{
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    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Vertical mixing\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import numpy as np\nfrom datetime import datetime, timedelta\nfrom opendrift.models.oceandrift import OceanDrift"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Configuration. Edit this section to see the differences.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "N = 10000  # Number of particles\nseed_depth = -10 # meters\nhours = 2  # Number of hours to mix particles\nsea_floor_depth = 100  # m\ntimestep_seconds = 60  # Timestep for vertical mixing\n\nterminal_velocity = 0  # Neutral particles\n#terminal_velocity = 0.005  # Rising particles\n#terminal_velocity = -0.005  # Sinking particles\n\n# Profile of diffusivities\nz = np.arange(0, -40, -1)\n\ndiffusivity = np.ones(z.shape)*.01  # Constant diffusivity\ndiffusivity[z<-20] = 0.001  # uncomment to reduce mixing below 20m"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Preparing mixing timestep\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "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(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.ocean_mixed_layer_thickness = np.ones(N)*50\no.environment_profiles = {\n        'z': z,\n        'ocean_vertical_diffusivity':\n         np.tile(diffusivity, (N, 1)).T}"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Calculate vertical mixing, and return particle depths at all positions\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "print('Calculating...')\ndepths = o.vertical_mixing(store_depths=True)\n\nprint('Making animation...')\no.animate_vertical_distribution(depths=depths)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "<img src=\"file://gallery/animations/example_vertical_mixing_0.gif\">\n\n"
      ]
    }
  ],
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      "display_name": "Python 3",
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      "file_extension": ".py",
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      "nbconvert_exporter": "python",
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