[skip ci] Updates

OpenDrift · Mar 29, 2024 · 040fa4d · 040fa4d
1 parent a2446cc
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 642146e8b99aada0158fefbb31cb31fb
+config: 14386eef9b4aae79c2f810df51e43a9a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_downloads/46b4cb42d5bb56cc39e2b5b2b520b38d/gallery_python.zip b/_downloads/46b4cb42d5bb56cc39e2b5b2b520b38d/gallery_python.zip
diff --git a/_downloads/88941f1f62ccc3a0ec3328b3bebf4549/example_vertical_mixing.py b/_downloads/88941f1f62ccc3a0ec3328b3bebf4549/example_vertical_mixing.py
@@ -38,8 +38,9 @@
 o.time = time
 o.time_step = timedelta(hours=hours)
 o.release_elements()
-o.environment = np.array(np.ones(N)*sea_floor_depth,
-                dtype=[('sea_floor_depth_below_sea_level', np.float32)]).view(np.recarray)
+o.environment = np.array(list(zip(np.ones(N)*sea_floor_depth, np.zeros(N))),
+                dtype=[('sea_floor_depth_below_sea_level', np.float32),
+                       ('sea_surface_height', np.float32)]).view(np.recarray)
 o.environment_profiles = {
         'z': z,
         'ocean_vertical_diffusivity':

diff --git a/_downloads/a39ec6912b86ec0c8b4a42df10fc243c/example_vertical_mixing.ipynb b/_downloads/a39ec6912b86ec0c8b4a42df10fc243c/example_vertical_mixing.ipynb
@@ -51,7 +51,7 @@
       },
       "outputs": [],
       "source": [
-        "time = datetime(2020, 1, 1, 0)\no = OceanDrift(loglevel=20)\no.set_config('drift:vertical_mixing', True)\no.set_config('vertical_mixing:diffusivitymodel', 'environment')\no.set_config('vertical_mixing:timestep', timestep_seconds)\no.set_config('environment:fallback:land_binary_mask', 0)\no.seed_elements(lon=4, lat=60, z=seed_depth, time=time, number=N, terminal_velocity=terminal_velocity)\no.time = time\no.time_step = timedelta(hours=hours)\no.release_elements()\no.environment = np.array(np.ones(N)*sea_floor_depth,\n                dtype=[('sea_floor_depth_below_sea_level', np.float32)]).view(np.recarray)\no.environment_profiles = {\n        'z': z,\n        'ocean_vertical_diffusivity':\n         np.tile(diffusivity, (N, 1)).T}"
+        "time = datetime(2020, 1, 1, 0)\no = OceanDrift(loglevel=20)\no.set_config('drift:vertical_mixing', True)\no.set_config('vertical_mixing:diffusivitymodel', 'environment')\no.set_config('vertical_mixing:timestep', timestep_seconds)\no.set_config('environment:fallback:land_binary_mask', 0)\no.seed_elements(lon=4, lat=60, z=seed_depth, time=time, number=N, terminal_velocity=terminal_velocity)\no.time = time\no.time_step = timedelta(hours=hours)\no.release_elements()\no.environment = np.array(list(zip(np.ones(N)*sea_floor_depth, np.zeros(N))),\n                dtype=[('sea_floor_depth_below_sea_level', np.float32),\n                       ('sea_surface_height', np.float32)]).view(np.recarray)\no.environment_profiles = {\n        'z': z,\n        'ocean_vertical_diffusivity':\n         np.tile(diffusivity, (N, 1)).T}"
       ]
     },
     {

diff --git a/_downloads/fcaddee3a42ae2e2c41e00ae08d70347/gallery_jupyter.zip b/_downloads/fcaddee3a42ae2e2c41e00ae08d70347/gallery_jupyter.zip
diff --git a/_images/example_2d_0.gif b/_images/example_2d_0.gif
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diff --git a/_images/sphx_glr_example_2d_001.png b/_images/sphx_glr_example_2d_001.png
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diff --git a/_images/sphx_glr_example_advection_schemes_eddy_thumb.png b/_images/sphx_glr_example_advection_schemes_eddy_thumb.png
diff --git a/_images/sphx_glr_example_biodegradation_001.png b/_images/sphx_glr_example_biodegradation_001.png
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diff --git a/_images/sphx_glr_example_chemicaldrift_thumb.png b/_images/sphx_glr_example_chemicaldrift_thumb.png
diff --git a/_images/sphx_glr_example_coastline_options_001.png b/_images/sphx_glr_example_coastline_options_001.png
diff --git a/_images/sphx_glr_example_coastline_options_thumb.png b/_images/sphx_glr_example_coastline_options_thumb.png
diff --git a/_images/sphx_glr_example_codegg_001.png b/_images/sphx_glr_example_codegg_001.png
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diff --git a/_images/sphx_glr_example_cone_thumb.png b/_images/sphx_glr_example_cone_thumb.png
diff --git a/_images/sphx_glr_example_depth_001.png b/_images/sphx_glr_example_depth_001.png
diff --git a/_images/sphx_glr_example_depth_thumb.png b/_images/sphx_glr_example_depth_thumb.png
diff --git a/_images/sphx_glr_example_ensemble_001.png b/_images/sphx_glr_example_ensemble_001.png
diff --git a/_images/sphx_glr_example_ensemble_thumb.png b/_images/sphx_glr_example_ensemble_thumb.png
diff --git a/_images/sphx_glr_example_entrainment_rate_oil_types_001.png b/_images/sphx_glr_example_entrainment_rate_oil_types_001.png
diff --git a/_images/sphx_glr_example_entrainment_rate_oil_types_002.png b/_images/sphx_glr_example_entrainment_rate_oil_types_002.png
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diff --git a/_images/sphx_glr_example_oilspill_seafloor_biodegradation_001.png b/_images/sphx_glr_example_oilspill_seafloor_biodegradation_001.png
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diff --git a/_images/sphx_glr_example_roms_native_001.png b/_images/sphx_glr_example_roms_native_001.png
diff --git a/_images/sphx_glr_example_roms_native_thumb.png b/_images/sphx_glr_example_roms_native_thumb.png
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diff --git a/_images/sphx_glr_example_sediments_resuspension_001.png b/_images/sphx_glr_example_sediments_resuspension_001.png
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diff --git a/_images/sphx_glr_example_sediments_thumb.png b/_images/sphx_glr_example_sediments_thumb.png
diff --git a/_images/sphx_glr_example_seed_from_shapefile_001.png b/_images/sphx_glr_example_seed_from_shapefile_001.png
diff --git a/_images/sphx_glr_example_seed_from_shapefile_thumb.png b/_images/sphx_glr_example_seed_from_shapefile_thumb.png
diff --git a/_images/sphx_glr_example_shipdrift_001.png b/_images/sphx_glr_example_shipdrift_001.png
diff --git a/_images/sphx_glr_example_shipdrift_leeway_001.png b/_images/sphx_glr_example_shipdrift_leeway_001.png
diff --git a/_images/sphx_glr_example_shipdrift_leeway_thumb.png b/_images/sphx_glr_example_shipdrift_leeway_thumb.png
diff --git a/_images/sphx_glr_example_shipdrift_thumb.png b/_images/sphx_glr_example_shipdrift_thumb.png
diff --git a/_modules/opendrift/readers/reader_ROMS_native.html b/_modules/opendrift/readers/reader_ROMS_native.html
@@ -587,7 +587,8 @@ <h1>Source code for opendrift.readers.reader_ROMS_native</h1><div class="highlig
             <span class="c1"># Transform z_rho to match convention of z.</span>
             <span class="n">z_rho</span> <span class="o">-=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">zeta</span><span class="p">)[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span>
 
-            <span class="k">assert</span> <span class="p">(</span><span class="n">z_rho</span> <span class="o">&lt;=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">()</span>
+            <span class="k">if</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="n">z_rho</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
+                <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s1">&#39;z_rho is positive, but should be negative or 0.&#39;</span><span class="p">)</span>
 
             <span class="c1"># Element indices must be relative to extracted subset</span>
             <span class="n">indx_el</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">indx_el</span> <span class="o">-</span> <span class="n">indx</span><span class="o">.</span><span class="n">min</span><span class="p">(),</span> <span class="mi">0</span><span class="p">,</span> <span class="n">z_rho</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>