Update documentation

latest/_sources/developers_guide/machines/chicoma.rst.txt

@@ -19,3 +19,22 @@ Then, you can build the MPAS model with
 .. code-block:: bash
 
     make [DEBUG=true] gnu-cray
+
+debug jobs
+~~~~~~~~~~
+
+In order to run jobs in the debug queue, you will need to use: 
+
+.. code-block:: cfg
+
+    # Config options related to creating a job script
+    [job]
+
+    # The job partition to use
+    partition = debug
+
+    # The job reservation to use (needed for debug jobs)
+    reservation = debug
+
+    # The job quality of service (QOS) to use
+    qos =

latest/_sources/users_guide/machines/chicoma.rst.txt

@@ -138,9 +138,12 @@ when setting up test cases or a test suite:
     # The job partition to use
     partition = standard
 
+    # The job reservation to use (needed for debug jobs)
+    reservation =
+
     # The job quality of service (QOS) to use
     qos = standard
-
+    
 
 Additionally, some relevant config options come from the
 `mache <https://github.com/E3SM-Project/mache/>`_ package:
@@ -213,4 +216,4 @@ To build the MPAS model with
 
 .. code-block:: bash
 
-    make [DEBUG=true] [OPENMP=true] [ALBANY=true] gnu-cray
+    make [DEBUG=true] [OPENMP=true] [ALBANY=true] gnu-cray

latest/developers_guide/landice/generated/compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP.html

@@ -134,7 +134,7 @@ <h1>compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP<a cla
 <span class="sig-prename descclassname"><span class="pre">compass.landice.tests.mismipplus.setup_mesh.</span></span><span class="sig-name descname"><span class="pre">mark_cull_cells_for_MISMIP</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ds_mesh</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/compass/landice/tests/mismipplus/setup_mesh.html#mark_cull_cells_for_MISMIP"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP" title="Link to this definition">¶</a></dt>
 <dd><dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>)</p>
+<dd class="field-odd"><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>)</p>
 </dd>
 </dl>
 </dd></dl>

latest/developers_guide/machines/chicoma.html

@@ -143,6 +143,23 @@ <h2>chicoma-cpu, gnu<a class="headerlink" href="#chicoma-cpu-gnu" title="Link to
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>make<span class="w"> </span><span class="o">[</span><span class="nv">DEBUG</span><span class="o">=</span>true<span class="o">]</span><span class="w"> </span>gnu-cray
 </pre></div>
 </div>
+<section id="debug-jobs">
+<h3>debug jobs<a class="headerlink" href="#debug-jobs" title="Link to this heading">¶</a></h3>
+<p>In order to run jobs in the debug queue, you will need to use:</p>
+<div class="highlight-cfg notranslate"><div class="highlight"><pre><span></span><span class="c1"># Config options related to creating a job script</span>
+<span class="k">[job]</span>
+
+<span class="c1"># The job partition to use</span>
+<span class="na">partition</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">debug</span>
+
+<span class="c1"># The job reservation to use (needed for debug jobs)</span>
+<span class="na">reservation</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">debug</span>
+
+<span class="c1"># The job quality of service (QOS) to use</span>
+<span class="na">qos</span><span class="w"> </span><span class="o">=</span>
+</pre></div>
+</div>
+</section>
 </section>
 </section>
 

latest/developers_guide/ocean/generated/compass.ocean.haney.compute_haney_number.html

@@ -136,9 +136,9 @@ <h1>compass.ocean.haney.compute_haney_number<a class="headerlink" href="#compass
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – A dataset with the MPAS-Ocean mesh</p></li>
-<li><p><strong>layer_thickness</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with layer thicknesses</p></li>
-<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with sea surface height</p></li>
+<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – A dataset with the MPAS-Ocean mesh</p></li>
+<li><p><strong>layer_thickness</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with layer thicknesses</p></li>
+<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – A data array with sea surface height</p></li>
 <li><p><strong>show_progress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to show a progress bar</p></li>
 </ul>
 </dd>

latest/developers_guide/ocean/generated/compass.ocean.iceshelf.compute_land_ice_pressure_and_draft.html

@@ -136,8 +136,8 @@ <h1>compass.ocean.iceshelf.compute_land_ice_pressure_and_draft<a class="headerli
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height (the ice draft)</p></li>
-<li><p><strong>modify_mask</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – A mask that is 1 where <code class="docutils literal notranslate"><span class="pre">landIcePressure</span></code> can be deviate from 0</p></li>
+<li><p><strong>ssh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – The sea surface height (the ice draft)</p></li>
+<li><p><strong>modify_mask</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – A mask that is 1 where <code class="docutils literal notranslate"><span class="pre">landIcePressure</span></code> can be deviate from 0</p></li>
 <li><p><strong>ref_density</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – A reference density for seawater displaced by the ice shelf</p></li>
 </ul>
 </dd>

latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_geom.html

@@ -137,8 +137,8 @@ <h1>compass.ocean.tests.isomip_plus.geom.interpolate_geom<a class="headerlink" h
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
-<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
+<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
+<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
 <a class="reference internal" href="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom.html#compass.ocean.tests.isomip_plus.process_geom.ProcessGeom" title="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom"><code class="xref py py-class docutils literal notranslate"><span class="pre">compass.ocean.tests.isomip_plus.process_geom.ProcessGeom</span></code></a></p></li>
 <li><p><strong>min_ocean_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – The minimum ocean fraction after interpolation, below which the cell
 is masked as land (which is not distinguished from grounded ice)</p></li>

latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask.html

@@ -139,8 +139,8 @@ <h1>compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask<a class="headerl
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
-<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
+<li><p><strong>ds_mesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – An MPAS-Ocean mesh</p></li>
+<li><p><strong>ds_geom</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – Ice-sheet topography produced by
 <a class="reference internal" href="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom.html#compass.ocean.tests.isomip_plus.process_geom.ProcessGeom" title="compass.ocean.tests.isomip_plus.process_geom.ProcessGeom"><code class="xref py py-class docutils literal notranslate"><span class="pre">compass.ocean.tests.isomip_plus.process_geom.ProcessGeom</span></code></a></p></li>
 <li><p><strong>min_ocean_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – The minimum ocean fraction after interpolation, below which the cell
 is masked as land (which is not distinguished from grounded ice)</p></li>

latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.html

@@ -169,8 +169,8 @@ <h1>compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter<a class="headerlink" h
 <li><p><strong>expt</strong> (<em>{'Ocean0'</em><em>, </em><em>'Ocean1'</em><em>, </em><em>'Ocean2'}</em>) – The name of the experiment</p></li>
 <li><p><strong>sectionY</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – The location along the y axis of a transect in the x-z plane to
 plot</p></li>
-<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – The MPAS mesh</p></li>
-<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – The time series output</p></li>
+<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – The MPAS mesh</p></li>
+<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – The time series output</p></li>
 <li><p><strong>showProgress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to show a progressbar</p></li>
 </ul>
 </dd>

latest/developers_guide/ocean/generated/compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.html

@@ -154,8 +154,8 @@ <h1>compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter<a class="headerli
 <li><p><strong>inFolder</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – The folder with simulation results</p></li>
 <li><p><strong>outFolder</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – The folder where images will be written</p></li>
 <li><p><strong>expt</strong> (<em>{'Ocean0'</em><em>, </em><em>'Ocean1'</em><em>, </em><em>'Ocean2'}</em><em>, </em><em>optional</em>) – The name of the experiment</p></li>
-<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The MPAS mesh</p></li>
-<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The time series output</p></li>
+<li><p><strong>dsMesh</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The MPAS mesh</p></li>
+<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a><em>, </em><em>optional</em>) – The time series output</p></li>
 </ul>
 </dd>
 </dl>

latest/developers_guide/ocean/generated/compass.ocean.vertical.init_vertical_coord.html

@@ -169,7 +169,7 @@ <h1>compass.ocean.vertical.init_vertical_coord<a class="headerlink" href="#compa
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>config</strong> (<a class="reference internal" href="../../generated/compass.config.CompassConfigParser.html#compass.config.CompassConfigParser" title="compass.config.CompassConfigParser"><em>compass.config.CompassConfigParser</em></a>) – Configuration options with parameters used to construct the vertical
 grid</p></li>
-<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.7.1.dev0)"><em>xarray.Dataset</em></a>) – A data set containing <code class="docutils literal notranslate"><span class="pre">bottomDepth</span></code> and <code class="docutils literal notranslate"><span class="pre">ssh</span></code> variables used to
+<li><p><strong>ds</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.9.1.dev0)"><em>xarray.Dataset</em></a>) – A data set containing <code class="docutils literal notranslate"><span class="pre">bottomDepth</span></code> and <code class="docutils literal notranslate"><span class="pre">ssh</span></code> variables used to
 construct the vertical coordinate</p></li>
 </ul>
 </dd>

latest/developers_guide/ocean/generated/compass.ocean.vertical.partial_cells.alter_bottom_depth.html

@@ -139,9 +139,9 @@ <h1>compass.ocean.vertical.partial_cells.alter_bottom_depth<a class="headerlink"
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>config</strong> (<a class="reference internal" href="../../generated/compass.config.CompassConfigParser.html#compass.config.CompassConfigParser" title="compass.config.CompassConfigParser"><em>compass.config.CompassConfigParser</em></a>) – Configuration options with parameters used to construct the vertical
 grid</p></li>
-<li><p><strong>bottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</p></li>
-<li><p><strong>refBottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the bottom of each z level</p></li>
-<li><p><strong>maxLevelCell</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.7.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
+<li><p><strong>bottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – The positive-down depth of the seafloor</p></li>
+<li><p><strong>refBottomDepth</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – A 1D array of positive-down depths of the bottom of each z level</p></li>
+<li><p><strong>maxLevelCell</strong> (<a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.DataArray.html#xarray.DataArray" title="(in xarray v2024.9.1.dev0)"><em>xarray.DataArray</em></a>) – The zero-based index of the bottom valid level</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>