Updates to google collab files

Author: michaeldenes

src/DRAKKAR workshop code/PlasticParcels/helper.py

@@ -3,6 +3,7 @@
 import xarray as xr
 
 
+import pandas as pd
 from parcels import FieldSet, Field, ParticleSet, JITParticle, Variable, AdvectionRK4, AdvectionRK4_3D
 from parcels.tools.converters import Geographic, GeographicPolar
 from datetime import datetime, timedelta
@@ -354,7 +355,63 @@ def create_particleset(fieldset, particle_settings):
                                     windage_coefficient=windage_coefficients
                                     )
     return pset
-        
+
+def create_particleset_from_file(fieldset, particle_settings):
+    """ Helper function to create a Parcels.ParicleSet
+
+    Parameters
+    ----------
+    model_settings :
+        A dictionary of model settings used to create the fieldset
+    particle_settings :
+        A dictionary of particle settings used to define some ....
+
+    Returns
+    -------
+    fieldset
+        A parcels.FieldSet object
+    """
+
+    # Load release type information
+    release_type = particle_settings['release_type']
+    if release_type == 'coastal':
+        release_file = './data/coastal_population_MPW_NEMO0083.csv'
+        release_quantity_name = 'MPW_Cell'
+    elif release_type == 'rivers':
+        release_file = './data/river_emissions_NEMO0083.csv'
+        release_quantity_name = 'Emissions'
+    elif release_type == 'fisheries':
+        release_file = './data/agg_data_fisheries_info.csv'
+        release_quantity_name = 'fishing_hours'
+
+    particle_locations = pd.read_csv(release_file)
+
+
+    # Select specific continent/region/subregion/country/economic status if applicable:
+    if 'continent' in particle_settings.keys():
+        particle_locations = particle_locations[particle_locations['Continent'] == particle_settings['continent']]
+    if 'region' in particle_settings.keys():
+        particle_locations = particle_locations[particle_locations['Region'] == particle_settings['region']]
+    if 'subregion' in particle_settings.keys():
+        particle_locations = particle_locations[particle_locations['Subregion'] == particle_settings['subregion']]
+    if 'country' in particle_settings.keys():
+        particle_locations = particle_locations[particle_locations['Country'] == particle_settings['country']]
+    if 'economicstatus' in particle_settings.keys():
+        particle_locations = particle_locations[particle_locations['Economic status'] == particle_settings['economicstatus']]
+
+    particle_locations = particle_locations.groupby(['Longitude', 'Latitude'])[release_quantity_name].agg('sum').reset_index()
+    particle_locations = particle_locations[particle_locations[release_quantity_name]>0]
+
+    release_locations = {'lons': particle_locations['Longitude'],
+                        'lats':  particle_locations['Latitude']}
+
+    particle_settings['release_locations'] = release_locations
+
+
+    return create_particleset(fieldset, particle_settings)
+
+
+
 def create_kernel(fieldset, pset):
     """_summary_
 

src/DRAKKAR workshop code/PlasticParcels/kernels.py

@@ -455,7 +455,12 @@ def biofouling(particle, fieldset, time):
     a_grazing = fieldset.algae_mortality_rate * particle.algae_amount
 
     ### ------ Compute the final algal amount ------
-    particle.algae_amount += (a_collision + algae_growth - a_grazing - a_respiration) * particle.dt
+    algae_amount_change = (a_collision + algae_growth - a_grazing - a_respiration) * particle.dt
+    if particle.algae_amount + algae_amount_change < 0.:
+        particle.algae_amount = 0.
+    else:
+        particle.algae_amount += algae_amount_change
+
 
     ### ------ Compute the new settling velocity
     particle_diameter = 2. * (total_radius)  # equivalent spherical diameter [m], calculated from Dietrich (1982) from A = pi/4 * dn**2
@@ -757,23 +762,24 @@ def unbeaching(particle, fieldset, time):
 
 
 def checkThroughBathymetry(particle, fieldset, time):
-    bathym = fieldset.bathymetry[time, particle.depth + particle_ddepth, particle.lat + particle_dlat, particle.lon + particle_dlon]
-
-    # If the particle is below the bathymetry
-    if particle.depth + particle_ddepth > bathym:
-        particle_ddepth = bathym - particle.depth - 5 # Move the particle 5 metres above the model bathymetry
-
+    bathymetry_local = fieldset.bathymetry[time, particle.depth + particle_ddepth, particle.lat + particle_dlat, particle.lon + particle_dlon]
+    potential_depth = particle.depth + particle_ddepth
+    min_depth = 0.5 #meters - maybe set this as a fieldset variable?
 
-
-
-
+    if potential_depth < min_depth:
+        particle_ddepth = fieldset.z_start - particle.depth # Stick particle to surface
+    elif potential_depth > bathymetry_local:
+        particle_ddepth = bathymetry_local - particle.depth # Stick particle at bottom of ocean
+    elif particle.depth > 100 and potential_depth > (bathymetry_local*0.99): # for deeper particles; since bathymetry can be quite rough (and is interpolated linearly) look at the 99% value instead
+        particle_ddepth = bathymetry_local*0.99 - particle.depth # Stick particle at the 99% point
+    
+    elif potential_depth > 3900: # If particle >3.9km deep, stick it there
+        particle_ddepth = 3900 - particle.depth
 
 
 
 
-
-
-
+