{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Radionuclides\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "from opendrift.readers import reader_netCDF_CF_generic\nfrom opendrift.models.radionuclides import RadionuclideDrift\nfrom datetime import timedelta, datetime\nimport numpy as np\n\n\no = RadionuclideDrift(loglevel=0, seed=0)  # Set loglevel to 0 for debug information\n\n# Norkyst\n#reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '/14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')\nreader_norkyst = reader_netCDF_CF_generic.Reader('https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')\n\no.add_reader([reader_norkyst])\n\n\n\n# Adjusting some configuration\no.set_config('drift:vertical_mixing', True)\n#o.set_config('vertical_mixing:diffusivitymodel','constant')  # include settling without vertical turbulent mixing\no.set_config('vertical_mixing:diffusivitymodel','environment')  # apply vertical diffusivity from ocean model\n# Vertical mixing requires fast time step\no.set_config('vertical_mixing:timestep', 600.) # seconds\no.set_config('drift:horizontal_diffusivity', 10)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "o.set_config('radionuclide:particle_diameter',5.e-6)  # m\n\no.set_config('radionuclide:sediment:resuspension_depth',2.)\no.set_config('radionuclide:sediment:resuspension_depth_uncert',0.1)\no.set_config('radionuclide:sediment:resuspension_critvel',0.15)\n\n\n#\no.set_config('radionuclide:isotope', '137Cs')\no.set_config('radionuclide:specie_setup','LMM + Rev')\n\n# By default, radionuclides do not strand towards coastline\no.set_config('general:coastline_action', 'previous')\no.set_config('general:seafloor_action','lift_to_seafloor')\n\n\no.set_config('seed:LMM_fraction',.45)\no.set_config('seed:particle_fraction',.55)\n\no.list_configspec()\n\n\n\n# SEEDING\n\ntd=datetime.today()\ntime = datetime(td.year, td.month, td.day, 0)\n\nlatseed= 60.0;   lonseed= 4.5 \n\nntraj=5000\niniz=np.random.rand(ntraj) * -10. # seeding the radionuclides in the upper 10m\n\no.seed_elements(lonseed, latseed, z=iniz, radius=1000,number=ntraj,\n                time=time, \n                )"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Running model\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "o.run(steps=24*2, time_step=1800, time_step_output=3600)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Print and plot results\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "print(o)\nprint('Final speciation:')\nfor isp,sp in enumerate(o.name_species):\n    print ('{:32}: {:>6}'.format(sp,sum(o.elements.specie==isp)))\n\nprint('Number of transformations:')\nfor isp in range(o.nspecies):\n    print('{}'.format(['{:>9}'.format(np.int32(item)) for item in o.ntransformations[isp,:]]) )\n\no.animation(color='specie',\n            vmin=0,vmax=o.nspecies-1,\n            colorbar=False,\n            legend=[o.specie_num2name(i) for i in range(o.nspecies)],\n            fast = True\n            )"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "<img src=\"file://gallery/animations/example_radionuclides_0.gif\">\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "o.plot_vertical_distribution()\n#o.plot_property('specie')\no.animation_profile(color='specie',\n            vmin=0,vmax=o.nspecies-1,\n            legend=[o.specie_num2name(i) for i in range(o.nspecies)],\n            legend_loc =3,\n#            markersize=10\n            )"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "<img src=\"file://gallery/animations/example_radionuclides_1.gif\">\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "o.plot(linecolor='specie',vmin=0,vmax=o.nspecies-1,fast=True,)\n\n\n\n# # Postprocessing: write to concentration netcdf file"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        ".. code:\n\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "o.write_netcdf_radionuclide_density_map('radio_conc.nc', pixelsize_m=500.,\n                                      zlevels=[-2.],\n                                      activity_unit='Bq',\n                                      horizontal_smoothing=True,\n                                      smoothing_cells=1,\n                                      time_avg_conc=True,\n                                      deltat=2., # hours\n#                                      llcrnrlon=4.4, llcrnrlat=59.9,\n#                                      urcrnrlon=4.8, urcrnrlat=60.2,\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"
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  "nbformat": 4,
  "nbformat_minor": 0
}