[skip ci] Updates

.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: e36d92882cbff06d990f33b55f556eca
+config: 5d9e0e9a7bc6ca85ecd21cda503e4d4b
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_downloads/db165b7788ff8b7c69580e0e56514a8c/example_biodegradation.ipynb

@@ -0,0 +1,140 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Biodegradation of oil\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "import numpy as np\nfrom datetime import datetime, timedelta\nfrom opendrift.readers import reader_netCDF_CF_generic\nfrom opendrift.models.openoil import OpenOil\n\no = OpenOil(loglevel=0)  # Set loglevel to 0 for debug information\ntime = datetime.now()\n\n# No motion is needed for this test\no.set_config('environment:constant', {k: 0 for k in\n             ['x_wind', 'y_wind', 'x_sea_water_velocity', 'y_sea_water_velocity']})\no.set_config('drift', {'current_uncertainty': 0, 'wind_uncertainty': 0})"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Seeding some particles\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "o.set_config('drift:vertical_mixing', False)  # Keeping oil at fixed depths\no.set_config('processes:biodegradation', True)\no.set_config('biodegradation:method', 'decay_rate')"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Fast decay for droplets, and slow decay for slick \n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "decay = {'biodegradation_decay_rate_slick': np.log(2)/timedelta(days=100).total_seconds(),\n         'biodegradation_decay_rate_droplet': np.log(2)/timedelta(days=3).total_seconds(),\n         'oil_type': 'GENERIC MEDIUM CRUDE'}"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Seed 5000 oil elements at surface, and 5000 elements at 100m depth\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "o.seed_elements(lon=4, lat=60.0, z=0, number=5000, time=datetime.now(), **decay)\no.seed_elements(lon=4, lat=60.0, z=-100, number=5000, time=datetime.now(), **decay)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Running model\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "o.run(duration=timedelta(hours=24), time_step=900)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Print and plot results\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "o.plot_oil_budget(show_watercontent_and_viscosity=False, show_wind_and_current=False)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "<img src=\"file://gallery/animations/example_biodegradation_0.gif\">\n\n"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.11.6"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

_downloads/db8475e1b1e79daba41dce5a4853bec8/example_biodegradation.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+"""
+Biodegradation of oil
+======================
+"""
+
+import numpy as np
+from datetime import datetime, timedelta
+from opendrift.readers import reader_netCDF_CF_generic
+from opendrift.models.openoil import OpenOil
+
+o = OpenOil(loglevel=0)  # Set loglevel to 0 for debug information
+time = datetime.now()
+
+# No motion is needed for this test
+o.set_config('environment:constant', {k: 0 for k in
+             ['x_wind', 'y_wind', 'x_sea_water_velocity', 'y_sea_water_velocity']})
+o.set_config('drift', {'current_uncertainty': 0, 'wind_uncertainty': 0})
+
+#%%
+# Seeding some particles
+o.set_config('drift:vertical_mixing', False)  # Keeping oil at fixed depths
+o.set_config('processes:biodegradation', True)
+o.set_config('biodegradation:method', 'decay_rate')
+
+#%%
+# Fast decay for droplets, and slow decay for slick 
+decay = {'biodegradation_decay_rate_slick': np.log(2)/timedelta(days=100).total_seconds(),
+         'biodegradation_decay_rate_droplet': np.log(2)/timedelta(days=3).total_seconds(),
+         'oil_type': 'GENERIC MEDIUM CRUDE'}
+
+#%%
+# Seed 5000 oil elements at surface, and 5000 elements at 100m depth
+o.seed_elements(lon=4, lat=60.0, z=0, number=5000, time=datetime.now(), **decay)
+o.seed_elements(lon=4, lat=60.0, z=-100, number=5000, time=datetime.now(), **decay)
+
+#%%
+# Running model
+o.run(duration=timedelta(hours=24), time_step=900) 
+
+#%%
+# Print and plot results
+o.plot_oil_budget(show_watercontent_and_viscosity=False, show_wind_and_current=False)
+
+#%%
+# .. image:: /gallery/animations/example_biodegradation_0.gif