44],queue:[2,4,10,11,12,13,15,30,43],queuenam:[4,10,13],queues_list:2,quick:[8,18,41,42],quick_start:45,quickli:[13,43],quota:43,r64:[4,10,13,30,32],radiat:[2,17,19],raid60:[10,45],rainfal:2,rais:[2,17],rang:[2,6,20,31,39,41,43],rare:43,rate:17,rather:21,raw:[2,15],reach:18,read:[2,6,12,13,15,20,21,32,33,39,43],read_ecenv:2,readi:[2,6,11],real:[23,30,31,32,43],real_tim:23,realis:17,realiti:17,realli:[21,43],reanalysi:[6,11,21,23,31,42],reason:[2,6,11,17,43],receiv:[30,43,44],recent:[10,43],recod:17,recommend:[6,17,21,31,43],reconstruct:[2,17],record:42,rectangular:12,red:17,reduc:[19,21,23],ref:[],refactor:36,refer:[2,14,39,43],regard:[5,18,44],regardless:42,region:21,regist:[22,31,33,42],registr:[6,14,22,23,31,33,41,44],regress:[36,41],regular:[2,20,43],regular_l:19,regularli:[],rel:[17,43],relat:43,releas:[2,41,42,43,44],relev:[2,5],reli:42,remain:[2,17],rememb:[34,42],remot:[2,4,6,7,9,10,12,13,14,15,18,20,30,41,42],remota:12,remov:[2,3,17],remove_old:2,renam:0,renew:30,repeat:2,rephras:[43,45],repo:42,report:[2,41],repositori:42,repr:[2,19],repres:[2,17,19,22,23,42,43],represent:[2,20],reqest:15,request:[2,4,5,6,10,11,13,15,17,22,36,43],request_numb:[2,19],requir:[2,13,14,17,20,21,30,31,32,39,41,42,43],rerun:11,research:39,resol:[2,5,6,10,19,21,43],resolut:[3,5,6,11,21,22,39,43],resolv:21,reson:[],respect:[2,5,15,17,18,19,31,39,42,43],respectivlei:[],respons:43,rest:[2,6],restrict:21,restructur:36,result:[2,15,19,21,43],retriev:[2,5,6,11,14,15,17,18,19,20,21,22,31,33,34,36,39,41,42,43],retrieve:5,return_list:2,review:6,revis:36,revtriev:2,right:[2,5,6,10,17,21,22,30,31,33,39,42,43,44],rla0:[2,13,19],rla1:[2,13,19],rlo0:[2,13,19],rlo1:[2,13,19],root:[2,4,12,13,18,31,32,42,43],round:12,rpath:[30,32],rpm:42,rrint:[2,5,6,10,11,43],rst:45,rthl:43,rudimentari:12,run:[2,5,6,7,8,10,13,15,18,19,22,30,31,42,43,44],run_loc:[15,43],runtim:10,rwgrib2:[30,31,32,36],sabin:2,sai:2,same:[2,6,11,22,30,31,33,43],sampl:[2,31,43],sardeshmukh:6,save:[11,19,21,31,43],sbatch:[4,10,13],scale:[2,11,17,19],scaveng:17,scenario:[14,17,43],schemat:17,scheme:[2,6,17,19,43],scientif:[23,34],scope:6,scp:32,scratch:[4,10,13,43],scriot:0,script:[5,6,13,14,15,16,17,18,19,20,21,23,30,31,32,36,42,43,44],scroll:42,sdor:19,second:[6,11],section:[5,12,18,22,31,36,37,39,40,42,43],see:[2,5,6,9,11,12,13,15,18,19,20,21,22,24,30,31,32,34,42,43],seem:43,seen:18,seibert:[2,6,17],select:[2,5,6,11,12,14,19,22,30,32,34,39,41,42],selectwher:2,send:[2,11,12,13,21,30,41,44],send_mail:2,sens:43,sensibl:[2,17,19],sent:[2,13,15,18,43],separ:[2,5,19,43],sepeart:[],seper:[2,6],septemb:[6,12,21],seqdiag:0,seqdiag_fontpath:0,sequenc:15,seri:[2,17],serv:[19,20,41,43],server:[2,4,5,6,7,9,10,11,12,13,14,15,18,20,22,23,30,31,32,36,42,43],servic:[30,39],session:[4,10],set:[0,2,4,5,6,8,9,10,11,12,13,17,18,19,20,21,22,23,30,31,32,33,34,36,39,42,43,44],set_kei:2,setup:[14,15,18,30,31,32,42,43],setup_controldata:2,sever:[9,12,13,19,42,43],sfc:[19,31],sgn:17,shade:17,share:[0,44],she:14,shell:[2,4,10,11,12,15,18,20,30,31,36,42,43],shift:17,shoot:23,shorten:43,shorter:2,shortli:43,shortnam:19,should:[0,2,6,9,12,13,17,21,30,31,32,33,36,39,42,43],shouldn:[6,43,45],show:[11,12,15,17,43],shown:[7,9,17,31,43],side:42,sign:[4,5,13,42],signal:43,silent_remov:2,similar:14,simpl:[6,17,31],simplest:17,simplifi:36,simul:2,sinc:[2,15,19,21,31,43,44],singl:[2,4,10,11,13,15,19,33,42,43],site:30,size:[34,43],sketch:[12,14],skip:[2,31],skt:19,slope:17,slurm:[13,23],small:[31,34,43],smaller:[2,6,11,19],smooth:[2,5,6,10,17,21,43],snippet:31,softwar:[2,6,12,13,14,20,21,23,30,31,32,41,42],solar:[2,17,19],sole:[6,19],solut:[2,44],solv:43,some:[0,2,4,5,6,8,10,11,12,13,14,15,18,19,20,22,31,32,39,42,43,44,45],someth:43,sometim:[6,43],soon:[6,43],sort:2,sourc:[0,2,4,9,10,11,12,13,18,20,31,33,34,36,41,42,43,45],south:[2,11],souther:[],southern:2,southernmost:2,space:[2,5,11,17,43],spar:2,spatial:[5,6,39],spdx:[11,12],speak:42,speci:17,special:[],specialis:43,specif:[2,4,5,6,9,10,11,13,14,17,19,20,21,36,39,41,42],specifc:[2,11],specifi:[2,6,11,12,17,30,31,32,43],spectral:[2,6,20,21,43],speed:43,sphere:6,spheric:19,sphinx:[36,45],sphinxcontrib:0,split:[15,17,19],sqrt:17,src:[],src_path:2,srvx8:10,ssh:[32,43],sshf:[17,19],ssr:[17,19],sss:6,stamp:19,standard:[2,9,17,21,30,31,32,42,43],start:[2,4,5,6,10,11,12,13,18,19,30,31,32,33,34,39,41,42],start_dat:[2,5,6,10,11,17,43],start_period:2,state:[2,12,14,22,23,24,30,31,39,42,43],statement:[2,30,32],statist:42,statu:[15,34,42],steer:2,step:[2,3,5,6,10,11,13,15,17,19,20,24,30,31,33,43],steprang:[2,11,19],still:[3,9,15,21,37,40,43],stl1:19,stop:[2,34,42,43],storag:[2,5],store:[2,6,10,11,12,15,19,21,22,23,31,42,43],str:2,str_of_list:2,straightawai:43,straightforeward:43,stream:[2,5,6,10,19,31,36,43],stress:[2,17,19],string:[2,5,6,11,12],structur:[10,36,39,43],studi:[21,39],style:36,sub:[2,17,19],subdirectori:43,subgrid:[2,11],subinterv:17,subject:[2,30,32,43],submiss:[2,4,10,12,20,43],submit:[4,5,10,12,13,14,15,18,19,30,32,43,44],submit_job_to_ecserv:2,subprocess:2,subsect:21,subsequ:6,subset:[6,11,43],substanti:43,substitut:[2,4,9,10,13,31,32,36,43],substr:2,subtract:[6,43],succeed:[30,31],success:[4,13,19,30,32],success_mod:2,successful:[18,42],successfulli:42,suffici:43,suggest:31,suit:[6,43],sum:[2,6,18,43],supplement:19,support:[2,17,23,39,41,42,43],suppos:2,sure:31,surfac:[2,6,15,17,19,21,22,34],swvl1:19,symmetri:17,syntax:[2,6],synthes:[6,36],system:[2,4,6,10,11,13,20,21,30,31,32,34,41,42,43],sytem:30,t1279:[21,43],t799:21,tab:42,tabl:[2,5,17,19,34,41,42,43],table128:2,take:[9,31,43],taken:[2,6,18,19,39,43],tar:[2,4,13,32,42],tarbal:[2,4,12,30,32],tarball_path:2,tarfil:32,target:[2,12,19,30,31,32],task:[2,18,20,43],tcc:19,team:41,technic:23,tell:[2,43],temp:[2,4,10,11,43],temperatur:[19,31],templat:[2,4,5,7,10,11,12,18,30,31,32,36,43],tempor:[5,6,17,19,22,39,43],temporal_properti:19,temporari:[2,6,11,43],tendenc:21,tenth:6,term:[42,43],termin:[30,31],test:[0,2,5,6,12,13,19,22,33,36,41,43],textbf:17,textrm:17,than:[2,3,6,9,11,19,21,31,34,44],thei:[0,2,5,6,9,11,12,13,15,17,18,19,31,39,43],them:[0,2,6,11,12,15,17,18,19,20],therebi:[17,21],therefor:[0,2,6,17,18,19,31,34,39,42,43],thi:[0,2,4,5,6,7,8,9,10,11,12,13,14,17,18,19,21,22,30,31,32,33,34,37,39,40,41,42,43,44,45],thick:17,thing:[],think:[2,42],third:[14,20,23,41],those:[5,43],thousandth:6,three:[2,11,17],through:[2,5,22,24,30,42,43],throughout:17,thu:[17,31,43],ticket:[34,41],time:[2,3,4,5,10,11,13,15,17,19,21,23,31,33,39,43,44],timeseri:[2,17],timespan:[2,17],timestamp:2,tld:32,tmc:[10,31,45],tmpdir:[10,13],to_list:2,to_param_id:2,to_param_id_with_tablenumb:2,todai:43,todo:[],togeth:[2,5,12,42,43],token:30,too:[6,11,17,31,34,43],tool:[4,10,14,15,43],toolkit:22,top:[11,12,18,34],topic:[],total:[2,19,43],touch:43,trace:17,train:23,transfer:[2,5,6,7,12,13,15,19,30,32,43],transferr:43,transform:2,transport:[20,41],trapezoid:12,treatment:39,tree:43,tri:[],triangular:[2,6],trigger:[2,21],troubl:23,troubleshoot:43,truetyp:0,truncat:[2,6],ttf:0,tupl:2,turbul:[17,19],twice:43,twiceadai:[],twicedaili:[8,43],two:[2,6,11,12,14,17,18,19,20,21,22,42,43],type:[0,2,3,4,5,6,10,11,13,17,18,19,30,31,32,42,43],typeoflevel:19,typic:[15,19,23,43,45],ubuntu:[30,31],udoc:2,uid:[12,32],un_tarbal:2,unavail:44,unchang:17,under:[0,2,11,12,13,14,17,19,26,27,28,29,30,31,37,38,40,41,43],undergo:[39,43],understand:[5,13,18],underw:[],undesir:17,unfortun:[17,22],uniqu:[2,19],unit:[0,17,21,36],univers:[2,35],univi:[10,35,44],unix:44,unless:[6,13],unload:[4,10,13],unrealist:17,unreason:36,untar:[2,4,12,32,42],until:[6,11,17,22,43],updat:41,upfront:[2,6],upgrad:36,upon:22,upper:[2,5,6,10,21,43],upstream:[],upto:[],usa:[2,11,12,41],usag:2,use:[0,2,6,9,12,17,18,20,21,22,30,31,32,33,34,36,42,43],used:[2,5,6,8,9,11,12,13,14,17,18,19,31,32,36,39,42,43,44],useful:[6,11,19,39,43],user:[2,4,5,10,11,12,13,14,18,20,22,23,24,30,31,32,33,36,39,42,43,44],user_group:[7,13],user_nam:[7,13],usergroup:13,usernam:[12,13,30,31,32],uses:[0,4,10,17,30,32,34,43],using:[2,4,6,11,12,17,18,19,30,31,32,42,43],usr:[0,4,10,13,30,31,32],usual:[5,6,11,15,19,31,43],utc:[6,11,19,43],util:[2,15],uza:35,v10:19,v20_update_protocol:21,v30_update_protocol:21,v40_update_protocol:21,v60_update_protocol:21,v703:[],v704:[],v711:[],v71:[],valid:[2,6,12,19,32,43],valu:[2,3,5,6,8,10,11,12,13,17,18,21,30,32,34,43],valuer:2,vanish:17,vari:[5,6,31,39,43],variabel:[],variabl:[2,4,6,10,11,13,17,20,31,33,36,39,43],varianc:[],variat:[6,19],vast:39,veloc:[15,19,20,43],veri:[2,6,11,17,21,31,43],version:[2,3,4,6,9,10,13,15,18,21,31,33,36,42,43,44],version_numb:13,vertic:[5,11,15,20,38,39,43],via:[2,11,14,15,22,23,30,31,32,36,43],vienna:[2,35],view:[2,11,12,41,44],virtual:42,visit:[2,11,12,30,41],vol:6,wai:[2,5,13,15,17,22,30,31,39,42,43],wait:22,want:[6,9,17,20,43],warn:[12,31],water:[2,6,19,43],wave:21,weather:[6,20,39,41],web:[2,6,11,14,22,23,24,33,36,42,43],webapi:[2,6],webserv:[],websit:[2,30,31,42,43,44],wedg:17,well:[2,6,15,21,34,39,42,43],were:[2,6,11,12,19,36,43],west:[2,11],western:2,westernmost:2,wet:17,wether:2,what:[3,5,23,31,41,43],whatev:43,when:[2,4,6,10,17],whenev:21,where:[2,6,9,11,12,13,17,19,21,31,42,43],wherea:[6,15,43],wherebi:[],wherekei:2,wherekeynam:2,wherekeyvalu:2,whether:[2,4,10,12,42],which:[0,2,3,4,5,6,7,9,10,11,12,14,15,17,18,19,20,21,22,30,31,36,39,42,43,44,45],whith:10,who:20,whole:[2,17,43,44],whose:[19,42],why:17,width:[],wiki:[2,6,32],wil:2,wildcard:43,wind:[5,19,39,43],window:[30,31,43],wish:42,within:[2,4,6,10,11,17,30,32,43],without:[2,13,22,33,42,43],word:2,work:[0,2,7,10,11,12,13,14,15,20,22,31,41,42,43],workdir:[4,10,13],workload:13,workspac:[10,19,43],workstep:[],would:[6,11,22,30,34,43,45],wrap:20,wrapper:[11,12,18],wrf:[2,5,10],write:[2,6,43,44],write_namelist:2,write_reqhead:2,written:[2,6,21,37,40],wrong:34,www:42,x86_64:31,xvf:[4,13,32,42],xxx:19,xxxx:6,xxxxx:43,xxyymmddhh:2,year:[19,31],yet:43,yield:[2,21],you:[0,3,5,6,9,13,21,24,30,31,32,33,34,42,43,44],your:[24,30,31,32,42,43,44],yourself:24,yymmdd:[6,19],yymmddhh:[6,19,21],yyyymmdd:[2,6,11],yyyymmddhh:[17,19],zamg:[36,44],zero:[17,21,34],zonal:21},titles:["Update Documentation","Auto-generated documentation for the Fortran programme","Auto-generated documentation for the Python scripts","CONTROL file changes","The compilation job script <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF user credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran makefile for <code class=\"docutils literal notranslate\"><span class=\"pre\">calc_etadot</span></code>","The job script <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The installation script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application modes","Program flow","Auto-generated documentation","Disaggregation of flux data","Control & input data","Output data","Overview","Vertical wind","Access modes","Link collection","Hints for data set selection","Available data sets for member-state users","Available data sets for public users","Metrics","Static code analysis","Test cases","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 Start","Support","ToDos"],titleterms:{"case":29,"class":2,"new":[19,36],"public":[26,42,43],"static":28,CDS:[31,34],The:[4,5,6,9,10,11,12],accept:42,access:22,addit:[0,6,19],adjust:43,agreement:[],analysi:28,api:[31,34],applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calc_etadot:[9,19,34],calcul:21,can:[24,33],cera:43,certain:43,chang:[3,36],changelog:36,check:2,code:[28,34],collect:23,combin:[42,43],comparison:29,compil:4,compilejob:[4,13],content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert:13,coordin:[],credenti:7,data:[6,17,18,19,24,25,26,34,39,43],dataset:[42,43],definit:43,depend:[30,31,32,42],destin:34,develop:[35,37],diagramm:0,differ:15,disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,download:42,eccod:34,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era5:34,era:43,error:34,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:[],fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,34,42],frequent:33,from:[21,33],full:42,gatewai:[30,34,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,hint:[24,43],horizont:21,how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,34,42],interim:43,issu:[34,44],job:[4,10,13,43],jobscript:10,known:[34,44],ksh:[4,10],level:25,librari:33,licenc:42,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],metric:27,mode:[14,15,22,30,31,32,43],model:25,modul:2,older:17,onlin:0,oper:43,option:[11,12],other:17,out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,34,43],parti:33,pre:21,precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,problem:34,program:[2,15,19,34,42],programm:1,proper:43,pure:19,python:2,question:33,quick:43,registr:42,releas:[34,36],remot:[32,43],report:44,request:[19,29],rest:[],retriev:[],run:11,script:[2,4,10,11,12],section:6,select:[24,43],sequenc:0,set:[15,24,25,26],setup:12,softwar:0,some:[],specif:43,specifi:[],sphinx:0,standard:19,start:43,state:25,submiss:11,submit:[2,11],support:44,surfac:25,system:44,team:35,temp:13,templat:13,temporari:19,test:[29,30,31,42],testcas:[],third:33,ticket:44,time:6,todo:[8,19,43,45],tool:2,uiofil:2,updat:0,usag:[11,12],user:[6,7,15,25,26,41],using:21,veloc:21,version:17,vertic:[6,19,21],web:31,welcom:41,what:[4,10,24,33],wind:[6,21],workflow:15}})
\ No newline at end of file
diff --git a/Documentation/html/todo.html b/Documentation/html/todo.html
index a8eebcd6cbde43c9a6fd606b73160191c6bb57dd..df9cdab887281b144b9aceac9ff068e544df0387 100644
--- a/Documentation/html/todo.html
+++ b/Documentation/html/todo.html
@@ -163,6 +163,31 @@
<div class="section" id="todos">
<h1>ToDos<a class="headerlink" href="#todos" title="Permalink to this headline">¶</a></h1>
+<div class="admonition-todo admonition">
+<p class="admonition-title">Todo</p>
+<p>#PS some information to be added.</p>
+</div>
+<p class="todo-source">(The <a class="reference internal" href="Documentation/Input/examples.html#id1"><em>original entry</em></a> is located in /raid60/nas/tmc/Anne/FLEX_EXTRACT_REPO/flex_extract/For_developers/Sphinx/source/Documentation/Input/examples.rst, line 38.)</p>
+<div class="admonition-todo admonition">
+<p class="admonition-title">Todo</p>
+<p>#PS NEEDS MORE DESCRIPTION</p>
+</div>
+<p class="todo-source">(The <a class="reference internal" href="Documentation/output.html#id1"><em>original entry</em></a> is located in /raid60/nas/tmc/Anne/FLEX_EXTRACT_REPO/flex_extract/For_developers/Sphinx/source/Documentation/output.rst, line 208.)</p>
+<div class="admonition-todo admonition">
+<p class="admonition-title">Todo</p>
+<p>#PS needs to be rephrased</p>
+</div>
+<p class="todo-source">(The <a class="reference internal" href="quick_start.html#id2"><em>original entry</em></a> is located in /raid60/nas/tmc/Anne/FLEX_EXTRACT_REPO/flex_extract/For_developers/Sphinx/source/quick_start.rst, line 420.)</p>
+<div class="admonition-todo admonition">
+<p class="admonition-title">Todo</p>
+<p>#PS shouldn’t we explain how to define a domain??</p>
+</div>
+<p class="todo-source">(The <a class="reference internal" href="quick_start.html#id3"><em>original entry</em></a> is located in /raid60/nas/tmc/Anne/FLEX_EXTRACT_REPO/flex_extract/For_developers/Sphinx/source/quick_start.rst, line 453.)</p>
+<div class="admonition-todo admonition">
+<p class="admonition-title">Todo</p>
+<p>#PS for which application would this be typical?</p>
+</div>
+<p class="todo-source">(The <a class="reference internal" href="quick_start.html#id4"><em>original entry</em></a> is located in /raid60/nas/tmc/Anne/FLEX_EXTRACT_REPO/flex_extract/For_developers/Sphinx/source/quick_start.rst, line 474.)</p>
</div>
diff --git a/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst b/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst
index f1bea12568b3b0aec245274df3fc82bab8bb6ece..16ad7c833688202b6aa5bce8814cc99aba7f1062 100644
--- a/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst
+++ b/For_developers/Sphinx/source/Documentation/Api/api_fortran.rst
@@ -1,6 +1,6 @@
-**************************************
+******************************************************
Auto-generated documentation for the Fortran programme
-**************************************
+******************************************************
.. contents::
:local:
diff --git a/For_developers/Sphinx/source/Documentation/Api/api_python.rst b/For_developers/Sphinx/source/Documentation/Api/api_python.rst
index 9fbfa052c28d1f8b75fba33d2468ada7589474ac..3be98adfa342acb7df40be76f0bca567bd5490d7 100644
--- a/For_developers/Sphinx/source/Documentation/Api/api_python.rst
+++ b/For_developers/Sphinx/source/Documentation/Api/api_python.rst
@@ -1,6 +1,6 @@
-*************************************
+***************************************************
Auto-generated documentation for the Python scripts
-*************************************
+***************************************************
.. contents::
:local:
diff --git a/For_developers/Sphinx/source/Documentation/Input/compilejob.rst b/For_developers/Sphinx/source/Documentation/Input/compilejob.rst
index cfc12eaa14df253e69dec97c7f826f8ac7d2631f..7eac32c0626ae8e63276c2a80f30eb6dc12eaed3 100644
--- a/For_developers/Sphinx/source/Documentation/Input/compilejob.rst
+++ b/For_developers/Sphinx/source/Documentation/Input/compilejob.rst
@@ -1,6 +1,6 @@
-********************************************
+*********************************************
The compilation job script ``compilejob.ksh``
-********************************************
+*********************************************
The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
diff --git a/For_developers/Sphinx/source/Documentation/Input/examples.rst b/For_developers/Sphinx/source/Documentation/Input/examples.rst
index 6ad28b0f34eedd11ced5e0b9e515fd95de022ae7..f69fd02641edbf9e42e102092decaf1b8286a96a 100644
--- a/For_developers/Sphinx/source/Documentation/Input/examples.rst
+++ b/For_developers/Sphinx/source/Documentation/Input/examples.rst
@@ -35,6 +35,8 @@ CONTROL.documentation
CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
+.. todo::
+
#PS some information to be added.
.. toctree::
diff --git a/For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst b/For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst
index 4c6b1a3af17185f7484025f8e2ced36f2a60b9d6..b88cbd41a0633cf36994cf752db41039504e9080 100644
--- a/For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst
+++ b/For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst
@@ -1,6 +1,6 @@
-**************************************
+****************************************
The Fortran makefile for ``calc_etadot``
-**************************************
+****************************************
.. _ref-convert:
diff --git a/For_developers/Sphinx/source/Documentation/Input/jobscript.rst b/For_developers/Sphinx/source/Documentation/Input/jobscript.rst
index 7510327253a52cd7c3fcc8ba70c1edb8ab9981dd..24ef07e50e18d14a50b0976fa50a222ed3e2f0fc 100644
--- a/For_developers/Sphinx/source/Documentation/Input/jobscript.rst
+++ b/For_developers/Sphinx/source/Documentation/Input/jobscript.rst
@@ -1,6 +1,6 @@
-*************************
+**************************
The job script ``job.ksh``
-*************************
+**************************
The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
@@ -19,7 +19,7 @@ The submission is done by the ``ECaccess`` tool from within ``flex_extract`` wit
What does the job script do?
----------------------------
+----------------------------
#. It sets necessary batch system parameters.
#. It prepares the job environment at the ECMWF servers by loading the necessary library modules.
diff --git a/For_developers/Sphinx/source/Documentation/Input/run.rst b/For_developers/Sphinx/source/Documentation/Input/run.rst
index 5baa5afa0782c38bc2809017f3944e8e5be4aac9..1e3ad685d5b5d23c1adea0e66b36a64a5f65aab1 100644
--- a/For_developers/Sphinx/source/Documentation/Input/run.rst
+++ b/For_developers/Sphinx/source/Documentation/Input/run.rst
@@ -14,7 +14,7 @@ Based on this input information, ``flex_extract`` applies one of the application
Submission parameters
---------------------
+---------------------
.. exceltable:: Parameters for submission
@@ -33,7 +33,7 @@ Content of ``run.sh``
:caption: run.sh
-.. _ref-install-script:
+
Usage of ``submit.py`` (optional)
---------------------------------
diff --git a/For_developers/Sphinx/source/Documentation/output.rst b/For_developers/Sphinx/source/Documentation/output.rst
index d8d7586814c2563f471f5e463cbb1a98d78ab131..8a25f252022e118e62de2570426b24f7619e6899 100644
--- a/For_developers/Sphinx/source/Documentation/output.rst
+++ b/For_developers/Sphinx/source/Documentation/output.rst
@@ -204,7 +204,10 @@ Index file
----------
This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
-#PS NEEDS MORE DESCRIPTION
+
+.. todo::
+
+ #PS NEEDS MORE DESCRIPTION
Flux files
diff --git a/For_developers/Sphinx/source/Documentation/vertco.rst b/For_developers/Sphinx/source/Documentation/vertco.rst
index e750454d1955780ec15e0b404bec675824b0ab41..fcc1d14faabe35e602a735b786c52f96c711c4d5 100644
--- a/For_developers/Sphinx/source/Documentation/vertco.rst
+++ b/For_developers/Sphinx/source/Documentation/vertco.rst
@@ -20,7 +20,7 @@ Calculation from the horizontal wind field is still required for historical case
Calculation of the vertical velocity from the horizontal wind using the continuity equation
-===================================================================================
+===========================================================================================
The vertical velocity in the ECMWF's eta vertical coordinate system is computed by the Fortran program ``calc_etadot``, using the continuity equation and thereby ensuring mass-consistent 3D wind fields. A detailed description of ``calc_etadot`` can be found in the
documents v20_update_protocol.pdf, V30_update_protocol.pdf and
@@ -41,7 +41,7 @@ following guidance can be given for choosing the right parameters:
Calculation of the vertical velocity from the pre-calculated MARS parameter 77
-======================================================================
+==============================================================================
Since November 2008, the parameter 77 (deta/dt) is stored in ``MARS`` on full model levels. ``FLEXTRA``/``FLEXPART`` in its current version requires ``deta/dt`` on model half levels, multiplied by ``dp/deta``. In ``flex_extract``, the program ``calc_etadot`` assumes that parameter 77 is available if the ``CONTROL`` parameter ``ETA`` is set to 1.
diff --git a/For_developers/Sphinx/source/Ecmwf/hintsecmwf.rst b/For_developers/Sphinx/source/Ecmwf/hintsecmwf.rst
index ac93b8ca1dca31c26c6db9810e9a5f12ab491a18..00e3bc105ca142ab96012e69b38d48d3b2c7b5ee 100644
--- a/For_developers/Sphinx/source/Ecmwf/hintsecmwf.rst
+++ b/For_developers/Sphinx/source/Ecmwf/hintsecmwf.rst
@@ -8,7 +8,7 @@ Hints for data set selection
How can I find out what data are available?
-==========================================
+===========================================
Go to the `Web Interface for accessing member-state data sets <http://apps.ecmwf.int/archive-catalogue/>`_
and click yourself through the steps to define your set of data and see what is available to you.
diff --git a/For_developers/Sphinx/source/index.rst b/For_developers/Sphinx/source/index.rst
index 04def90b123a55441c469874a3a57785d6643b23..be0f055ced67a84c805ceb789406db524a059c4c 100644
--- a/For_developers/Sphinx/source/index.rst
+++ b/For_developers/Sphinx/source/index.rst
@@ -77,8 +77,8 @@ Welcome to ``flex_extract``'s user documentation!
<h2><a href="dev_guide.html">Developer</a></h2>
<ul>
<li><a href="Developers/gen_docu.html">Updateing the documentation</a></li>
-<!-- <li><a href=""></a><Placeholder></li>
- <li><a href=""></a><Placeholder></li>-->
+ <li><a href=""></a><Placeholder></li>
+ <li><a href=""></a><Placeholder></li>
</ul>
</td>
</tr>
diff --git a/For_developers/Sphinx/source/quick_start.rst b/For_developers/Sphinx/source/quick_start.rst
index 6ae04c4105ac9b3925f3e2e5890e27d2ec2fec0b..5b927c2c8f3477a8a1e12dc1d35850999fefeb3a 100644
--- a/For_developers/Sphinx/source/quick_start.rst
+++ b/For_developers/Sphinx/source/quick_start.rst
@@ -336,7 +336,7 @@ It is available for the period from 1 January 1979 to 31 August 2019. The ``etad
Operational data
----------------
-This data set provides the output of the real-time atmospheric model runs in high resolution, including 10-day forecasts. The model undergoes frequent adaptations and improvements. Thus, retrieving data from this dataset requires extra attention in selecting correct settings of the parameters. See :ref:`ref-tab-dataset-cmp` for the most important parameters.
+This data set provides the output of the real-time atmospheric model runs in high resolution, including 10-day forecasts. The model undergoes frequent adaptations and improvements. Thus, retrieving data from this dataset requires extra attention in selecting correct settings of the parameters. See :ref:`[Table of datasets]<ref-tab-dataset-cmp>` for the most important parameters.
Currently, fields can be retrieved at 1 h temporal resolution by filling the gaps between analysis fields with 1-hourly forecast fields. Since 4 June 2008, the eta coordinate vertical velocity is directly available from MARS, therefore ``ETA`` should be set to ``1`` to save computation time. The horizontal resolution can be up to ``0.1°`` and in combination with ``137`` vertical levels can lead to problems in terms of job duration and disk space quota.
It is recommended to submit such high resolution cases as single day retrievals (see ``JOB_CHUNK`` parameter in ``run.sh`` script) to avoid job failures due to exceeding limits.
@@ -404,8 +404,7 @@ doubleelda
debug
If set to ``1``, all temporary files are preserved. Otherwise, everything except the final output files will be deleted.
request
- This produces an extra *csv* file ``mars_requests.csv`` where the content of each MARS request submitted within the job is stored, which is useful for debugging and documentation.
-Possible values are 0 for normal data retrieval, 1 for not retrieving data and just writing out the MARS requests, and 2 to retrieve data and write out requests.
+ This produces an extra *csv* file ``mars_requests.csv`` where the content of each MARS request submitted within the job is stored, which is useful for debugging and documentation. Possible values are 0 for normal data retrieval, 1 for not retrieving data and just writing out the MARS requests, and 2 to retrieve data and write out requests.
mailfail
As a default, e-mails are sent to the mail address defined for the ECMWF user account. It is possible to overwrite this by specifying one or more e-mail addresses (comma-separated list). In order to include the e-mail associated with the user account, add ``${USER}`` to the list.
@@ -417,7 +416,10 @@ Field type and time
This combination is very important. It defines the temporal resolution and which field type is extracted on each time step.
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
-# needs to be rephrased
+
+ .. todo::
+
+ #PS needs to be rephrased
.. code-block:: bash
:caption: Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.
@@ -430,8 +432,8 @@ Field type and time
Vertical velocity
The vertical velocity for ``FLEXPART`` is not directly available from MARS and has to be calculated.
- There are several options for this, and the following parameters are responsible for the selection. See :doc:`Documentation/vertco` for a detailed explanation. Using ``ETADIFF 1``, ``OMEGA 1`` and ``OMEGADIFF 1`` is recommended for debugging and testing only.
- Usually, one has to decide between ``GAUSS 1`` and ``ETA 1``. ``GAUSS 1`` means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. ``ETA 1`` means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use ``ETA 1`` where possible, as there is a substantial computational overhead for solving the continuity equation.
+ There are several options for this, and the following parameters are responsible for the selection. See :doc:`Documentation/vertco` for a detailed explanation. Using ``ETADIFF 1``, ``OMEGA 1`` and ``OMEGADIFF 1`` is recommended for debugging and testing only.
+ Usually, one has to decide between ``GAUSS 1`` and ``ETA 1``. ``GAUSS 1`` means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. ``ETA 1`` means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use ``ETA 1`` where possible, as there is a substantial computational overhead for solving the continuity equation.
.. code-block:: bash
:caption: Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).
@@ -447,7 +449,11 @@ Vertical velocity
Grid resolution and domain
The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
-#PS shouldn't we explain how to define a domain??
+
+ .. todo::
+
+ #PS shouldn't we explain how to define a domain??
+
The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
.. code-block:: bash
@@ -465,9 +471,13 @@ Grid resolution and domain
Flux data
Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
+ .. todo::
+
+ #PS for which application would this be typical?
+
.. code-block:: bash
:caption: Example setting for the definition of flux fields.
-#PS for which application would this be typical?
+
DTIME 3
ACCTYPE FC
diff --git a/For_developers/Sphinx/source/todo.rst b/For_developers/Sphinx/source/todo.rst
index 902e69e5f3b60fdd23fb121dc013416d5b0c212c..f8607af19b164a45a339d6978bdd062a7c60ac90 100644
--- a/For_developers/Sphinx/source/todo.rst
+++ b/For_developers/Sphinx/source/todo.rst
@@ -6,3 +6,5 @@ ToDos
.. todolist::
+
+