{
  "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, 'horizontal_diffusivity': 10})"
      ]
    },
    {
      "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', True)\no.set_config('processes:biodegradation', True)\no.set_config('biodegradation:method', 'half_time')"
      ]
    },
    {
      "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": [
        "kwargs = {'biodegradation_half_time_slick': 3, # days\n          'biodegradation_half_time_droplet': 1, # days\n          'oil_type': 'GENERIC MEDIUM CRUDE', 'm3_per_hour': .5, 'diameter': 1e-5}  # small droplets"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Seed 500 oil elements at surface, and 500 elements at 50m 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=500, time=datetime.now(), **kwargs)\no.seed_elements(lon=4, lat=60.0, z=-50, number=500, time=datetime.now(), **kwargs)"
      ]
    },
    {
      "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=72), time_step=3600, outfile='oil.nc')"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "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": [
        "Custom oil budget plot\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "b = o.get_oil_budget()\nimport matplotlib.pyplot as plt\ntime, time_relative = o.get_time_array()\ntime = np.array([t.total_seconds() / 3600. for t in time_relative])\nfig, ax = plt.subplots()\nax.plot(time, b['mass_submerged'], label='Submerged oil mass')\nax.plot(time, b['mass_surface'], label='Surface oil mass')\nax.plot(time, b['mass_biodegraded'], label='Biodegraded oil mass')\nax.set_title(f'{o.get_oil_name()},  {b[\"oil_density\"].max():.2f} kg/m3')\nplt.legend()\nplt.xlabel('Time [hours]')\nplt.ylabel('Mass oil [kg]')\nplt.show()"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Animation of vertical behaviour\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "o.animation_profile(markersize='mass_oil', markersize_scaling=50, color='z', alpha=.5)"
      ]
    },
    {
      "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
}