Merge pull request #32 from OceanParcels/add_makeyourown_kernel_tutorial

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

Author: michaeldenes

docs/examples.rst

@@ -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
+

docs/examples/example_Croatian_fisheries.ipynb

@@ -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"
+    }
+}