Adding example_Italy_coastline

Author: erikvansebille

docs/examples/default_settings.json

@@ -2,16 +2,16 @@
     "use_3D": true,
     "allow_time_extrapolation": false,
     "verbose_delete": false,
-    "mixing_f": false,
-    "biofouling_f": false,
-    "stokes_f": false,
-    "wind_f": false,
+    "use_mixing": false,
+    "use_biofouling": false,
+    "use_stokes": false,
+    "use_wind": false,
     "ocean": {
         "modelname": "NEMO0083",
-        "directory": "data/input_data/MOi/",
+        "directory": "/storage/shared/oceanparcels/input_data/MOi/",
         "filename_style": "psy4v3r1/psy4v3r1-daily_",
-        "ocean_mesh": "domain_ORCA0083-N006/coordinates.nc",
-        "bathymetry_mesh": "domain_ORCA0083-N006/bathymetry_ORCA12_V3.3.nc",
+        "ocean_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_hgr.nc",
+        "bathymetry_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_zgr.nc",
         "variables": {
             "U": "vozocrtx",
             "V": "vomecrty",
@@ -53,7 +53,7 @@
         },
         "indices": {},
         "bathymetry_variables": {
-            "bathymetry": "Bathymetry"
+            "bathymetry": "mbathy"
         },
         "bathymetry_dimensions": {
             "lon": "nav_lon",
@@ -70,7 +70,7 @@
         }
     },
     "bgc": {
-        "directory": "data/input_data/MOi/",
+        "directory": "/storage/shared/oceanparcels/input_data/MOi/",
         "filename_style": "biomer4v2r1/biomer4v2r1-weekly_",
         "bgc_mesh": "domain_ORCA025-N006/mesh_hgr_PSY4V3_deg.nc",
         "variables": {
@@ -113,7 +113,7 @@
         }
     },
     "stokes": {
-        "directory": "data/input_data/ERA5/waves/",
+        "directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/waves/",
         "filename_style": "ERA5_global_waves_monthly_",
         "variables": {
             "Stokes_U": "ust",
@@ -128,7 +128,7 @@
         "indices": {}
     },
     "wind": {
-        "directory": "data/input_data/ERA5/wind/",
+        "directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/wind/",
         "filename_style": "ERA5_global_wind_monthly_",
         "variables": {
             "Wind_U": "u10",
@@ -142,7 +142,7 @@
         "indices": {}
     },
     "unbeaching": {
-        "directory": "data/output_data/masks/",
+        "directory": "input_data/NEMO0083/",
         "filename": "land_current_NEMO0083.nc",
         "variables": {
             "unbeach_U": "land_current_u",
@@ -160,9 +160,9 @@
         "dt_timestep": null
     },
     "release_maps": {
-        "coastal": "data/release/generated_files/coastal_population_MPW_NEMO0083.csv",
-        "rivers": "data/release/generated_files/river_emissions_NEMO0083.csv",
-        "fisheries": "data/release/generated_files/agg_data_fisheries_info_NEMO0083.csv",
+        "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.csv",
         "global_concentrations": null
     }
 }

docs/examples/example_Italy_coast.ipynb

@@ -182,7 +182,7 @@ def create_fieldset(settings):
 
     # Apply unbeaching currents when Stokes/Wind can push particles into land cells
     if fieldset.use_stokes or fieldset.use_wind > 0:
-        unbeachfiles = settings['unbeaching']['filename']
+        unbeachfiles = os.path.join(settings['unbeaching']['directory'], settings['unbeaching']['filename'])
         filenames_unbeach = {'unbeach_U': unbeachfiles,
                              'unbeach_V': unbeachfiles}