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Updating Italy coast example settings to include global concentrations release map, and creating a Greek coastline global concentrations example
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‎docs/examples/example_Greece_coast.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# PlasticParcels Example\n",
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"## The pathways and fate of existing plastic pollution along Greek coastlines\n",
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"In this example, we will use `plasticparcels` to run a basic simulation of microplastic pollution along the Greek coastline."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Library imports\n",
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"from datetime import datetime, timedelta\n",
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"\n",
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"# Parcels and PlasticParcels imports\n",
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"import os\n",
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"os.chdir('../../')\n",
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"import plasticparcels as pp\n",
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"\n",
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"# Plotting imports\n",
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"import matplotlib.pyplot as plt\n",
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"import cartopy.crs as ccrs\n",
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"import xarray as xr"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Load the model settings\n",
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"settings_file = 'docs/examples/example_Greece_coast_settings.json'\n",
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"settings = pp.utils.load_settings(settings_file)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the simulation settings\n",
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"settings['simulation'] = {\n",
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" 'start_date': datetime.strptime('2019-01-10-00:00:00', '%Y-%m-%d-%H:%M:%S'), # Start date of simulation\n",
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" 'runtime': timedelta(days=30), # Runtime of simulation, use negative if releasing particles backwards in time\n",
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" 'dt_write': timedelta(hours=12), # Timestep of output\n",
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" 'dt_timestep': timedelta(minutes=20), # Timestep of advection\n",
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" }\n",
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"\n",
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"# Overwrite some settings\n",
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"settings['use_3D'] = False\n",
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"settings['use_biofouling'] = False\n",
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"settings['use_stokes'] = True\n",
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"settings['use_wind'] = True\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the particle release settings\n",
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"settings['release'] = {\n",
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" 'initialisation_type': 'global_concentrations',\n",
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" 'concentration_type': 'Beach',\n",
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" 'country': 'Greece',\n",
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"}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the plastic type settings\n",
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"settings['plastictype'] = {\n",
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" 'wind_coefficient' : 0.01, # Percentage of wind to apply to particles\n",
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" 'plastic_diameter' : 0.001, # Plastic particle diameter (m)\n",
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" 'plastic_density' : 1030., # Plastic particle density (kg/m^3)\n",
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"}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"settings['ocean']['indices'] = {'lon':range(3300, 4000), 'lat':range(1850, 2400)}#, 'depth':range(0,2)}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Download the mask and release data\n",
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"#settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the fieldset\n",
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"fieldset = pp.constructors.create_fieldset(settings)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the particleset\n",
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"pset = pp.constructors.create_particleset_from_map(fieldset, settings)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the applicable kernels to the plastic particles\n",
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"kernels = pp.constructors.create_kernel(fieldset)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Define the runtime, the timestepping, and the output frequency of the simulation from the settings\n",
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"runtime = settings['simulation']['runtime']\n",
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"dt_timestep = settings['simulation']['dt_timestep']\n",
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"dt_write = settings['simulation']['dt_write']"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Create the particle file where output will be stored\n",
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"pfile = pp.ParticleFile('example_Italy_coast.zarr', pset, settings=settings, outputdt=dt_write)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Execute the simulation\n",
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"pset.execute(kernels, runtime=runtime, dt=dt_timestep, output_file=pfile)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Plot the trajectories\n",
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"ds = xr.open_zarr('example_Italy_coast.zarr')\n",
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"\n",
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"ax = plt.subplot(111, projection=ccrs.PlateCarree())\n",
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"ax.coastlines(zorder=20)\n",
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"ax.plot(ds['lon'].T, ds['lat'].T, transform=ccrs.PlateCarree())\n",
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"\n",
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"plt.show()"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "py3_parcels",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.4"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎docs/examples/example_Greece_coast_settings.json‎

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{
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"use_3D": true,
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"allow_time_extrapolation": false,
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"verbose_delete": false,
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"use_mixing": false,
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"use_biofouling": false,
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"use_stokes": false,
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"use_wind": false,
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"ocean": {
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"modelname": "NEMO0083",
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"directory": "/storage/shared/oceanparcels/input_data/MOi/",
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"filename_style": "psy4v3r1/psy4v3r1-daily_",
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"ocean_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_hgr.nc",
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"bathymetry_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_zgr.nc",
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"variables": {
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"U": "vozocrtx",
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"V": "vomecrty",
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"W": "vovecrtz",
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"conservative_temperature": "votemper",
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"absolute_salinity": "vosaline"
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},
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"dimensions": {
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"U": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"V": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"W": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"conservative_temperature": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"absolute_salinity": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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}
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},
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"indices": {},
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"bathymetry_variables": {
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"bathymetry": "mbathy"
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},
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"bathymetry_dimensions": {
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"lon": "nav_lon",
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"lat": "nav_lat"
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},
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"mixing_variables": {
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"mixing_kz": "votkeavt"
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},
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"mixing_dimensions": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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}
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},
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"bgc": {
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"directory": "/storage/shared/oceanparcels/input_data/MOi/",
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"filename_style": "biomer4v2r1/biomer4v2r1-weekly_",
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"bgc_mesh": "domain_ORCA025-N006/mesh_hgr_PSY4V3_deg.nc",
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"variables": {
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"pp_phyto": "nppv",
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"bio_nanophy": "phy",
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"bio_diatom": "phy2"
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},
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"dimensions": {
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"pp_phyto": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"bio_nanophy": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"bio_diatom": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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}
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},
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"indices": {},
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"constants": {
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"biofilm_density": 1388.0,
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"algae_cell_volume": 2e-16,
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"K": 1.3805834190672156e-23,
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"R20": 1.1574074074074074e-06,
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"Q10": 2.13,
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"Gamma": 2.0,
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"carbon_molecular_weight": 12.0,
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"collision_probability": 1.0,
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"algae_mortality_rate": 1.0,
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"algae_respiration_f": 1.0
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}
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},
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"stokes": {
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"directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/waves/",
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"filename_style": "ERA5_global_waves_monthly_",
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"variables": {
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"Stokes_U": "ust",
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"Stokes_V": "vst",
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"wave_Tp": "pp1d"
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},
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"dimensions": {
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"lat": "latitude",
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"lon": "longitude",
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"time": "time"
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},
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"indices": {}
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},
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"wind": {
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"directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/wind/",
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"filename_style": "ERA5_global_wind_monthly_",
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"variables": {
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"Wind_U": "u10",
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"Wind_V": "v10"
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},
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"dimensions": {
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"lat": "latitude",
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"lon": "longitude",
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"time": "time"
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},
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"indices": {}
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},
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"unbeaching": {
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"directory": "input_data/NEMO0083/",
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"filename": "land_current_NEMO0083.nc",
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"variables": {
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"unbeach_U": "land_current_u",
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"unbeach_V": "land_current_v"
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},
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"dimensions": {
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"lat": "lat",
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"lon": "lon"
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}
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},
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"simulation": {
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"start_date": null,
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"runtime": null,
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"dt_write": null,
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"dt_timestep": null
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},
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"release_maps": {
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"coastal": "input_data/NEMO0083/coastal_population_MPW_NEMO0083.csv",
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"rivers": "input_data/NEMO0083/river_emissions_NEMO0083.csv",
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"fisheries": "input_data/NEMO0083/agg_data_fisheries_info_NEMO0083.csv",
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"global_concentrations": "input_data/NEMO0083/global_concentrations_NEMO0083.csv"
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}
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}

‎docs/examples/example_Italy_coast_settings.json‎

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"release_maps": {
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"coastal": "input_data/NEMO0083/coastal_population_MPW_NEMO0083.csv",
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"rivers": "input_data/NEMO0083/river_emissions_NEMO0083.csv",
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"fisheries": "input_data/NEMO0083/agg_data_fisheries_info.csv",
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"global_concentrations": null
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"fisheries": "input_data/NEMO0083/agg_data_fisheries_info_NEMO0083.csv",
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"global_concentrations": "input_data/NEMO0083/global_concentrations_NEMO0083.csv"
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}
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}

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