Update cesm2.1 docs with changes from #187

versions/cesm2.1/html/_sources/cesm_configurations.rst.txt

@@ -108,13 +108,62 @@ The CESM2 components can be combined in numerous ways to carry out
 various scientific or software experiments. A particular mix of
 components, *along with* component-specific configuration and/or
 namelist settings is called a `component set or compset
-<http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html>`_.  CESM
-has a shorthand naming convention for component sets that are
-supported out-of-the-box.
-
-The compset name usually has a well defined first letter followed by
-some characters that are indicative of the configuration setup. Each
-compset name has a corresponding short name. 
+<http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html>`_. CESM has a
+shorthand naming convention (known as an alias) for component sets that
+are supported out-of-the-box. The compset alias usually has a
+well-defined first letter followed by some characters that are
+indicative of the configuration setup.
+
+The first letter in a compset alias generally indicates which of the
+components are fully active (prognostic), which are data components, and
+which are completely absent (or stub). For the most part, this first
+letter refers only to the atmosphere (atm), land (lnd), sea ice (ice)
+and ocean (ocn) components. The type of component used for river (rof),
+land ice (glc) and ocean wave (wav) is either specified in some other
+way in the alias or is not specified explicitly. For example, an
+evolving land ice (glc) model is denoted by a capital G near the end of
+the compset alias (e.g., B1850G is similar to B1850 but with an evolving
+Greenland ice sheet). In some cases, the distinction between prognostic
+and data components is not clear-cut -- for example, when using a data
+ocean model in slab ocean model (SOM) mode, or when using a prognostic
+sea ice model (CICE) in prescribed mode.
+
+The following table summarizes these first-letter designations in
+compset aliases:
+
+.. table::
+
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | Designation | Active Components  | Data Components | Notes                                                                    |
+    +=============+====================+=================+==========================================================================+
+    | A           | --                 | various         | All data components; used for software testing                           |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | B           | atm, lnd, ice, ocn | --              | Fully active components                                                  |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | C           | ocn                | atm, ice, rof   | \                                                                        |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | D           | ice                | atm, ocn, rof   | Slab ocean model (SOM)                                                   |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | E           | atm, lnd, ice      | ocn             | Slab ocean model (SOM)                                                   |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | F           | atm, lnd           | ice, ocn        | Sea ice in prescribed mode; some F compsets use fewer surface components |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | G           | ice, ocn           | atm, rof        | \                                                                        |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | I           | lnd                | atm             | \                                                                        |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | J           | lnd, ice, ocn      | atm             | Can be used to spin up the surface components                            |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | P           | atm                | --              | CAM PORT compsets                                                        |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | Q           | atm                | ocn             | Aquaplanet compsets                                                      |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | S           | --                 | --              | No components present; used for software testing                         |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | T           | glc                | lnd             | \                                                                        |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
+    | X           | --                 | --              | Coupler-test components; used for software testing                       |
+    +-------------+--------------------+-----------------+--------------------------------------------------------------------------+
 
 See `supported component sets
 <http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html>`_ for a

versions/cesm2.1/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -764,6 +764,7 @@ div.code-block-caption code {
 }
 
 table.highlighttable td.linenos,
+span.linenos,
 div.doctest > div.highlight span.gp {  /* gp: Generic.Prompt */
     user-select: none;
 }

versions/cesm2.1/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -285,9 +285,10 @@ var Documentation = {
   initOnKeyListeners: function() {
     $(document).keydown(function(event) {
       var activeElementType = document.activeElement.tagName;
-      // don't navigate when in search box or textarea
+      // don't navigate when in search box, textarea, dropdown or button
       if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
-          && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
+          && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
+          && !event.shiftKey) {
         switch (event.keyCode) {
           case 37: // left
             var prevHref = $('link[rel="prev"]').prop('href');

versions/cesm2.1/html/_static/language_data.js

@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

versions/cesm2.1/html/_static/pygments.css

@@ -1,8 +1,8 @@
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-span.linenos.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; }
+pre { line-height: 125%; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
 .highlight { background: #eeffcc; }
 .highlight .c { color: #408090; font-style: italic } /* Comment */

versions/cesm2.1/html/_static/searchtools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -59,10 +59,10 @@ var Search = {
   _pulse_status : -1,
 
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-      var htmlElement = document.createElement('span');
-      htmlElement.innerHTML = htmlString;
-      $(htmlElement).find('.headerlink').remove();
-      docContent = $(htmlElement).find('[role=main]')[0];
+      var virtualDocument = document.implementation.createHTMLDocument('virtual');
+      var htmlElement = $(htmlString, virtualDocument);
+      htmlElement.find('.headerlink').remove();
+      docContent = htmlElement.find('[role=main]')[0];
       if(docContent === undefined) {
           console.warn("Content block not found. Sphinx search tries to obtain it " +
                        "via '[role=main]'. Could you check your theme or template.");

versions/cesm2.1/html/cesm_configurations.html

@@ -420,12 +420,113 @@ <h2>CESM2 Component Sets<a class="headerlink" href="#cesm2-component-sets" title
 <p>The CESM2 components can be combined in numerous ways to carry out
 various scientific or software experiments. A particular mix of
 components, <em>along with</em> component-specific configuration and/or
-namelist settings is called a <a class="reference external" href="http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html">component set or compset</a>.  CESM
-has a shorthand naming convention for component sets that are
-supported out-of-the-box.</p>
-<p>The compset name usually has a well defined first letter followed by
-some characters that are indicative of the configuration setup. Each
-compset name has a corresponding short name.</p>
+namelist settings is called a <a class="reference external" href="http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html">component set or compset</a>. CESM has a
+shorthand naming convention (known as an alias) for component sets that
+are supported out-of-the-box. The compset alias usually has a
+well-defined first letter followed by some characters that are
+indicative of the configuration setup.</p>
+<p>The first letter in a compset alias generally indicates which of the
+components are fully active (prognostic), which are data components, and
+which are completely absent (or stub). For the most part, this first
+letter refers only to the atmosphere (atm), land (lnd), sea ice (ice)
+and ocean (ocn) components. The type of component used for river (rof),
+land ice (glc) and ocean wave (wav) is either specified in some other
+way in the alias or is not specified explicitly. For example, an
+evolving land ice (glc) model is denoted by a capital G near the end of
+the compset alias (e.g., B1850G is similar to B1850 but with an evolving
+Greenland ice sheet). In some cases, the distinction between prognostic
+and data components is not clear-cut – for example, when using a data
+ocean model in slab ocean model (SOM) mode, or when using a prognostic
+sea ice model (CICE) in prescribed mode.</p>
+<p>The following table summarizes these first-letter designations in
+compset aliases:</p>
+<table class="docutils align-default">
+<colgroup>
+<col style="width: 10%" />
+<col style="width: 16%" />
+<col style="width: 14%" />
+<col style="width: 60%" />
+</colgroup>
+<thead>
+<tr class="row-odd"><th class="head"><p>Designation</p></th>
+<th class="head"><p>Active Components</p></th>
+<th class="head"><p>Data Components</p></th>
+<th class="head"><p>Notes</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>A</p></td>
+<td><p>–</p></td>
+<td><p>various</p></td>
+<td><p>All data components; used for software testing</p></td>
+</tr>
+<tr class="row-odd"><td><p>B</p></td>
+<td><p>atm, lnd, ice, ocn</p></td>
+<td><p>–</p></td>
+<td><p>Fully active components</p></td>
+</tr>
+<tr class="row-even"><td><p>C</p></td>
+<td><p>ocn</p></td>
+<td><p>atm, ice, rof</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p>D</p></td>
+<td><p>ice</p></td>
+<td><p>atm, ocn, rof</p></td>
+<td><p>Slab ocean model (SOM)</p></td>
+</tr>
+<tr class="row-even"><td><p>E</p></td>
+<td><p>atm, lnd, ice</p></td>
+<td><p>ocn</p></td>
+<td><p>Slab ocean model (SOM)</p></td>
+</tr>
+<tr class="row-odd"><td><p>F</p></td>
+<td><p>atm, lnd</p></td>
+<td><p>ice, ocn</p></td>
+<td><p>Sea ice in prescribed mode; some F compsets use fewer surface components</p></td>
+</tr>
+<tr class="row-even"><td><p>G</p></td>
+<td><p>ice, ocn</p></td>
+<td><p>atm, rof</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p>I</p></td>
+<td><p>lnd</p></td>
+<td><p>atm</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p>J</p></td>
+<td><p>lnd, ice, ocn</p></td>
+<td><p>atm</p></td>
+<td><p>Can be used to spin up the surface components</p></td>
+</tr>
+<tr class="row-odd"><td><p>P</p></td>
+<td><p>atm</p></td>
+<td><p>–</p></td>
+<td><p>CAM PORT compsets</p></td>
+</tr>
+<tr class="row-even"><td><p>Q</p></td>
+<td><p>atm</p></td>
+<td><p>ocn</p></td>
+<td><p>Aquaplanet compsets</p></td>
+</tr>
+<tr class="row-odd"><td><p>S</p></td>
+<td><p>–</p></td>
+<td><p>–</p></td>
+<td><p>No components present; used for software testing</p></td>
+</tr>
+<tr class="row-even"><td><p>T</p></td>
+<td><p>glc</p></td>
+<td><p>lnd</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p>X</p></td>
+<td><p>–</p></td>
+<td><p>–</p></td>
+<td><p>Coupler-test components; used for software testing</p></td>
+</tr>
+</tbody>
+</table>
 <p>See <a class="reference external" href="http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html">supported component sets</a> for a
 complete list of supported compset options. Running <strong>query_config</strong>
 with the <code class="docutils literal notranslate"><span class="pre">--compsets</span></code> option will also provide a listing of the
@@ -555,7 +656,6 @@ <h2>CESM2 Validation<a class="headerlink" href="#cesm2-validation" title="Permal
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/pop_ver.js"></script>
 
 

versions/cesm2.1/html/downloading_cesm.html

@@ -359,7 +359,6 @@ <h2>Downloading input data<a class="headerlink" href="#downloading-input-data" t
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/pop_ver.js"></script>
 
 

versions/cesm2.1/html/genindex.html

@@ -215,7 +215,6 @@ <h1 id="index">Index</h1>
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/pop_ver.js"></script>
 
 

versions/cesm2.1/html/index.html

@@ -260,7 +260,6 @@ <h2>Table of contents<a class="headerlink" href="#table-of-contents" title="Perm
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/pop_ver.js"></script>
 
 

versions/cesm2.1/html/introduction.html

@@ -328,7 +328,6 @@ <h2>CESM2 Software/Operating System Prerequisites<a class="headerlink" href="#ce
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/pop_ver.js"></script>
 
 

versions/cesm2.1/html/quickstart.html

@@ -401,7 +401,6 @@ <h2>Run the case<a class="headerlink" href="#run-the-case" title="Permalink to t
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/pop_ver.js"></script>
 
 

versions/cesm2.1/html/search.html

@@ -221,7 +221,6 @@
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
         <script src="_static/searchtools.js"></script>
         <script src="_static/pop_ver.js"></script>