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Adding a 'makeyourown' kernel tutorial, and a 'varying biofouling parameters' tutorial. #32

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Merged
michaeldenes merged 10 commits into from
May 28, 2024
Merged

Adding a 'makeyourown' kernel tutorial, and a 'varying biofouling parameters' tutorial. #32

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a819fcb
Starting to develop a 'make your own kernel' tutorial
michaeldenes May 23, 2024
6b48123
Finalised 'make your own kernel' tutorial
michaeldenes May 24, 2024
6b1acc8
changing name of settings file
michaeldenes May 24, 2024
9b084b8
Adding a biofouling sensitivity analysis tutorial
michaeldenes May 24, 2024
e183fc3
Adding two tutorials to readthedocs
michaeldenes May 24, 2024
48fd7f6
Updates to fisheries example - shorter title and removing minor imports
michaeldenes May 27, 2024
b77f7e5
Renaming the 'add your own kernel' tutorial, removing unnecessary imp…
michaeldenes May 27, 2024
b00be0b
Merge branch 'main' into add_makeyourown_kernel_tutorial
michaeldenes May 28, 2024
de6168d
Changing headings in ipynb for better readability on readthedocs
michaeldenes May 28, 2024
033b97a
Changing title of initialisation maps tutorial to be clearer.
michaeldenes May 28, 2024
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3 changes: 3 additions & 0 deletions docs/examples.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,7 @@ PlasticParcels has a few example notebooks, see below.

examples/example_Italy_coast.ipynb
examples/example_Greece_coast.ipynb
examples/example_Croatian_fisheries.ipynb
examples/example_add_your_own_kernel.ipynb
examples/example_initialisation_maps.ipynb

448 changes: 448 additions & 0 deletions docs/examples/example_Croatian_fisheries.ipynb
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167 changes: 167 additions & 0 deletions docs/examples/example_Croatian_fisheries_settings.json
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@@ -0,0 +1,167 @@
{
"use_3D": true,
"allow_time_extrapolation": false,
"verbose_delete": false,
"use_mixing": false,
"use_biofouling": false,
"use_stokes": false,
"use_wind": false,
"ocean": {
"modelname": "NEMO0083",
"directory": "/storage/shared/oceanparcels/input_data/MOi/",
"filename_style": "psy4v3r1/psy4v3r1-daily_",
"ocean_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_hgr.nc",
"bathymetry_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_zgr.nc",
"variables": {
"U": "vozocrtx",
"V": "vomecrty",
"W": "vovecrtz",
"conservative_temperature": "votemper",
"absolute_salinity": "vosaline"
},
"dimensions": {
"U": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
},
"V": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
},
"W": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
},
"conservative_temperature": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
},
"absolute_salinity": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
}
},
"indices": {},
"bathymetry_variables": {
"bathymetry": "mbathy"
},
"bathymetry_dimensions": {
"lon": "nav_lon",
"lat": "nav_lat"
},
"mixing_variables": {
"mixing_kz": "votkeavt"
},
"mixing_dimensions": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
}
},
"bgc": {
"directory": "/storage/shared/oceanparcels/input_data/MOi/",
"filename_style": "biomer4v2r1/biomer4v2r1-weekly_",
"bgc_mesh": "domain_ORCA025-N006/mesh_hgr_PSY4V3_deg.nc",
"variables": {
"pp_phyto": "nppv",
"bio_nanophy": "phy",
"bio_diatom": "phy2"
},
"dimensions": {
"pp_phyto": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
},
"bio_nanophy": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
},
"bio_diatom": {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter"
}
},
"indices": {},
"constants": {
"biofilm_density": 1388.0,
"algae_cell_volume": 2e-16,
"K": 1.3805834190672156e-23,
"R20": 1.1574074074074074e-06,
"Q10": 2.13,
"Gamma": 2.0,
"carbon_molecular_weight": 12.0,
"collision_probability": 1.0,
"algae_mortality_rate": 1.0,
"algae_respiration_f": 1.0
}
},
"stokes": {
"directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/waves/",
"filename_style": "ERA5_global_waves_monthly_",
"variables": {
"Stokes_U": "ust",
"Stokes_V": "vst",
"wave_Tp": "pp1d"
},
"dimensions": {
"lat": "latitude",
"lon": "longitude",
"time": "time"
},
"indices": {}
},
"wind": {
"directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/wind/",
"filename_style": "ERA5_global_wind_monthly_",
"variables": {
"Wind_U": "u10",
"Wind_V": "v10"
},
"dimensions": {
"lat": "latitude",
"lon": "longitude",
"time": "time"
},
"indices": {}
},
"unbeaching": {
"filename": "input_data/NEMO0083/land_current_NEMO0083.nc",
"variables": {
"unbeach_U": "land_current_u",
"unbeach_V": "land_current_v"
},
"dimensions": {
"lat": "lat",
"lon": "lon"
}
},
"simulation": {
"start_date": null,
"runtime": null,
"dt_write": null,
"dt_timestep": null
},
"release_maps": {
"coastal": "input_data/NEMO0083/coastal_population_MPW_NEMO0083.csv",
"rivers": "input_data/NEMO0083/river_emissions_NEMO0083.csv",
"fisheries": "input_data/NEMO0083/agg_data_fisheries_info_NEMO0083.csv",
"global_concentrations": "input_data/NEMO0083/global_concentrations_NEMO0083.csv"
}
}
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