.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/example_vertical_mixing.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_gallery_example_vertical_mixing.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_gallery_example_vertical_mixing.py:


Vertical mixing
===============

.. GENERATED FROM PYTHON SOURCE LINES 6-11

.. code-block:: Python


    import numpy as np
    from datetime import datetime, timedelta
    from opendrift.models.oceandrift import OceanDrift








.. GENERATED FROM PYTHON SOURCE LINES 12-13

Configuration. Edit this section to see the differences.

.. GENERATED FROM PYTHON SOURCE LINES 13-29

.. code-block:: Python

    N = 10000  # Number of particles
    seed_depth = -10 # meters
    hours = 2  # Number of hours to mix particles
    sea_floor_depth = 100  # m
    timestep_seconds = 60  # Timestep for vertical mixing

    terminal_velocity = 0  # Neutral particles
    #terminal_velocity = 0.005  # Rising particles
    #terminal_velocity = -0.005  # Sinking particles

    # Profile of diffusivities
    z = np.arange(0, -40, -1)

    diffusivity = np.ones(z.shape)*.01  # Constant diffusivity
    diffusivity[z<-20] = 0.001  # uncomment to reduce mixing below 20m








.. GENERATED FROM PYTHON SOURCE LINES 30-31

Preparing mixing timestep

.. GENERATED FROM PYTHON SOURCE LINES 31-50

.. code-block:: Python

    time = datetime(2020, 1, 1, 0)
    o = OceanDrift(loglevel=20)
    o.set_config('drift:vertical_mixing', True)
    o.set_config('vertical_mixing:diffusivitymodel', 'environment')
    o.set_config('vertical_mixing:timestep', timestep_seconds)
    o.set_config('environment:fallback:land_binary_mask', 0)
    o.seed_elements(lon=4, lat=60, z=seed_depth, time=time, number=N, terminal_velocity=terminal_velocity)
    o.time = time
    o.time_step = timedelta(hours=hours)
    o.release_elements()
    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.ocean_mixed_layer_thickness = np.ones(N)*50
    o.environment_profiles = {
            'z': z,
            'ocean_vertical_diffusivity':
             np.tile(diffusivity, (N, 1)).T}





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    17:14:12 INFO    opendrift:513: OpenDriftSimulation initialised (version 1.14.2 / v1.14.2-88-gf09b7bd)
    17:14:12 INFO    opendrift.models.basemodel.environment:206: Adding a global landmask from GSHHG
    17:14:16 INFO    opendrift.models.basemodel.environment:229: Fallback values will be used for the following variables which have no readers: 
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    x_sea_water_velocity: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    y_sea_water_velocity: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    sea_surface_height: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    x_wind: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    y_wind: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    upward_sea_water_velocity: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    ocean_vertical_diffusivity: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    sea_surface_wave_significant_height: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    sea_surface_wave_stokes_drift_x_velocity: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    sea_surface_wave_stokes_drift_y_velocity: 0.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    ocean_mixed_layer_thickness: 50.000000
    17:14:16 INFO    opendrift.models.basemodel.environment:232:    sea_floor_depth_below_sea_level: 10000.000000




.. GENERATED FROM PYTHON SOURCE LINES 51-52

Calculate vertical mixing, and return particle depths at all positions

.. GENERATED FROM PYTHON SOURCE LINES 52-58

.. code-block:: Python

    print('Calculating...')
    depths = o.vertical_mixing(store_depths=True)

    print('Making animation...')
    o.animate_vertical_distribution(depths=depths)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Calculating...
    Making animation...
    17:14:17 INFO    opendrift:4553: Saving animation to /root/project/docs/source/gallery/animations/example_vertical_mixing_0.gif...
    17:14:38 INFO    opendrift.models.oceandrift:633: Time to make animation: 0:00:21.678440




.. GENERATED FROM PYTHON SOURCE LINES 59-60

.. image:: /gallery/animations/example_vertical_mixing_0.gif


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 31.324 seconds)


.. _sphx_glr_download_gallery_example_vertical_mixing.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: example_vertical_mixing.ipynb <example_vertical_mixing.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: example_vertical_mixing.py <example_vertical_mixing.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: example_vertical_mixing.zip <example_vertical_mixing.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_