Update documentation

latest/_modules/compass/ocean/tests/global_ocean/files_for_e3sm.html

@@ -153,6 +153,9 @@ <h1>Source code for compass.ocean.tests.global_ocean.files_for_e3sm</h1><div cla
 <span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.files_for_e3sm.seaice_mesh</span> <span class="kn">import</span> <span class="p">(</span>  <span class="c1"># noqa: E501</span>
     <span class="n">SeaiceMesh</span><span class="p">,</span>
 <span class="p">)</span>
+<span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct</span> <span class="kn">import</span> <span class="p">(</span>  <span class="c1"># noqa: E501</span>
+    <span class="n">WriteCoeffsReconstruct</span><span class="p">,</span>
+<span class="p">)</span>
 <span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.forward</span> <span class="kn">import</span> <span class="n">get_forward_subdir</span>
 <span class="kn">from</span> <span class="nn">compass.testcase</span> <span class="kn">import</span> <span class="n">TestCase</span>
 
@@ -228,7 +231,11 @@ <h1>Source code for compass.ocean.tests.global_ocean.files_for_e3sm</h1><div cla
             <span class="n">test_case</span><span class="o">=</span><span class="bp">self</span><span class="p">))</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">add_step</span><span class="p">(</span><span class="n">RemapIcebergClimatology</span><span class="p">(</span>
-            <span class="n">test_case</span><span class="o">=</span><span class="bp">self</span><span class="p">))</span></div>
+            <span class="n">test_case</span><span class="o">=</span><span class="bp">self</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">mesh</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">init</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_step</span><span class="p">(</span><span class="n">WriteCoeffsReconstruct</span><span class="p">(</span>
+                <span class="n">test_case</span><span class="o">=</span><span class="bp">self</span><span class="p">,</span> <span class="n">mesh</span><span class="o">=</span><span class="n">mesh</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="n">init</span><span class="p">))</span></div>
 
 <div class="viewcode-block" id="FilesForE3SM.configure"><a class="viewcode-back" href="../../../../../developers_guide/ocean/generated/compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM.configure.html#compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM.configure">[docs]</a>    <span class="k">def</span> <span class="nf">configure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>

latest/_modules/compass/ocean/tests/global_ocean/forward.html

@@ -154,7 +154,7 @@ <h1>Source code for compass.ocean.tests.global_ocean.forward</h1><div class="hig
 <div class="viewcode-block" id="ForwardStep.__init__"><a class="viewcode-back" href="../../../../../developers_guide/ocean/generated/compass.ocean.tests.global_ocean.forward.ForwardStep.html#compass.ocean.tests.global_ocean.forward.ForwardStep.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">test_case</span><span class="p">,</span> <span class="n">mesh</span><span class="p">,</span> <span class="n">time_integrator</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">name</span><span class="o">=</span><span class="s1">&#39;forward&#39;</span><span class="p">,</span> <span class="n">subdir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ntasks</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">min_tasks</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">openmp_threads</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">get_dt_from_min_res</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-                 <span class="n">land_ice_flux_mode</span><span class="o">=</span><span class="s1">&#39;pressure_only&#39;</span><span class="p">):</span>
+                 <span class="n">land_ice_flux_mode</span><span class="o">=</span><span class="s1">&#39;pressure_only&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Create a new step</span>
 
@@ -206,7 +206,7 @@ <h1>Source code for compass.ocean.tests.global_ocean.forward</h1><div class="hig
             <span class="n">min_tasks</span> <span class="o">=</span> <span class="n">ntasks</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">test_case</span><span class="o">=</span><span class="n">test_case</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span> <span class="n">subdir</span><span class="o">=</span><span class="n">subdir</span><span class="p">,</span>
                          <span class="n">ntasks</span><span class="o">=</span><span class="n">ntasks</span><span class="p">,</span> <span class="n">min_tasks</span><span class="o">=</span><span class="n">min_tasks</span><span class="p">,</span>
-                         <span class="n">openmp_threads</span><span class="o">=</span><span class="n">openmp_threads</span><span class="p">)</span>
+                         <span class="n">openmp_threads</span><span class="o">=</span><span class="n">openmp_threads</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="p">(</span><span class="n">ntasks</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">)</span> <span class="o">!=</span> <span class="p">(</span><span class="n">openmp_threads</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">):</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;You must specify both ntasks and openmp_threads &#39;</span>
@@ -293,7 +293,8 @@ <h1>Source code for compass.ocean.tests.global_ocean.forward</h1><div class="hig
                                            <span class="s1">&#39;config_btr_dt&#39;</span><span class="p">:</span> <span class="n">btr_dt</span><span class="p">})</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="c1"># RK4, so use the smaller time step</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">add_namelist_options</span><span class="p">({</span><span class="s1">&#39;config_dt&#39;</span><span class="p">:</span> <span class="n">btr_dt</span><span class="p">})</span></div>
+                <span class="bp">self</span><span class="o">.</span><span class="n">add_namelist_options</span><span class="p">({</span><span class="s1">&#39;config_dt&#39;</span><span class="p">:</span> <span class="n">btr_dt</span><span class="p">})</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">setup</span><span class="p">()</span></div>
 
     <span class="k">def</span> <span class="nf">constrain_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">available_resources</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
@@ -321,11 +322,13 @@ <h1>Source code for compass.ocean.tests.global_ocean.forward</h1><div class="hig
             <span class="k">else</span><span class="p">:</span>
                 <span class="c1"># RK4, so use the smaller time step</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">update_namelist_at_runtime</span><span class="p">({</span><span class="s1">&#39;config_dt&#39;</span><span class="p">:</span> <span class="n">btr_dt</span><span class="p">})</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">runtime_setup</span><span class="p">()</span>
 
 <div class="viewcode-block" id="ForwardStep.run"><a class="viewcode-back" href="../../../../../developers_guide/ocean/generated/compass.ocean.tests.global_ocean.forward.ForwardStep.run.html#compass.ocean.tests.global_ocean.forward.ForwardStep.run">[docs]</a>    <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Run this step of the testcase</span>
 <span class="sd">        &quot;&quot;&quot;</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
         <span class="n">update_pio</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">getboolean</span><span class="p">(</span><span class="s1">&#39;global_ocean&#39;</span><span class="p">,</span>
                                             <span class="s1">&#39;forward_update_pio&#39;</span><span class="p">)</span>
         <span class="n">run_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">update_pio</span><span class="o">=</span><span class="n">update_pio</span><span class="p">)</span>

latest/_modules/index.html

@@ -265,6 +265,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="compass/ocean/tests/global_ocean/files_for_e3sm/seaice_graph_partition.html">compass.ocean.tests.global_ocean.files_for_e3sm.seaice_graph_partition</a></li>
 <li><a href="compass/ocean/tests/global_ocean/files_for_e3sm/seaice_initial_condition.html">compass.ocean.tests.global_ocean.files_for_e3sm.seaice_initial_condition</a></li>
 <li><a href="compass/ocean/tests/global_ocean/files_for_e3sm/seaice_mesh.html">compass.ocean.tests.global_ocean.files_for_e3sm.seaice_mesh</a></li>
+<li><a href="compass/ocean/tests/global_ocean/files_for_e3sm/write_coeffs_reconstruct.html">compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct</a></li>
 </ul><li><a href="compass/ocean/tests/global_ocean/forward.html">compass.ocean.tests.global_ocean.forward</a></li>
 <li><a href="compass/ocean/tests/global_ocean/init.html">compass.ocean.tests.global_ocean.init</a></li>
 <ul><li><a href="compass/ocean/tests/global_ocean/init/initial_state.html">compass.ocean.tests.global_ocean.init.initial_state</a></li>

latest/_sources/developers_guide/ocean/api.rst.txt

@@ -203,6 +203,8 @@ test cases and steps
    files_for_e3sm.remap_sea_surface_salinity_restoring.RemapSeaSurfaceSalinityRestoring.run
    files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology
    files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run
+   files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct
+   files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run
 
    init.Init
    init.Init.configure

latest/_sources/developers_guide/ocean/generated/compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.rst.txt

@@ -0,0 +1,37 @@
+compass.ocean.tests.global\_ocean.files\_for\_e3sm.write\_coeffs\_reconstruct.WriteCoeffsReconstruct
+====================================================================================================
+
+.. currentmodule:: compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct
+
+.. autoclass:: WriteCoeffsReconstruct
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~WriteCoeffsReconstruct.__init__
+      ~WriteCoeffsReconstruct.add_input_file
+      ~WriteCoeffsReconstruct.add_model_as_input
+      ~WriteCoeffsReconstruct.add_namelist_file
+      ~WriteCoeffsReconstruct.add_namelist_options
+      ~WriteCoeffsReconstruct.add_output_file
+      ~WriteCoeffsReconstruct.add_streams_file
+      ~WriteCoeffsReconstruct.constrain_resources
+      ~WriteCoeffsReconstruct.process_inputs_and_outputs
+      ~WriteCoeffsReconstruct.run
+      ~WriteCoeffsReconstruct.runtime_setup
+      ~WriteCoeffsReconstruct.set_resources
+      ~WriteCoeffsReconstruct.setup
+      ~WriteCoeffsReconstruct.update_namelist_at_runtime
+      ~WriteCoeffsReconstruct.update_namelist_pio
+      ~WriteCoeffsReconstruct.update_streams_at_runtime
+
+
+
+
+
+

latest/_sources/developers_guide/ocean/generated/compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run.rst.txt

@@ -0,0 +1,6 @@
+compass.ocean.tests.global\_ocean.files\_for\_e3sm.write\_coeffs\_reconstruct.WriteCoeffsReconstruct.run
+========================================================================================================
+
+.. currentmodule:: compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct
+
+.. automethod:: WriteCoeffsReconstruct.run

latest/_sources/developers_guide/ocean/test_groups/global_ocean.rst.txt

@@ -1380,6 +1380,12 @@ The test case is made up of 10 steps:
     the MPAS mesh.  This dataset is used in E3SM for compsets with data iceberg
     freshwater fluxes (``DIB``).
 
+:py:class:`compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct`
+    is used to do a one-time-step forward run to write out coefficients
+    ``coeff_reconstruct`` for reconstructing vector fields at cell centers from
+    normal values at edges.  These can be used in combination with the
+
+
 files_for_e3sm for an existing mesh
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

latest/developers_guide/ocean/api.html

@@ -525,6 +525,12 @@ <h4>test cases and steps<a class="headerlink" href="#test-cases-and-steps" title
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run.html#compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run" title="compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run"><code class="xref py py-obj docutils literal notranslate"><span class="pre">files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run</span></code></a>()</p></td>
 <td><p>Run this step of the test case</p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.html#compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct" title="compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct"><code class="xref py py-obj docutils literal notranslate"><span class="pre">files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct</span></code></a>(...)</p></td>
+<td><p>A step for writing out <code class="docutils literal notranslate"><span class="pre">coeffs_reconstruct</span></code> for a given MPAS mesh</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run.html#compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run" title="compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run"><code class="xref py py-obj docutils literal notranslate"><span class="pre">files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run</span></code></a>()</p></td>
+<td><p>Run this step of the testcase</p></td>
+</tr>
 <tr class="row-even"><td><p><a class="reference internal" href="generated/compass.ocean.tests.global_ocean.init.Init.html#compass.ocean.tests.global_ocean.init.Init" title="compass.ocean.tests.global_ocean.init.Init"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init.Init</span></code></a>(test_group, mesh, initial_condition)</p></td>
 <td><p>A test case for creating initial conditions on a global MPAS-Ocean mesh</p></td>
 </tr>

latest/developers_guide/ocean/generated/compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run.html

@@ -20,7 +20,7 @@
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
-    <link rel="next" title="compass.ocean.tests.global_ocean.init.Init" href="compass.ocean.tests.global_ocean.init.Init.html" />
+    <link rel="next" title="compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct" href="compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.html" />
     <link rel="prev" title="compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology" href="compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.html" /> 
 </head>
 
@@ -143,7 +143,7 @@ <h1>compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.Re
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.html" class="btn btn-neutral float-left" title="compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="compass.ocean.tests.global_ocean.init.Init.html" class="btn btn-neutral float-right" title="compass.ocean.tests.global_ocean.init.Init" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.html" class="btn btn-neutral float-right" title="compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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