.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/example_long_radionuclides.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_long_radionuclides.py>`
        to download the full example code.

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

.. _sphx_glr_gallery_example_long_radionuclides.py:


Radionuclides
=============

.. GENERATED FROM PYTHON SOURCE LINES 6-31

.. code-block:: Python


    from opendrift.readers import reader_netCDF_CF_generic
    from opendrift.models.radionuclides import RadionuclideDrift
    from datetime import timedelta, datetime
    import numpy as np


    o = RadionuclideDrift(loglevel=0, seed=0)  # Set loglevel to 0 for debug information

    # Norkyst
    #reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '/14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
    reader_norkyst = reader_netCDF_CF_generic.Reader('https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')

    o.add_reader([reader_norkyst])



    # Adjusting some configuration
    o.set_config('drift:vertical_mixing', True)
    #o.set_config('vertical_mixing:diffusivitymodel','constant')  # include settling without vertical turbulent mixing
    o.set_config('vertical_mixing:diffusivitymodel','environment')  # apply vertical diffusivity from ocean model
    # Vertical mixing requires fast time step
    o.set_config('vertical_mixing:timestep', 600.) # seconds
    o.set_config('drift:horizontal_diffusivity', 10)


.. GENERATED FROM PYTHON SOURCE LINES 32-70

.. code-block:: Python

    o.set_config('radionuclide:particle_diameter',5.e-6)  # m

    o.set_config('radionuclide:sediment:resuspension_depth',2.)
    o.set_config('radionuclide:sediment:resuspension_depth_uncert',0.1)
    o.set_config('radionuclide:sediment:resuspension_critvel',0.15)


    #
    o.set_config('radionuclide:isotope', '137Cs')
    o.set_config('radionuclide:specie_setup','LMM + Rev')

    # By default, radionuclides do not strand towards coastline
    o.set_config('general:coastline_action', 'previous')
    o.set_config('general:seafloor_action','lift_to_seafloor')


    o.set_config('seed:LMM_fraction',.45)
    o.set_config('seed:particle_fraction',.55)

    o.list_configspec()



    # SEEDING

    td=datetime.today()
    time = datetime(td.year, td.month, td.day, 0)

    latseed= 60.0;   lonseed= 4.5 

    ntraj=5000
    iniz=np.random.rand(ntraj) * -10. # seeding the radionuclides in the upper 10m

    o.seed_elements(lonseed, latseed, z=iniz, radius=1000,number=ntraj,
                    time=time, 
                    )



.. GENERATED FROM PYTHON SOURCE LINES 71-72

Running model

.. GENERATED FROM PYTHON SOURCE LINES 72-75

.. code-block:: Python

    o.run(steps=24*2, time_step=1800, time_step_output=3600)



.. GENERATED FROM PYTHON SOURCE LINES 76-77

Print and plot results

.. GENERATED FROM PYTHON SOURCE LINES 77-92

.. code-block:: Python

    print(o)
    print('Final speciation:')
    for isp,sp in enumerate(o.name_species):
        print ('{:32}: {:>6}'.format(sp,sum(o.elements.specie==isp)))

    print('Number of transformations:')
    for isp in range(o.nspecies):
        print('{}'.format(['{:>9}'.format(np.int32(item)) for item in o.ntransformations[isp,:]]) )

    o.animation(color='specie',
                vmin=0,vmax=o.nspecies-1,
                colorbar=False,
                legend=[o.specie_num2name(i) for i in range(o.nspecies)],
                fast = True
                )

.. GENERATED FROM PYTHON SOURCE LINES 93-94

.. image:: /gallery/animations/example_radionuclides_0.gif

.. GENERATED FROM PYTHON SOURCE LINES 94-103

.. code-block:: Python


    o.plot_vertical_distribution()
    #o.plot_property('specie')
    o.animation_profile(color='specie',
                vmin=0,vmax=o.nspecies-1,
                legend=[o.specie_num2name(i) for i in range(o.nspecies)],
                legend_loc =3,
    #            markersize=10
                )

.. GENERATED FROM PYTHON SOURCE LINES 104-105

.. image:: /gallery/animations/example_radionuclides_1.gif

.. GENERATED FROM PYTHON SOURCE LINES 105-112

.. code-block:: Python


    o.plot(linecolor='specie',vmin=0,vmax=o.nspecies-1,fast=True,)



    # # Postprocessing: write to concentration netcdf file


.. GENERATED FROM PYTHON SOURCE LINES 113-115

.. code:


.. GENERATED FROM PYTHON SOURCE LINES 116-129

.. code-block:: Python

    o.write_netcdf_radionuclide_density_map('radio_conc.nc', pixelsize_m=500.,
                                          zlevels=[-2.],
                                          activity_unit='Bq',
                                          horizontal_smoothing=True,
                                          smoothing_cells=1,
                                          time_avg_conc=True,
                                          deltat=2., # hours
    #                                      llcrnrlon=4.4, llcrnrlat=59.9,
    #                                      urcrnrlon=4.8, urcrnrlat=60.2,
                                         )





.. _sphx_glr_download_gallery_example_long_radionuclides.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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