Merge pull request #1319 from magnesim/magnesim/radionuclide

Magnesim/radionuclide
OpenDrift · Jun 17, 2024 · c196bbc · c196bbc
2 parents 25a02ff + 9ddab2e
commit c196bbc
Show file tree

Hide file tree

Showing 3 changed files with 402 additions and 335 deletions.
diff --git a/examples/example_radionuclides.py b/examples/example_radionuclides.py
@@ -22,50 +22,27 @@
 
 # Adjusting some configuration
 o.set_config('drift:vertical_mixing', True)
-#o.set_config('environment:constant:ocean_vertical_diffusivity', 0)
 #o.set_config('vertical_mixing:diffusivitymodel','constant')  # include settling without vertical turbulent mixing
-o.set_config('vertical_mixing:diffusivitymodel','environment')  # include settling without vertical turbulent mixing
+o.set_config('vertical_mixing:diffusivitymodel','environment')  # apply vertical diffusivity from ocean model
 # Vertical mixing requires fast time step
 o.set_config('vertical_mixing:timestep', 600.) # seconds
 o.set_config('drift:horizontal_diffusivity', 10)
 
 #%%
-# Activate the desired species
-#o.set_config('radionuclide:species:LMM', True)
-#o.set_config('radionuclide:species:LMMcation', True)
-#o.set_config('radionuclide:species:LMManion', True)
-#o.set_config('radionuclide:species:Colloid', True)
-#o.set_config('radionuclide:species:Humic_colloid', True)
-#o.set_config('radionuclide:species:Polymer', True)
-#o.set_config('radionuclide:species:Particle_reversible', True)
-#o.set_config('radionuclide:species:Particle_irreversible', True)
-#o.set_config('radionuclide:species:Particle_slowly_reversible', True)
-
-#o.set_config('radionuclide:species:Sediment_reversible', True)
-#o.set_config('radionuclide:species:Sediment_irreversible', True)
-#o.set_config('radionuclide:species:Sediment_slowly_reversible', True)
-
 o.set_config('radionuclide:particle_diameter',5.e-6)  # m
-#o.set_config('radionuclide:particle_diameter_uncertainty',1.e-7) # m
-o.set_config('radionuclide:transformations:Kd',2.e0) # (m3/kg)
-#o.set_config('radionuclide:transformations:slow_coeff',1.e-6)
 
 o.set_config('radionuclide:sediment:resuspension_depth',2.)
 o.set_config('radionuclide:sediment:resuspension_depth_uncert',0.1)
 o.set_config('radionuclide:sediment:resuspension_critvel',0.15)
 
 
 #
-#o.set_config('radionuclide:transfer_setup','custom')
-o.set_config('radionuclide:transfer_setup','Bokna_137Cs')
-#o.set_config('radionuclide:transfer_setup','137Cs_rev')
-#o.set_config('radionuclide:transfer_setup','Sandnesfj_Al')
+o.set_config('radionuclide:isotope', '137Cs')
+o.set_config('radionuclide:specie_setup','LMM + Rev')
 
 # By default, radionuclides do not strand towards coastline
 o.set_config('general:coastline_action', 'previous')
 o.set_config('general:seafloor_action','lift_to_seafloor')
-#o.set_config('general:seafloor_action','previous')
-#o.set_config('general:use_auto_landmask',False)
 
 
 o.set_config('seed:LMM_fraction',.45)
@@ -80,20 +57,13 @@
 td=datetime.today()
 time = datetime(td.year, td.month, td.day, 0)
 
-#latseed= 61.2; lonseed= 4.3    # Sognesjen
-#latseed= 59.0;   lonseed= 10.75 # Hvaler/Koster
-#latseed= 57.5;   lonseed= 9.3 # Kattegat
-latseed= 60.0;   lonseed= 4.5 # Bergen (?)
+latseed= 60.0;   lonseed= 4.5 
 
 ntraj=5000
 iniz=np.random.rand(ntraj) * -10. # seeding the radionuclides in the upper 10m
 
 o.seed_elements(lonseed, latseed, z=iniz, radius=1000,number=ntraj,
                 time=time, 
-#                LMM_fraction=0.25,
-#                particle_fraction=0.75
-#                diameter=99.e-6#diam, 
-                #specie=init_speciation
                 )
 
 
@@ -137,17 +107,7 @@
 
 
 
-# Postprocessing: write to concentration netcdf file
-o.conc_lat  = reader_norkyst.get_variables('latitude',
-                                       x=[reader_norkyst.xmin,reader_norkyst.xmax],
-                                       y=[reader_norkyst.ymin,reader_norkyst.ymax])['latitude'][:]
-o.conc_lon  = reader_norkyst.get_variables('longitude',
-                                       x=[reader_norkyst.xmin,reader_norkyst.xmax],
-                                       y=[reader_norkyst.ymin,reader_norkyst.ymax])['longitude'][:]
-o.conc_topo  = reader_norkyst.get_variables('sea_floor_depth_below_sea_level',
-                                       x=[reader_norkyst.xmin,reader_norkyst.xmax],
-                                       y=[reader_norkyst.ymin,reader_norkyst.ymax])['sea_floor_depth_below_sea_level'][:]
-#o.conc_mask  = reader_norkyst.land_binary_mask
+# # Postprocessing: write to concentration netcdf file
 
 #%%
 #
@@ -160,8 +120,8 @@
                                       smoothing_cells=1,
                                       time_avg_conc=True,
                                       deltat=2., # hours
-                                      llcrnrlon=4.4, llcrnrlat=59.9,
-                                      urcrnrlon=4.8, urcrnrlat=60.2,
+#                                      llcrnrlon=4.4, llcrnrlat=59.9,
+#                                      urcrnrlon=4.8, urcrnrlat=60.2,
                                      )