split env

examples/example_advection_schemes_eddy.py

@@ -21,9 +21,9 @@
         o = OceanDrift(loglevel=50)
         o.set_config('environment:fallback:land_binary_mask', 0)
         o.set_config('drift:advection_scheme', scheme)
+        o.set_config('drift:vertical_mixing', False)
         o.add_reader(fake_eddy)
         o.seed_elements(lon=2.0, lat=63.0, time=datetime.utcnow())
-        o.set_config('drift:vertical_mixing', False)
         o.run(duration=timedelta(days=9), time_step=time_step)
         runs.append(o)
 

examples/example_backandforth.py

@@ -18,14 +18,14 @@
 
 o.add_reader(reader_norkyst)
 o.set_config('environment:fallback:land_binary_mask', 0)
+o.disable_vertical_motion()
 
 #%%
 # Forward run
 # Seeding some particles
 lon = 4.2; lat = 60.1;
 time = reader_norkyst.start_time
 o.seed_elements(lon, lat, radius=1000, number=100, time=time)
-o.disable_vertical_motion()
 
 o.run(steps=50*4, time_step=900, time_step_output=3600, outfile=ncfile)
 
@@ -43,9 +43,9 @@
 del o
 o = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information
 o.set_config('environment:fallback:land_binary_mask', 0)
+o.disable_vertical_motion()
 o.add_reader(reader_norkyst)
 o.schedule_elements(elements_final, time_final)
-o.disable_vertical_motion()
 
 #%%
 # Running model backwards from end of forward simulation

examples/example_coastline.py

@@ -10,7 +10,7 @@
 from opendrift.models.oceandrift import OceanDrift
 
 o = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information
-o.max_speed = 3
+o.set_config('drift:max_speed', 3)
 
 # This example works better using hourly input from Thredds than the daily data from test folder
 reader_current = reader_netCDF_CF_generic.Reader('https://thredds.met.no/thredds/dodsC/cmems/topaz6/dataset-topaz6-arc-15min-3km-be.ncml')

examples/example_codegg.py

@@ -15,6 +15,14 @@
     'https://thredds.met.no/thredds/dodsC/cmems/topaz6/dataset-topaz6-arc-15min-3km-be.ncml',
     'https://thredds.met.no/thredds/dodsC/mepslatest/meps_lagged_6_h_latest_2_5km_latest.nc'])
 
+#%%
+# Adjusting some configuration
+o.set_config('drift:vertical_mixing', True)
+o.set_config('vertical_mixing:diffusivitymodel', 'windspeed_Sundby1983') # windspeed parameterization for eddy diffusivity
+#%%
+# Vertical mixing requires fast time step
+o.set_config('vertical_mixing:timestep', 60.) # seconds
+
 #%%
 # spawn NEA cod eggs at defined position and time
 time = datetime.utcnow()
@@ -27,14 +35,6 @@
 o.seed_elements(13., 67.8, z=-40, radius=2000, number=500,
                 time=time, diameter=0.0014, neutral_buoyancy_salinity=31.25)
 
-#%%
-# Adjusting some configuration
-o.set_config('drift:vertical_mixing', True)
-o.set_config('vertical_mixing:diffusivitymodel', 'windspeed_Sundby1983') # windspeed parameterization for eddy diffusivity
-#%%
-# Vertical mixing requires fast time step
-o.set_config('vertical_mixing:timestep', 60.) # seconds
-
 #%%
 # Running model
 o.run(duration=timedelta(hours=48), time_step=3600)

examples/example_cone.py

@@ -15,6 +15,15 @@
 o.add_readers_from_list([
     'https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be'])
 
+#%%
+# Adjusting some configuration
+o.set_config('processes:dispersion', True)
+o.set_config('processes:evaporation', False)
+o.set_config('processes:emulsification', True)
+o.disable_vertical_motion()
+#o.set_config('drift:vertical_mixing', False)
+#o.set_config('drift:vertical_mixing', False)
+
 #%%
 # Seed elements along cone, e.g. ship track with
 # increasing uncertainty in position
@@ -23,21 +32,11 @@
 latend = 69.991446
 lonend = 17.760061
 time = [datetime.utcnow(), datetime.utcnow() + timedelta(hours=12)]
-
 o.seed_cone(lon=[lonstart, lonend], lat=[latstart, latend],
             oil_type='EKOFISK', radius=[100, 800], number=10000, time=[time])
 
 print(o)
 
-#%%
-# Adjusting some configuration
-o.set_config('processes:dispersion', True)
-o.set_config('processes:evaporation', False)
-o.set_config('processes:emulsification', True)
-o.disable_vertical_motion()
-#o.set_config('drift:vertical_mixing', False)
-#o.set_config('drift:vertical_mixing', False)
-
 #%%
 # Running model for 24 hours
 o.run(steps=24*2, time_step=1800, time_step_output=3600)

examples/example_depth.py

@@ -15,6 +15,10 @@
 o.add_readers_from_list([
     'https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be'])
 
+#%%
+# Adding some diffusion
+o.set_config('drift:horizontal_diffusivity', 10)  # m2/s
+
 #%%
 # Seed 1000 elements at random depths
 z = -np.random.rand(2000)*50
@@ -23,10 +27,6 @@
 
 print(o)
 
-#%%
-# Adding some diffusion
-o.set_config('drift:horizontal_diffusivity', 10)  # m2/s
-
 #%%
 # Running model
 o.run(duration=timedelta(hours=24), time_step=1800)

examples/example_dominating.py

@@ -18,10 +18,10 @@
 t = datetime.now()
 
 o = OceanDrift(loglevel=20)
+o.set_config('environment:constant:y_sea_water_velocity', .1)
 
 for i, lon in enumerate(lons):
     o.seed_elements(lon=lon, lat=60, radius=3000, number=2000, time=t, origin_marker_name='Lon %f' % lon)
-o.set_config('environment:constant:y_sea_water_velocity', .1)
 o.run(steps=15, outfile=of)
 
 #%%

examples/example_double_gyre_LCS_particles.py

@@ -44,13 +44,13 @@
 #%%
 # Make run with particles for the same period
 o.reset()
+o.disable_vertical_motion()
 x = [.9]
 y = [.5]
 lon, lat = double_gyre.xy2lonlat(x, y)
 
 o.seed_elements(lon, lat, radius=.15, number=2000,
                 time=double_gyre.initial_time)
-o.disable_vertical_motion()
 o.run(duration=duration, time_step=time_step,
       time_step_output=time_step_output)
 o.animation(buffer=0, lcs=lcs, hide_landmask=True)

examples/example_drifter.py

@@ -21,6 +21,9 @@
 
 o.add_reader([reader_current, reader_wind])
 
+# Prevent mixing elements downwards
+o.set_config('drift:vertical_mixing', False)
+
 #%%
 # Seeding elements
 #
@@ -41,9 +44,6 @@
                 time=reader_current.start_time,
                 wind_drift_factor=wind_drift_factor)
 
-# Prevent mixing elements downwards
-o.set_config('drift:vertical_mixing', False)
-
 #%%
 # Running model
 o.run(time_step=timedelta(minutes=15),

examples/example_generic.py

@@ -28,10 +28,6 @@
         reader_arome.start_time + timedelta(hours=30)]
 #time = reader_arome.start_time
 
-# Seed oil elements at defined position and time
-o.seed_elements(lon=4.6, lat=60.0, radius=50, number=3000, time=time,
-                wind_drift_factor=.02)
-
 #%%
 # Adjusting some configuration
 o.set_config('drift:vertical_mixing', False)
@@ -41,6 +37,10 @@
 o.set_config('drift:current_uncertainty', .1)
 o.set_config('drift:wind_uncertainty', 1)
 
+# Seed oil elements at defined position and time
+o.seed_elements(lon=4.6, lat=60.0, radius=50, number=3000, time=time,
+                wind_drift_factor=.02)
+
 #%%
 # Running model
 o.run(end_time=reader_norkyst.end_time, time_step=1800,

examples/example_horizontal_diffusion.py

@@ -24,33 +24,33 @@
 #reader_norkyst = reader_netCDF_CF_generic.Reader('https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
 
 o.add_reader([reader_norkyst, reader_arome])
-time = reader_arome.start_time
-o.seed_elements(lon, lat, radius=500, number=2000, time=time)
 
 #%%
 # First run, with no horizontal diffusion
 o.set_config('drift:current_uncertainty', 0)
 o.set_config('drift:wind_uncertainty', 0)
+time = reader_arome.start_time
+o.seed_elements(lon, lat, radius=500, number=2000, time=time)
 o.run(duration=timedelta(hours=24))
 
 #%%
 # Second run, identical, except for added diffusion
 o2 = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information
 o2.add_reader([reader_norkyst, reader_arome])
-o2.seed_elements(lon, lat, radius=500, number=2000, time=time)
 #o2.set_config('drift:current_uncertainty', .2) # Difference from first run
 #o2.set_config('drift:wind_uncertainty', 1)     # Difference from first run
 o2.set_config('drift:horizontal_diffusivity', 10)     # Difference from first run
+o2.seed_elements(lon, lat, radius=500, number=2000, time=time)
 o2.run(duration=timedelta(hours=24))
 
 #%%
 # Third run, identical, except for diffusion and shorter timestep
 o3 = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information
 o3.add_reader([reader_norkyst, reader_arome])
-o3.seed_elements(lon, lat, radius=500, number=2000, time=time)
 #o3.set_config('drift:current_uncertainty', .2) # Difference from first run
 #o3.set_config('drift:wind_uncertainty', 1)     # Difference from first run
 o3.set_config('drift:horizontal_diffusivity', 10)     # Difference from first run
+o3.seed_elements(lon, lat, radius=500, number=2000, time=time)
 o3.run(duration=timedelta(hours=24), time_step=300, time_step_output=3600)
 
 #%%

examples/example_huge_output.py

@@ -13,21 +13,21 @@
 #%%
 # First make a simulation with two seedings, marked by *origin_marker*
 o = OceanDrift(loglevel=50)
+o.set_config('drift:horizontal_diffusivity', 10)
 t1 = datetime.now()
 t2 = t1 + timedelta(hours=6)
 number = 10000
 outfile = 'simulation.nc'  # Raw simulation output
-o.seed_elements(time=t1, lon=4, lat=60, number=number,
-                origin_marker=0)
-o.seed_elements(time=[t1, t2], lon=4.2, lat=60.4, number=number,
-                origin_marker=1)
-
 reader_x = reader_oscillating.Reader('x_sea_water_velocity',
                 amplitude=1, zero_time=t1)
 reader_y = reader_oscillating.Reader('y_sea_water_velocity',
                 amplitude=1, zero_time=t2)
 o.add_reader([reader_x, reader_y])
-o.set_config('drift:horizontal_diffusivity', 10)
+o.seed_elements(time=t1, lon=4, lat=60, number=number,
+                origin_marker=0)
+o.seed_elements(time=[t1, t2], lon=4.2, lat=60.4, number=number,
+                origin_marker=1)
+
 o.run(duration=timedelta(hours=24),
       time_step=900, time_step_output=1800, outfile=outfile)
 

examples/example_larvae.py

@@ -10,20 +10,20 @@
 
 o = LarvalFish(loglevel=50)
 
-#%%
-# Seeding 20 fish eggs, which will hatch as larvae after some time, depending om temperature
-time = datetime(2020, 7, 1, 12)
-o.seed_elements(lon=4, lat=60, time=[time, time+timedelta(hours=24)], number=20)
-
 #%%
 # No horizontal movement, here only investigating vertical mixing and swimming
 r = ConstantReader(
         {'x_sea_water_velocity': 0, 'y_sea_water_velocity': 0, 'x_wind': 0, 'y_wind': 0,
          'sea_water_temperature': 10,
          'land_binary_mask': 0, 'ocean_vertical_diffusivity': .02})
 o.add_reader(r)
-
 o.set_config('general:use_auto_landmask', False)
+
+#%%
+# Seeding 20 fish eggs, which will hatch as larvae after some time, depending om temperature
+time = datetime(2020, 7, 1, 12)
+o.seed_elements(lon=4, lat=60, time=[time, time+timedelta(hours=24)], number=20)
+
 o.run(duration=timedelta(days=40))
 
 #%%

examples/example_mixed_layer_depth.py

@@ -18,13 +18,13 @@
 #%%
 # First with Sundby1983 parameterization of diffusivity, based on wind and MLD
 o = OceanDrift(loglevel=50)
-o.seed_cone(lon=[2, 4], lat=[60, 60], time=datetime.now(), number=5000)
 o.add_reader([r1, r2])
 o.set_config('environment:constant:y_wind', 8)  # Some wind for mixing
 o.set_config('drift:vertical_mixing', True)
 o.set_config('vertical_mixing:diffusivitymodel', 'windspeed_Sundby1983')
 # Increasing background diffusivity beyond default (1.2e-5) to avoid artefact due to sharp gradient at MLD
 o.set_config('vertical_mixing:background_diffusivity', 0.001)
+o.seed_cone(lon=[2, 4], lat=[60, 60], time=datetime.now(), number=5000)
 o.run(duration=timedelta(hours=48))
 o.animation_profile()
 
@@ -34,12 +34,12 @@
 #%%
 # Same, but with Large1994 parameterization of diffusivity
 o = OceanDrift(loglevel=50)
-o.seed_cone(lon=[2, 4], lat=[60, 60], time=datetime.now(), number=5000)
 o.add_reader([r1, r2])
 o.set_config('environment:constant:y_wind', 8)  # Some wind for mixing
 o.set_config('drift:vertical_mixing', True)
 o.set_config('vertical_mixing:diffusivitymodel', 'windspeed_Large1994')
 o.set_config('vertical_mixing:background_diffusivity', 0.001)
+o.seed_cone(lon=[2, 4], lat=[60, 60], time=datetime.now(), number=5000)
 o.run(duration=timedelta(hours=48))
 o.animation_profile()
 
@@ -49,12 +49,12 @@
 #%%
 # Using Large1994, but with 0 diffusivity below MLD
 o = OceanDrift(loglevel=50)
-o.seed_cone(lon=[2, 4], lat=[60, 60], time=datetime.now(), number=5000)
 o.add_reader([r1, r2])
 o.set_config('environment:constant:y_wind', 8)  # Some wind for mixing
 o.set_config('drift:vertical_mixing', True)
 o.set_config('vertical_mixing:diffusivitymodel', 'windspeed_Large1994')
 o.set_config('vertical_mixing:background_diffusivity', 0)
+o.seed_cone(lon=[2, 4], lat=[60, 60], time=datetime.now(), number=5000)
 o.run(duration=timedelta(hours=48))
 o.animation_profile()
 

examples/example_model_landmask.py

@@ -22,25 +22,24 @@
 # First run, with default GSHHG vector landmask
 o.add_reader([reader_nordic])
 time = reader_nordic.start_time
-o.seed_elements(lon, lat, radius=3000, number=1000, time=time)
 o.set_config('general:use_auto_landmask', True)
+o.seed_elements(lon, lat, radius=3000, number=1000, time=time)
 o.run(end_time=reader_nordic.end_time, time_step=1800, time_step_output=3*3600)
 
 #%%
 # Second run, with landmask from ocean model
 o2 = OceanDrift(loglevel=20)
 o2.add_reader([reader_nordic])
 lon = 14.75; lat = 68.1
-o2.seed_elements(lon, lat, radius=3000, number=1000, time=time)
 o2.set_config('general:use_auto_landmask', False)
+o2.seed_elements(lon, lat, radius=3000, number=1000, time=time)
 o2.run(end_time=reader_nordic.end_time, time_step=1800, time_step_output=3*3600)
 
 #%% Prepare cusom colormap/colors for land and ocean
 from matplotlib.colors import ListedColormap
 import cartopy.feature as cfeature
-#cmap = ListedColormap(('blue', 'red'))
-cmap = ListedColormap((cfeature.COLORS['water'],
-                       cfeature.COLORS['land']))
+cmap = ListedColormap([cfeature.COLORS['water'],
+                       cfeature.COLORS['land']])
 
 #%%
 # .. _model_landmask_only_model: