def test_stranding_3d(self):
o = PelagicEggDrift(loglevel=30)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
o.add_reader(reader_nordic)
o.fallback_values['y_wind'] = 10 # Some wind for mixing
o.seed_elements(
lon=14.0,
lat=68.15,
radius=2000,
number=100,
time=[reader_nordic.start_time, reader_nordic.end_time],
z=0)
o.set_config('general:coastline_action', 'stranding')
o.set_config('turbulentmixing:timestep', 120)
o.max_speed = .1
o.run(end_time=reader_nordic.end_time, time_step=3600 * 6)
self.assertEqual(o.status_categories[1], 'stranded')
self.assertEqual(o.elements_deactivated.status.min(), 1)
self.assertEqual(o.elements_deactivated.status.max(), 1)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 79)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 21)
self.assertEqual(o.num_elements_total(), 100)
def test_stranding_3d(self):
o = PelagicEggDrift(loglevel=30)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
o.add_reader(reader_nordic)
o.set_config('environment:fallback:y_wind', 10) # Some wind for mixing
o.seed_elements(
lon=14.0,
lat=68.15,
radius=2000,
number=100,
time=[reader_nordic.start_time, reader_nordic.end_time],
z=0)
o.set_config('general:coastline_action', 'stranding')
o.set_config('vertical_mixing:timestep', 120)
o.max_speed = .1
o.run(end_time=reader_nordic.end_time, time_step=3600 * 6)
self.assertEqual(o.status_categories[1], 'stranded')
self.assertEqual(o.elements_deactivated.status.min(), 1)
self.assertEqual(o.elements_deactivated.status.max(), 1)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 81)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 19)
self.assertEqual(o.num_elements_total(), 100)
# Check calculated trajectory lengths and speeds
total_length, distances, speeds = o.get_trajectory_lengths()
self.assertAlmostEqual(total_length.max(), 14978.3, 1)
self.assertAlmostEqual(total_length.min(), 1225.2, 1)
self.assertAlmostEqual(speeds.max(), 0.127, 1)
self.assertAlmostEqual(distances.max(), 2859.0, 1)
def test_reader_boundary(self):
o = PelagicEggDrift(loglevel=0)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() + "2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc"
)
reader_arctic = reader_netCDF_CF_generic.Reader(
o.test_data_folder() + "2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc"
)
######################################################
# Vertical interpolation is another issue to be fixed:
reader_nordic.zlevels = reader_arctic.z
######################################################
o.add_reader([reader_nordic, reader_arctic])
o.fallback_values["land_binary_mask"] = 0
o.fallback_values["x_wind"] = 10 # Some wind for mixing
# Seed close to Nordic boundary
o.seed_elements(lon=14.9, lat=71.1, radius=2000, number=100, time=reader_nordic.start_time, z=0)
o.set_config("turbulentmixing:timestep", 20)
o.set_config("turbulentmixing:verticalresolution", 1)
o.set_config("drift:scheme", "runge-kutta")
o.run(steps=5, time_step=3600, time_step_output=3600)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertAlmostEqual(o.elements.lat[0], 71.15, 2)
self.assertAlmostEqual(o.elements.z.min(), -35.0, 3)
self.assertAlmostEqual(o.elements.z.max(), -0.5, 3)
self.assertAlmostEqual(o.elements.lon.max(), 14.87, 2)
def test_reader_boundary(self):
o = PelagicEggDrift(loglevel=0)
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
reader_arctic = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc')
######################################################
# Vertical interpolation is another issue to be fixed:
reader_nordic.zlevels = reader_arctic.z
######################################################
o.add_reader([reader_nordic, reader_arctic])
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 10 # Some wind for mixing
# Seed close to Nordic boundary
o.seed_elements(lon=14.9,
lat=71.1,
radius=2000,
number=100,
time=reader_nordic.start_time,
z=0)
o.set_config('turbulentmixing:timestep', 20)
o.set_config('drift:scheme', 'runge-kutta')
o.run(steps=5, time_step=3600, time_step_output=3600)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertAlmostEqual(o.elements.lat[0], 71.16, 1)
#self.assertAlmostEqual(o.elements.z.min(), -41.92, 1) # With past ROMS-masking
self.assertAlmostEqual(o.elements.z.min(), -40.1, 1)
self.assertAlmostEqual(o.elements.z.max(), -0.01, 1)
#self.assertAlmostEqual(o.elements.lon.max(), 14.949, 2)
self.assertAlmostEqual(o.elements.lon.max(), 14.87, 2)
def test_stranding_roms(self):
o = PelagicEggDrift(loglevel=0)
reader_arctic = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc')
reader_nordic = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
o.add_reader(reader_arctic)
o.add_reader(reader_nordic)
o.fallback_values['x_sea_water_velocity'] = 1
o.seed_elements(
lon=13.0,
lat=68.0,
radius=20000,
number=100,
time=[reader_arctic.start_time, reader_nordic.end_time],
z=-30)
o.set_config('general:coastline_action', 'previous')
o.set_config('processes:turbulentmixing', False)
o.max_speed = 1
o.run(end_time=reader_nordic.end_time, time_step=3600 * 36)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), 100)
def test_outside_reader_time_coverage(self):
o = PelagicEggDrift()
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader(reader)
o.fallback_values['x_sea_water_velocity'] = 1
o.fallback_values['land_binary_mask'] = 0
o.set_config('processes:turbulentmixing', False)
o.seed_elements(lon=4.8, lat=60, number=1, time=reader.end_time)
o.run(steps=2)
# Check that fallback value is used when outside time coverage
self.assertEqual(o.history['x_sea_water_velocity'][0][-1], 1.0)
def test_outside_reader_time_coverage(self):
o = PelagicEggDrift()
reader = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader(reader)
o.fallback_values['x_sea_water_velocity'] = 1
o.fallback_values['land_binary_mask'] = 0
o.set_config('processes:turbulentmixing', False)
o.seed_elements(lon=4.8, lat=60, number=1, time=reader.end_time)
o.run(steps=2)
# Check that fallback value is used when outside time coverage
self.assertEqual(o.history['x_sea_water_velocity'][0][-1], 1.0)
def atest_reader_boundary_thredds(self):
o = PelagicEggDrift(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_nordic = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/fou-hi/nordic4km-1h/Nordic-4km_SURF_1h_avg_00.nc')
o.add_reader([reader_norkyst, reader_nordic])
o.fallback_values['land_binary_mask'] = 0
lon = 0.2; lat = 61.0; # Close to NorKyst boundary
time = reader_nordic.start_time
o.seed_elements(lon, lat, radius=5000, number=100, time=time, z=0)
o.set_config('turbulentmixing:timestep', 5)
o.run(steps=5, time_step=3600,
time_step_output=3600)
def atest_reader_boundary_thredds(self):
o = PelagicEggDrift(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_nordic = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/fou-hi/nordic4km-1h/Nordic-4km_SURF_1h_avg_00.nc')
o.add_reader([reader_norkyst, reader_nordic])
o.fallback_values['land_binary_mask'] = 0
lon = 0.2; lat = 61.0; # Close to NorKyst boundary
time = reader_nordic.start_time
o.seed_elements(lon, lat, radius=5000, number=100, time=time, z=0)
o.set_config('turbulentmixing:timestep', 5)
o.run(steps=5, time_step=3600,
time_step_output=3600)
def test_stranding_3d(self):
o = PelagicEggDrift(loglevel=30)
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader(reader_nordic)
o.fallback_values['y_wind'] = 10 # Some wind for mixing
o.seed_elements(lon=14.0, lat=68.15, radius=2000, number=100,
time=[reader_nordic.start_time,
reader_nordic.end_time], z=0)
o.set_config('general:coastline_action', 'stranding')
o.set_config('turbulentmixing:timestep', 60)
o.set_config('turbulentmixing:verticalresolution', 10)
o.run(end_time=reader_nordic.end_time, time_step=3600*3)
self.assertEqual(o.status_categories[1], 'stranded')
self.assertEqual(o.elements_deactivated.status.min(), 1)
self.assertEqual(o.elements_deactivated.status.max(), 1)
def test_vertical_mixing(self):
# Export to file only at end
o1 = PelagicEggDrift(loglevel=20) # Profiles and vertical mixing
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o1.add_reader([norkyst])
o1.fallback_values['x_wind'] = 8
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.1, 63.3, radius=1000, number=100,
time=norkyst.start_time)
o1.set_config('turbulentmixing:timestep', 20.) # seconds
o1.set_config('turbulentmixing:verticalresolution', 1.) # m
o1.run(steps=20, time_step=300, time_step_output=1800,
export_buffer_length=10, outfile='verticalmixing.nc')
self.assertAlmostEqual(o1.history['z'].min(), -25.0)
self.assertAlmostEqual(o1.history['z'].max(), 0.0)
os.remove('verticalmixing.nc')
def test_vertical_mixing(self):
# Export to file only at end
o1 = PelagicEggDrift(loglevel=20) # Profiles and vertical mixing
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o1.add_reader([norkyst])
o1.fallback_values['x_wind'] = 8
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.1, 63.3, radius=1000, number=100,
time=norkyst.start_time)
o1.set_config('turbulentmixing:timestep', 20.) # seconds
o1.run(steps=20, time_step=300, time_step_output=1800,
export_buffer_length=10, outfile='verticalmixing.nc')
self.assertAlmostEqual(o1.history['z'].min(), -38.1, 1)
self.assertAlmostEqual(o1.history['z'].max(), 0.0, 1)
os.remove('verticalmixing.nc')
def test_stranding_roms(self):
o = PelagicEggDrift(loglevel=0)
reader_arctic = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Arctic20_1to5Feb_2016.nc')
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader(reader_arctic)
o.add_reader(reader_nordic)
o.fallback_values['x_sea_water_velocity'] = 1
o.seed_elements(lon=13.0, lat=68.0, radius=20000, number=100,
time=[reader_arctic.start_time,
reader_nordic.end_time], z=-30)
o.set_config('general:basemap_resolution', 'c')
o.set_config('general:coastline_action', 'previous')
o.set_config('processes:turbulentmixing', False)
o.max_speed=1
o.run(end_time=reader_nordic.end_time, time_step=3600*36)
self.assertEqual(o.num_elements_scheduled(), 0)
self.assertEqual(o.num_elements_active(), 100)
self.assertEqual(o.num_elements_activated(), 100)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), 100)
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)
#%%
# Print and plot results.
# At the end the wind vanishes, and eggs come to surface
print(o)
o.plot(fast=True)
o.animation(fast=True, color='z')
#%%
# .. image:: /gallery/animations/example_codegg_0.gif
#%% Vertical distribution of particles
o.animate_vertical_distribution()
# spawn NEA cod eggs at defined position and time
o.seed_elements(14. , 68.1, z=-40, radius=2000, number=500,
time=time, diameter=0.0014, neutral_buoyancy_salinity=31.25)
o.seed_elements(12.5, 68.5, z=-40, radius=2000, number=500,
time=time, diameter=0.0014, neutral_buoyancy_salinity=31.25)
# Adjusting some configuration
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:diffusivitymodel', 'windspeed_Sundby1983') # windspeed parameterization for eddy diffusivity
#o.set_config('turbulentmixing:diffusivitymodel', 'environment') # use eddy diffusivity from ocean model
# Vertical resolution and time step should be adjusted so to avoid getting
# output warnings like 'DEBUG: WARNING! some elements have p+q>1.'
o.set_config('turbulentmixing:timestep', 10.) # seconds
o.set_config('turbulentmixing:verticalresolution', 2.) # m
o.set_config('turbulentmixing:TSprofiles', True) # update T,S frequently in each inner loop for turbulent
o.set_config('turbulentmixing:TSprofiles', False) # False is faster
# Running model (until end of driver data)
o.run(steps=6*2, time_step=1800)
# Print and plot results
print o
o.plot()
o.animation()
o.plot_vertical_distribution()
o.add_reader([reader_norkyst, reader_arome])
# spawn NEA cod eggs at defined position and time
time = reader_arome.start_time
o.seed_elements(14. , 68.1, z=-40, radius=2000, number=500,
time=time, diameter=0.0014, neutral_buoyancy_salinity=31.25)
o.seed_elements(12.5, 68.5, z=-40, radius=2000, number=500,
time=time, diameter=0.0014, neutral_buoyancy_salinity=31.25)
# Adjusting some configuration
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:diffusivitymodel', 'windspeed_Sundby1983') # windspeed parameterization for eddy diffusivity
#o.set_config('turbulentmixing:diffusivitymodel', 'environment') # use eddy diffusivity from ocean model
# Vertical resolution and time step should be adjusted so to avoid getting
# output warnings like 'DEBUG: WARNING! some elements have p+q>1.'
o.set_config('turbulentmixing:timestep', 10.) # seconds
o.set_config('turbulentmixing:verticalresolution', 2.) # m
# Running model (until end of driver data)
o.run(steps=6*2, time_step=1800)
# Print and plot results
print o
o.plot()
o.animation()
o.plot_vertical_distribution()
number=500,
time=time,
diameter=0.0014,
neutral_buoyancy_salinity=31.25)
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('processes:turbulentmixing', True)
#o.set_config('turbulentmixing:diffusivitymodel', 'windspeed_Sundby1983') # windspeed parameterization for eddy diffusivity
o.set_config('turbulentmixing:diffusivitymodel',
'environment') # use eddy diffusivity from ocean model
# Vertical mixing requires fast time step
o.set_config('turbulentmixing:timestep', 60.) # seconds
# Running model (until end of driver data)
o.run(steps=96, time_step=3600)
# Print and plot results
print(o)
o.plot(filename='codegg_forecast.png')
o.animation(filename='codegg_forecast.gif')
o.plot_vertical_distribution(filename='codegg_vertical.png')