Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
@github-actions
github-actions[bot] committed Sep 20, 2024
1 parent a0bce3d commit 70f4b13
Show file tree
Hide file tree
Showing 32 changed files with 224 additions and 236 deletions.
Binary file removed latest/_images/sowisc12to60.png
View file
Binary file not shown.
38 changes: 29 additions & 9 deletions latest/_modules/compass/ocean/plot.html
View file

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion latest/_modules/compass/ocean/tests/global_ocean.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ <h1>Source code for compass.ocean.tests.global_ocean</h1><div class="highlight">

<span class="bp">self</span><span class="o">.</span><span class="n">_add_tests</span><span class="p">(</span><span class="n">mesh_names</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;ARRM10to60&#39;</span><span class="p">,</span> <span class="s1">&#39;ARRMwISC10to60&#39;</span><span class="p">])</span>

<span class="bp">self</span><span class="o">.</span><span class="n">_add_tests</span><span class="p">(</span><span class="n">mesh_names</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;SO12to60&#39;</span><span class="p">,</span> <span class="s1">&#39;SOwISC12to60&#39;</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_add_tests</span><span class="p">(</span><span class="n">mesh_names</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;SO12to30&#39;</span><span class="p">,</span> <span class="s1">&#39;SOwISC12to30&#39;</span><span class="p">])</span>

<span class="bp">self</span><span class="o">.</span><span class="n">_add_tests</span><span class="p">(</span><span class="n">mesh_names</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;WC14&#39;</span><span class="p">,</span> <span class="s1">&#39;WCwISC14&#39;</span><span class="p">])</span>

Expand Down
41 changes: 34 additions & 7 deletions latest/_modules/compass/ocean/tests/global_ocean/init/initial_state.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,7 @@ <h1>Source code for compass.ocean.tests.global_ocean.init.initial_state</h1><div
<span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">importlib.resources</span> <span class="kn">import</span> <span class="n">contents</span><span class="p">,</span> <span class="n">read_text</span>

<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">xarray</span> <span class="k">as</span> <span class="nn">xr</span>
<span class="kn">from</span> <span class="nn">jinja2</span> <span class="kn">import</span> <span class="n">Template</span>
<span class="kn">from</span> <span class="nn">mpas_tools.io</span> <span class="kn">import</span> <span class="n">write_netcdf</span>
Expand Down Expand Up @@ -319,7 +320,7 @@ <h1>Source code for compass.ocean.tests.global_ocean.init.initial_state</h1><div
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span>
<span class="n">section</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s1">&#39;global_ocean&#39;</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_smooth_topography</span><span class="p">()</span>
<span class="n">topo_filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_smooth_topography</span><span class="p">()</span>

<span class="n">interfaces</span> <span class="o">=</span> <span class="n">generate_1d_grid</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">config</span><span class="p">)</span>

Expand Down Expand Up @@ -348,8 +349,16 @@ <h1>Source code for compass.ocean.tests.global_ocean.init.initial_state</h1><div
<span class="n">namelist</span><span class="p">[</span><span class="s1">&#39;config_rx1_min_layer_thickness&#39;</span><span class="p">]</span> <span class="o">=</span> \
<span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">cavity_min_layer_thickness</span><span class="si">}</span><span class="s1">&#39;</span>

<span class="n">min_water_column_thickness</span> <span class="o">=</span> \
<span class="n">cavity_min_layer_thickness</span> <span class="o">*</span> <span class="n">cavity_min_levels</span>

<span class="n">topo_filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dig_cavity_bed_elevation</span><span class="p">(</span>
<span class="n">topo_filename</span><span class="p">,</span> <span class="n">min_water_column_thickness</span><span class="p">)</span>

<span class="bp">self</span><span class="o">.</span><span class="n">update_namelist_at_runtime</span><span class="p">(</span><span class="n">namelist</span><span class="p">)</span>

<span class="n">symlink</span><span class="p">(</span><span class="n">target</span><span class="o">=</span><span class="n">topo_filename</span><span class="p">,</span> <span class="n">link_name</span><span class="o">=</span><span class="s1">&#39;topography.nc&#39;</span><span class="p">)</span>

<span class="n">update_pio</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;init_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>

Expand All @@ -376,10 +385,8 @@ <h1>Source code for compass.ocean.tests.global_ocean.init.initial_state</h1><div
<span class="n">section</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s1">&#39;global_ocean&#39;</span><span class="p">]</span>
<span class="n">num_passes</span> <span class="o">=</span> <span class="n">section</span><span class="o">.</span><span class="n">getint</span><span class="p">(</span><span class="s1">&#39;topo_smooth_num_passes&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">num_passes</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># just symlink the culled topography to be the topography used for</span>
<span class="c1"># the initial condition</span>
<span class="n">symlink</span><span class="p">(</span><span class="n">target</span><span class="o">=</span><span class="s1">&#39;topography_culled.nc&#39;</span><span class="p">,</span> <span class="n">link_name</span><span class="o">=</span><span class="s1">&#39;topography.nc&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="c1"># just return the culled topography file name</span>
<span class="k">return</span> <span class="s1">&#39;topography_culled.nc&#39;</span>

<span class="n">distance_limit</span> <span class="o">=</span> <span class="n">section</span><span class="o">.</span><span class="n">getfloat</span><span class="p">(</span><span class="s1">&#39;topo_smooth_distance_limit&#39;</span><span class="p">)</span>
<span class="n">std_deviation</span> <span class="o">=</span> <span class="n">section</span><span class="o">.</span><span class="n">getfloat</span><span class="p">(</span><span class="s1">&#39;topo_smooth_std_deviation&#39;</span><span class="p">)</span>
Expand All @@ -400,15 +407,35 @@ <h1>Source code for compass.ocean.tests.global_ocean.init.initial_state</h1><div
<span class="n">check_call</span><span class="p">(</span><span class="n">args</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;ocean_smooth_topo_before_init&#39;</span><span class="p">],</span>
<span class="n">logger</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">logger</span><span class="p">)</span>

<span class="k">with</span> <span class="p">(</span><span class="n">xr</span><span class="o">.</span><span class="n">open_dataset</span><span class="p">(</span><span class="s1">&#39;topography_culled.nc&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">ds_topo</span><span class="p">):</span>
<span class="n">out_filename</span> <span class="o">=</span> <span class="s1">&#39;topography_smoothed.nc&#39;</span>
<span class="k">with</span> <span class="n">xr</span><span class="o">.</span><span class="n">open_dataset</span><span class="p">(</span><span class="s1">&#39;topography_culled.nc&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">ds_topo</span><span class="p">:</span>
<span class="k">with</span> <span class="n">xr</span><span class="o">.</span><span class="n">open_dataset</span><span class="p">(</span><span class="s1">&#39;topography_orig_and_smooth.nc&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">ds_smooth</span><span class="p">:</span>
<span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;bed_elevation&#39;</span><span class="p">,</span> <span class="s1">&#39;landIceDraftObserved&#39;</span><span class="p">,</span>
<span class="s1">&#39;landIceThkObserved&#39;</span><span class="p">]:</span>
<span class="n">attrs</span> <span class="o">=</span> <span class="n">ds_topo</span><span class="p">[</span><span class="n">field</span><span class="p">]</span><span class="o">.</span><span class="n">attrs</span>
<span class="n">ds_topo</span><span class="p">[</span><span class="n">field</span><span class="p">]</span> <span class="o">=</span> <span class="n">ds_smooth</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">field</span><span class="si">}</span><span class="s1">New&#39;</span><span class="p">]</span>
<span class="n">ds_topo</span><span class="p">[</span><span class="n">field</span><span class="p">]</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="n">attrs</span>

<span class="n">write_netcdf</span><span class="p">(</span><span class="n">ds_topo</span><span class="p">,</span> <span class="s1">&#39;topography.nc&#39;</span><span class="p">)</span></div>
<span class="n">write_netcdf</span><span class="p">(</span><span class="n">ds_topo</span><span class="p">,</span> <span class="n">out_filename</span><span class="p">)</span>
<span class="k">return</span> <span class="n">out_filename</span>

<span class="k">def</span> <span class="nf">_dig_cavity_bed_elevation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">in_filename</span><span class="p">,</span>
<span class="n">min_water_column_thickness</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot; Dig bed elevation to preserve minimum water-column thickness &quot;&quot;&quot;</span>

<span class="n">out_filename</span> <span class="o">=</span> <span class="s1">&#39;topography_dig_bed.nc&#39;</span>
<span class="k">with</span> <span class="n">xr</span><span class="o">.</span><span class="n">open_dataset</span><span class="p">(</span><span class="n">in_filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">ds_topo</span><span class="p">:</span>
<span class="n">bed</span> <span class="o">=</span> <span class="n">ds_topo</span><span class="o">.</span><span class="n">bed_elevation</span>
<span class="n">attrs</span> <span class="o">=</span> <span class="n">bed</span><span class="o">.</span><span class="n">attrs</span>
<span class="n">draft</span> <span class="o">=</span> <span class="n">ds_topo</span><span class="o">.</span><span class="n">landIceDraftObserved</span>
<span class="n">max_bed</span> <span class="o">=</span> <span class="n">draft</span> <span class="o">-</span> <span class="n">min_water_column_thickness</span>
<span class="n">mask</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_or</span><span class="p">(</span><span class="n">draft</span> <span class="o">==</span> <span class="mf">0.</span><span class="p">,</span> <span class="n">bed</span> <span class="o">&lt;</span> <span class="n">max_bed</span><span class="p">)</span>
<span class="n">bed</span> <span class="o">=</span> <span class="n">xr</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">mask</span><span class="p">,</span> <span class="n">bed</span><span class="p">,</span> <span class="n">max_bed</span><span class="p">)</span>
<span class="n">ds_topo</span><span class="p">[</span><span class="s1">&#39;bed_elevation&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">bed</span>
<span class="n">ds_topo</span><span class="p">[</span><span class="s1">&#39;bed_elevation&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="n">attrs</span>

<span class="n">write_netcdf</span><span class="p">(</span><span class="n">ds_topo</span><span class="p">,</span> <span class="n">out_filename</span><span class="p">)</span>
<span class="k">return</span> <span class="n">out_filename</span></div>

</pre></div>

Expand Down
6 changes: 3 additions & 3 deletions latest/_modules/compass/ocean/tests/global_ocean/mesh.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ <h1>Source code for compass.ocean.tests.global_ocean.mesh</h1><div class="highli
<span class="n">QUMeshFromConfigStep</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.mesh.rrs6to18</span> <span class="kn">import</span> <span class="n">RRS6to18BaseMesh</span>
<span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.mesh.so12to60</span> <span class="kn">import</span> <span class="n">SO12to60BaseMesh</span>
<span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.mesh.so12to30</span> <span class="kn">import</span> <span class="n">SO12to30BaseMesh</span>
<span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.mesh.wc14</span> <span class="kn">import</span> <span class="n">WC14BaseMesh</span>
<span class="kn">from</span> <span class="nn">compass.ocean.tests.global_ocean.metadata</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">get_author_and_email_from_git</span><span class="p">,</span>
Expand Down Expand Up @@ -216,8 +216,8 @@ <h1>Source code for compass.ocean.tests.global_ocean.mesh</h1><div class="highli
<span class="n">base_mesh_step</span> <span class="o">=</span> <span class="n">ARRM10to60BaseMesh</span><span class="p">(</span><span class="bp">self</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="k">elif</span> <span class="n">mesh_name</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;RRS6to18&#39;</span><span class="p">,</span> <span class="s1">&#39;RRSwISC6to18&#39;</span><span class="p">]:</span>
<span class="n">base_mesh_step</span> <span class="o">=</span> <span class="n">RRS6to18BaseMesh</span><span class="p">(</span><span class="bp">self</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="k">elif</span> <span class="n">mesh_name</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;SO12to60&#39;</span><span class="p">,</span> <span class="s1">&#39;SOwISC12to60&#39;</span><span class="p">]:</span>
<span class="n">base_mesh_step</span> <span class="o">=</span> <span class="n">SO12to60BaseMesh</span><span class="p">(</span><span class="bp">self</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="k">elif</span> <span class="n">mesh_name</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;SO12to30&#39;</span><span class="p">,</span> <span class="s1">&#39;SOwISC12to30&#39;</span><span class="p">]:</span>
<span class="n">base_mesh_step</span> <span class="o">=</span> <span class="n">SO12to30BaseMesh</span><span class="p">(</span><span class="bp">self</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="k">elif</span> <span class="n">mesh_name</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;FRIS01to60&#39;</span><span class="p">,</span> <span class="s1">&#39;FRISwISC01to60&#39;</span><span class="p">]:</span>
<span class="n">base_mesh_step</span> <span class="o">=</span> <span class="n">FRIS01to60BaseMesh</span><span class="p">(</span><span class="bp">self</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="k">elif</span> <span class="n">mesh_name</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;FRIS02to60&#39;</span><span class="p">,</span> <span class="s1">&#39;FRISwISC02to60&#39;</span><span class="p">]:</span>
Expand Down
Loading

0 comments on commit 70f4b13

Please sign in to comment.