def test_buffer_length_stranding(self):
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=1, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='i', projection='merc')
o1.add_reader([basemap])
o1.fallback_values['x_sea_water_velocity'] = 1.0 # onshore drift
o1.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o1.run(steps=100,
time_step=900,
time_step_output=3600,
export_buffer_length=10)
# Without buffer
o2 = OceanDrift(loglevel=20)
o2.add_reader([basemap])
o2.fallback_values['x_sea_water_velocity'] = 1.0 # onshore drift
o2.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o2.run(steps=100,
time_step=900,
time_step_output=3600,
outfile='test_buffer_length_stranding.nc')
self.assertItemsEqual(o1.history['lon'].compressed(),
o2.history['lon'].compressed())
self.assertItemsEqual(o1.history['status'].compressed(),
o2.history['status'].compressed())
os.remove('test_buffer_length_stranding.nc')
def test_reader_boundary(self):
# Check that the element outside reader coverage is
# not deactivated if fallback value exist
o = OceanDrift()
nordic3d = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
lon = [12.0, 12.0]
lat = [70.0, 70.5]
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 2)
self.assertEqual(o.num_elements_deactivated(), 0)
# Check that the outside element is deactivated,
# if no fallback value exists
o = OceanDrift()
del o.fallback_values['x_sea_water_velocity']
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
def test_stranding_options(self):
reader_osc = reader_oscillating.Reader(
'x_sea_water_velocity', amplitude=1,
zero_time=datetime.now())
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=12, llcrnrlat=67.6,
urcrnrlon=13.6, urcrnrlat=68.1,
resolution='i', projection='merc')
# Three different stranding options, with
# expected final status and position
options = ['stranding', 'previous', 'none']
status = ['stranded', 'active', 'active']
lons = [12.930, 13.348, 12.444]
for i, option in enumerate(options):
o = OceanDrift(loglevel=30)
o.set_config('general:coastline_action', option)
o.add_reader([reader_osc, reader_basemap])
# Adding northwards drift
o.fallback_values['y_sea_water_velocity'] = .2
o.seed_elements(lon=12.2, lat=67.7, radius=0,
time=reader_osc.zero_time)
o.run(steps=28, time_step=3600*2)
print 'Testing stranding: %s' % option
if len(o.elements) == 1:
el = o.elements
else:
el = o.elements_deactivated
self.assertEqual(o.status_categories[int(el.status)], status[i])
self.assertAlmostEqual(el.lon, lons[i], 2)
def test_output_time_step(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4.5, llcrnrlat=60.0,
urcrnrlon=5.2, urcrnrlat=60.5,
resolution='i', projection='merc')
o1.add_reader([basemap, norkyst])
o1.seed_elements(4.96, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=30)
o2.add_reader([basemap, norkyst])
o2.seed_elements(4.96, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100,25))
self.assertEqual(o2.history.shape, (100,13))
# Check that start and end conditions (longitudes) are idential
self.assertItemsEqual(o1.history['lon'][:,24].compressed(),
o2.history['lon'][:,12].compressed())
self.assertItemsEqual(o1.history['lon'][:,0].compressed(),
o2.history['lon'][:,0].compressed())
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertItemsEqual(o2i.history['lon'][:,12].compressed(),
o2.history['lon'][:,12].compressed())
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
def test_adding_readers(self):
o = OceanDrift()
r = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader([r, basemap])
self.assertEqual(o.priority_list['land_binary_mask'],
['roms native', 'basemap_landmask'])
self.assertEqual(o.priority_list['x_sea_water_velocity'],
['roms native'])
# Switch order
o = OceanDrift()
o.add_reader([basemap, r])
self.assertEqual(o.priority_list['land_binary_mask'],
['basemap_landmask', 'roms native'])
self.assertEqual(o.priority_list['x_sea_water_velocity'],
['roms native'])
def test_reader_order(self):
# Check that we get the same output indepenently of reader order
o = OceanDrift(loglevel=50)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=2, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='c', projection='merc')
lon=4.; lat=60.
# First run
o.add_reader([basemap, norkyst, arome])
o.seed_elements(lon, lat, time=norkyst.start_time)
o.run(steps=30)
# Second run
# Check that we get almost identical results with other projection
o1 = OceanDrift(loglevel=50)
o1.add_reader([norkyst, arome, basemap])
o1.seed_elements(lon, lat, time=norkyst.start_time)
o1.run(steps=30)
self.assertAlmostEqual(o.elements.lon, o1.elements.lon, 2)
self.assertAlmostEqual(o.elements.lat, o1.elements.lat, 2)
# Third run
# Check that this is identical to run 1 if projection set equal
o2 = OceanDrift(loglevel=50)
o2.add_reader([norkyst, arome, basemap])
o2.seed_elements(lon, lat, time=norkyst.start_time)
o2.set_projection(basemap.proj4)
o2.run(steps=30)
self.assertEqual(o.elements.lon, o2.elements.lon)
def test_export_step_interval(self):
# Export to file only at end
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o1.add_reader(norkyst)
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o1.run(steps=40)
# Export to file during simulation
o2 = OceanDrift(loglevel=20)
o2.add_reader(norkyst)
o2.fallback_values['land_binary_mask'] = 0
o2.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o2.run(steps=40, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertItemsEqual(o1.history['lon'].compressed(),
o2.history['lon'].compressed())
# Finally check when steps is multiple of export_buffer_length
o3 = OceanDrift(loglevel=20)
o3.add_reader(norkyst)
o3.fallback_values['land_binary_mask'] = 0
o3.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o3.run(steps=42)
# Export to file during simulation
o4 = OceanDrift(loglevel=20)
o4.add_reader(norkyst)
o4.fallback_values['land_binary_mask'] = 0
o4.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o4.run(steps=42, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertItemsEqual(o3.history['lon'].compressed(),
o4.history['lon'].compressed())
os.remove('export_step_interval.nc')
from datetime import datetime
from opendrift.readers import reader_basemap_landmask
from opendrift.readers import reader_ArtificialOceanEddy
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=-1.5, llcrnrlat=59,
urcrnrlon=7, urcrnrlat=64, resolution='h')
o.add_reader([fake_eddy, reader_basemap])
lon = 2.0; lat = 63.0; # Close to Station M
# First run, with Euler scheme:
o.set_config('drift:scheme', 'euler')
o.seed_elements(lon, lat, radius=0, number=1, time=datetime(2015,1,1))
o.run(steps=300, time_step=3600)
# Second run, with Runge-Kutta scheme:
o2 = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
o2.add_reader([fake_eddy, reader_basemap])
o2.set_config('drift:scheme', 'runge-kutta')
o2.seed_elements(lon, lat, radius=0, number=1, time=datetime(2015,1,1))
o2.run(steps=300, time_step=3600)
o.plot(compare=o2, legend=['Euler scheme', 'Runge-Kutta scheme'])
Grid
=============
"""
import numpy as np
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
# Norkyst
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader(reader_norkyst)
#o.fallback_values['land_binary_mask'] = 0
#%%
# Seeding some particles
lons = np.linspace(3.5, 5.0, 100)
lats = np.linspace(60, 61, 100)
lons, lats = np.meshgrid(lons, lats)
lons = lons.ravel()
lats = lats.ravel()
#%%
# Seed oil elements at defined position and time
o.seed_elements(lons,
lats,
radius=0,
"""
import numpy as np
from opendrift.readers import reader_global_landmask
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
# Norkyst
#reader_norkyst = reader_netCDF_CF_generic.Reader('https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader([reader_norkyst])
o.set_config('drift:vertical_mixing', False)
#%%
# Seeding particles in a checkerboard pattern
di = 5 # Horizontal number of particles per square
dj = 5 # Vertical number of particles per square
lons = np.linspace(3.5, 5.0, 100)
lats = np.linspace(60, 61, 100)
ii = np.arange(len(lons)) // di
jj = np.arange(len(lats)) // dj
ii, jj = np.meshgrid(ii, jj)
board = (ii + jj) % 2 > 0
lons, lats = np.meshgrid(lons, lats)
class TestRun(unittest.TestCase):
"""Tests for (non-scalar) LagrangianArray"""
def make_OceanDrift_object(self):
self.o = OceanDrift(loglevel=30)
self.fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
self.reader_landmask = reader_global_landmask.Reader(
extent=[-1.5, 59, 7, 64])
self.o.add_reader([self.fake_eddy, self.reader_landmask])
def test_seed(self):
"""Test seeding"""
o = OceanDrift(loglevel=20)
number = 3
lonvec = np.linspace(2, 5, number)
latvec = np.linspace(60, 61, number)
o.seed_elements(lonvec,
latvec,
number=number,
time=datetime(2015, 1, 1, 12, 5, 17))
#time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.num_elements_active(), 0)
self.assertEqual(o.num_elements_activated(), 0)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), number)
def test_seed_cone(self):
o = OceanDrift(loglevel=20)
o.seed_cone(time=[datetime.now(),
datetime.now() + timedelta(hours=3)],
number=100,
lat=[60.5, 60.6],
lon=[4.4, 4.5])
self.assertAlmostEqual(o.elements_scheduled.lon[50], 4.450, 2)
def test_seed_outside_coverage(self):
"""Test seeding"""
o = OpenOil(loglevel=0)
norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
landmask = reader_global_landmask.Reader(extent=[4, 6, 60, 64])
o.add_reader([landmask, norkyst])
o.set_config('environment:fallback:x_wind', 0)
o.set_config('environment:fallback:y_wind', 0)
o.set_config('seed:oil_type', 'SNORRE B 2004')
o.seed_elements(5,
63,
number=5,
time=norkyst.start_time - 24 * timedelta(hours=24))
# Check that the oiltype is taken from config
self.assertEqual(o.oil_name, o.get_config('seed:oil_type'))
self.assertEqual(o.oil_name, 'SNORRE B 2004')
with self.assertRaises(ValueError):
o.run(steps=3, time_step=timedelta(minutes=15))
def test_invalid_config(self):
o = OceanDrift(loglevel=20)
with self.assertRaises(ValueError): # outside min-max
o.set_config('seed:number', 0)
with self.assertRaises(ValueError): # not in list/enum
o.set_config('vertical_mixing:diffusivitymodel', 'not_in_list')
o.set_config('seed:number', 100)
self.assertEqual(o.get_config('seed:number'), 100)
def test_config_suggestion(self):
o = Leeway(loglevel=20)
try:
o.set_config('seed:object_type', 'person')
except Exception as e:
self.assertTrue('Did you mean' in str(e))
def test_config_seed(self):
#o = Leeway(loglevel=20)
o = OceanDrift(loglevel=20)
o.list_configspec()
def test_config_constant_fallback(self):
o = OceanDrift(loglevel=0)
reader_arome = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
print(reader_norkyst, reader_arome)
o.add_reader([reader_norkyst, reader_arome])
o.seed_elements(lon=4,
lat=60,
time=reader_arome.end_time - timedelta(hours=3),
number=1)
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:x_sea_water_velocity', 1)
o.set_config('environment:fallback:y_sea_water_velocity', 0)
o.set_config('environment:constant:x_wind', 0)
o.set_config('environment:constant:y_wind', 5)
o.run(duration=timedelta(hours=6))
y_wind = np.array(o.get_property('y_wind')[0][:, 0])
x_current = np.array(o.get_property('x_sea_water_velocity')[0][:, 0])
# Check that constant wind is used for whole simulation
self.assertAlmostEqual(y_wind[0], 5, 2)
self.assertAlmostEqual(y_wind[-1], 5, 2)
# Check that fallback current is used only after end of reader
self.assertAlmostEqual(x_current[0], 0.155, 2)
self.assertAlmostEqual(x_current[-1], 1, 2)
def test_runge_kutta(self):
number = 50
# With Euler
o = OceanDrift(loglevel=30, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.set_config('environment:fallback:land_binary_mask', 0)
o.add_reader([norkyst])
z = -40 * np.random.rand(number)
o.seed_elements(5,
62.5,
number=number,
radius=5000,
z=z,
time=norkyst.start_time)
o.run(steps=4 * 3, time_step=timedelta(minutes=15))
# With Runge-Kutta
o2 = OceanDrift(loglevel=30, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o2.set_config('environment:fallback:land_binary_mask', 0)
o2.add_reader([norkyst])
z = -40 * np.random.rand(number)
o2.seed_elements(5,
62.5,
number=number,
radius=5000,
z=z,
time=norkyst.start_time)
o2.set_config('drift:advection_scheme', 'runge-kutta')
o2.run(steps=4 * 3, time_step=timedelta(minutes=15))
# And finally repeating the initial run to check that indetical
o3 = OceanDrift(loglevel=30, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o3.set_config('environment:fallback:land_binary_mask', 0)
o3.add_reader([norkyst])
z = -40 * np.random.rand(number)
o3.seed_elements(5,
62.5,
number=number,
radius=5000,
z=z,
time=norkyst.start_time)
o3.run(steps=4 * 3, time_step=timedelta(minutes=15))
# Check that we get some difference with Runge-Kutta:
self.assertIsNone(
np.testing.assert_array_almost_equal(
(o2.elements.lon - o.elements.lon).max(), 0.0015, 3))
#(o2.elements.lon-o.elements.lon).max(), 0.013, 3))
# Check that runs with Euler are identical
self.assertIsNone(
np.testing.assert_array_almost_equal(
(o3.elements.lon - o.elements.lon).max(), 0))
def test_seed_polygon(self):
o = OpenOil(loglevel=0)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time = datetime(2015, 1, 1, 12, 5, 17)
o.set_config('seed:oil_type', 'HEIDRUN')
o.seed_within_polygon(lonvec,
latvec,
number=number,
time=time,
wind_drift_factor=.09)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time)
self.assertAlmostEqual(o.elements_scheduled.wind_drift_factor, .09)
# Check that oil type is taken fom config
self.assertEqual(o.oil_name, 'HEIDRUN')
def test_seed_polygon_timespan(self):
o = OceanDrift(loglevel=20)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time = [
datetime(2015, 1, 1, 12, 5, 17),
datetime(2015, 1, 1, 18, 5, 17)
]
o.seed_within_polygon(lonvec, latvec, number=number, time=time)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time[0])
self.assertEqual(o.elements_scheduled_time[-1], time[-1])
@unittest.skipIf(has_ogr is False, 'OGR library needed to parse WKT')
def test_seed_wkt(self):
wkt = 'MULTIPOLYGON(((7.784889 64.353442,7.777561 64.353842,7.774236 64.354707,7.770215 64.355829,7.774269 64.356015,7.776829 64.356863,7.779107 64.3578,7.782827 64.358355,7.786346 64.359615,7.787109 64.361975,7.790125 64.361132,7.794584 64.359908,7.798455 64.359624,7.797258 64.358193,7.79978 64.356904,7.795957 64.356494,7.792955 64.355335,7.789134 64.355339,7.784889 64.353442)))'
o = OceanDrift(loglevel=20)
o.set_config('seed:number', 100)
o.seed_from_wkt(wkt, time=datetime.now())
wkt_multi = 'MULTIPOLYGON(((2.458058 59.178919,2.456276 59.179283,2.454867 59.180692,2.45277 59.182852,2.452521 59.183759,2.452675 59.184726,2.451365 59.18534,2.451436 59.186609,2.450835 59.188138,2.449576 59.189435,2.447393 59.190818,2.447211 59.191915,2.446273 59.193573,2.445551 59.19423,2.446597 59.195015,2.44838 59.194651,2.450277 59.193,2.452377 59.191919,2.453315 59.19026,2.45457 59.187885,2.455473 59.186131,2.457033 59.18461,2.458774 59.181992,2.458971 59.180403,2.459775 59.179444,2.459606 59.178969,2.458058 59.178919)),((2.442682 59.197444,2.440531 59.198922,2.439575 59.199994,2.440874 59.200951,2.439596 59.20166,2.436232 59.202958,2.433255 59.203728,2.42982 59.203756,2.428 59.202946,2.425857 59.200693,2.42454 59.199149,2.422418 59.198563,2.419404 59.198158,2.417332 59.197175,2.41514 59.19532,2.412395 59.194596,2.410072 59.194519,2.409481 59.193397,2.408199 59.191947,2.405959 59.190489,2.403129 59.188988,2.401292 59.18759,2.398331 59.187867,2.395639 59.187825,2.393585 59.187428,2.389665 59.187697,2.38736 59.188208,2.386923 59.189132,2.390625 59.188785,2.392191 59.189424,2.395825 59.188887,2.398602 59.188627,2.402104 59.189869,2.403773 59.191871,2.407276 59.193113,2.407648 59.194158,2.407751 59.195522,2.410008 59.196488,2.411979 59.197187,2.41439 59.19912,2.415839 59.199965,2.417946 59.201043,2.417796 59.202235,2.414886 59.203195,2.411923 59.203473,2.40923 59.203431,2.409753 59.204363,2.412549 59.20469,2.415342 59.203937,2.41891 59.20321,2.420325 59.203961,2.420463 59.20542,2.419357 59.207683,2.4218 59.208631,2.420303 59.209262,2.418925 59.210766,2.421401 59.21073,2.424984 59.20951,2.425201 59.208508,2.425939 59.207359,2.428832 59.205812,2.431004 59.206001,2.433124 59.205507,2.436926 59.204365,2.439568 59.203724,2.441518 59.202755,2.442879 59.201744,2.443246 59.20063,2.443311 59.199741,2.444589 59.199032,2.445428 59.198168,2.445088 59.197218,2.442682 59.197444)))'
o.seed_from_wkt(wkt_multi, time=datetime.now(), number=200)
self.assertEqual(len(o.elements_scheduled), 300)
self.assertAlmostEqual(o.elements_scheduled.lat.max(), 64.36, 2)
self.assertAlmostEqual(o.elements_scheduled.lat.min(), 59.18, 2)
@unittest.skipIf(has_ogr is False, 'OGR library needed to read shapefiles')
def test_seed_shapefile(self):
o = OceanDrift(loglevel=20)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=100,
layername=None,
featurenum=[2, 4],
time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 100)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=300,
layername=None,
featurenum=None,
time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 400)
self.assertAlmostEqual(o.elements_scheduled.lat[-1], 52.5, 2)
#@unittest.skipIf(has_ogr is False,
# 'GDAL library needed to read shapefiles')
#def test_write_geotiff(self):
# o = OceanDrift(loglevel=20)
# o.seed_elements(lon=4, lat=60, time=datetime(2016, 1, 1))
# o.run(steps=3)
# o.write_geotiff('geotiff.tif')
def test_seed_single_point_over_time(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements(2.0,
61.0,
radius=0,
number=9,
time=[datetime(2015, 1, 1),
datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30)
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 5)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
def test_temporal_seed(self):
self.o = OceanDrift(loglevel=20)
self.o.set_config('environment:fallback:x_sea_water_velocity', 1)
self.o.set_config('environment:fallback:land_binary_mask', 0)
# Seed elements on a grid at regular time interval
start_time = datetime(2016, 9, 16)
time_step = timedelta(hours=6)
num_steps = 10
lon = 4.4
lat = 60.0
for i in range(num_steps + 1):
self.o.seed_elements(lon,
lat,
radius=0,
number=2,
time=start_time + i * time_step)
# Running model
self.o.run(steps=20, time_step=3600, outfile='temporal_seed.nc')
self.o = OceanDrift(loglevel=20)
# Check that data imported is properly masked
self.o.io_import_file('temporal_seed.nc')
self.assertTrue(self.o.history['lon'].max() < 1000)
self.assertTrue(self.o.history['lon'].min() > -1000)
self.assertTrue(self.o.history['lon'].mask[5, 5])
self.assertFalse(self.o.history['lon'].mask[1, 1])
os.remove('temporal_seed.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.set_config('environment:fallback:x_wind', 8)
o1.set_config('environment:fallback:land_binary_mask', 0)
o1.seed_elements(4.1,
63.3,
radius=1000,
number=100,
time=norkyst.start_time)
o1.set_config('vertical_mixing: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(), -44.4, 1)
self.assertAlmostEqual(o1.history['z'].max(), 0.0, 1)
os.remove('verticalmixing.nc')
def test_vertical_mixing_profiles(self):
# Testing an isolated mixing timestep
cases = [ # Some cases with expected outcome
{
'vt': 0,
'K': 0,
'K_below': .01,
'T': 60, # No mixing
'zmin': -10,
'zmax': -10,
'zmean': -10
},
{
'vt': -.005,
'K': 0,
'K_below': .01,
'T': 60, # Sinking
#'zmin': -74.0, 'zmax': -21.4, 'zmean': -50.2}, # With old seed_elements
'zmin': -74.79,
'zmax': -21.6,
'zmean': -49.97
},
{
'vt': 0,
'K': .01,
'K_below': .01,
'T': 60, # Mixing
#'zmin': -39.8, 'zmax': -0.1, 'zmean': -14.5},
'zmin': -42.76,
'zmax': -0.02,
'zmean': -14.38
},
{
'vt': .005,
'K': .01,
'K_below': .01,
'T': 60, # Mixing and rising
#'zmin': -8.1, 'zmax': -0.01, 'zmean': -2.1},
'zmin': -7.86,
'zmax': -0.01,
'zmean': -2.1
},
{
'vt': -0.005,
'K': .01,
'K_below': .01,
'T': 60, # Mixing and sinking
#'zmin': -75.8, 'zmax': -20.7, 'zmean': -48.1},
'zmin': -78.76,
'zmax': -19.74,
'zmean': -48.0
},
{
'vt': 0,
'K': .02,
'K_below': .001,
'T': 60, # Mixing in mixed layer
#'zmin': -22.8, 'zmax': -0.1, 'zmean': -9.8},
'zmin': -21.3,
'zmax': -0.1,
'zmean': -9.55
},
]
N = 100
z = np.arange(0, -30, -2)
time = datetime.now()
for case in cases:
diffusivity = np.ones(z.shape) * case['K']
diffusivity[z < -15] = case['K_below']
o = OceanDrift(loglevel=20)
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:diffusivitymodel', 'environment')
o.set_config('vertical_mixing:timestep', case['T'])
o.seed_elements(lon=4,
lat=60,
z=-10,
time=time,
number=N,
terminal_velocity=case['vt'])
o.time = time
o.time_step = timedelta(hours=2)
o.release_elements()
o.set_config('environment:fallback:land_binary_mask', 0)
o.environment = np.array(np.ones(N) * 100,
dtype=[('sea_floor_depth_below_sea_level',
np.float32)]).view(np.recarray)
o.environment_profiles = {
'z': z,
'ocean_vertical_diffusivity': np.tile(diffusivity, (N, 1)).T
}
o.set_fallback_values()
o.vertical_mixing()
self.assertAlmostEqual(o.elements.z.min(), case['zmin'], 1)
self.assertAlmostEqual(o.elements.z.max(), case['zmax'], 1)
self.assertAlmostEqual(o.elements.z.mean(), case['zmean'], 1)
def test_export_step_interval(self):
# Export to file only at end
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(
o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o1.add_reader(norkyst)
o1.set_config('environment:fallback:land_binary_mask', 0)
o1.seed_elements(4.25,
60.2,
radius=1000,
number=10,
time=norkyst.start_time)
o1.run(steps=40)
# Export to file during simulation
o2 = OceanDrift(loglevel=20)
o2.add_reader(norkyst)
o2.set_config('environment:fallback:land_binary_mask', 0)
o2.seed_elements(4.25,
60.2,
radius=1000,
number=10,
time=norkyst.start_time)
o2.run(steps=40,
export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertIsNone(
np.testing.assert_array_equal(o1.history['lon'].compressed(),
o2.history['lon'].compressed()))
# Finally check when steps is multiple of export_buffer_length
o3 = OceanDrift(loglevel=20)
o3.add_reader(norkyst)
o3.set_config('environment:fallback:land_binary_mask', 0)
o3.seed_elements(4.25,
60.2,
radius=1000,
number=10,
time=norkyst.start_time)
o3.run(steps=42)
# Export to file during simulation
o4 = OceanDrift(loglevel=20)
o4.add_reader(norkyst)
o4.set_config('environment:fallback:land_binary_mask', 0)
o4.seed_elements(4.25,
60.2,
radius=1000,
number=10,
time=norkyst.start_time)
o4.run(steps=42,
export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertIsNone(
np.testing.assert_array_equal(o3.history['lon'].compressed(),
o4.history['lon'].compressed()))
os.remove('export_step_interval.nc')
def test_export_final_timestep(self):
o = OceanDrift()
o.set_config('environment:constant:land_binary_mask', 0)
o.set_config('general:use_auto_landmask', False)
o.seed_elements(lon=0,
lat=0,
radius=500,
number=100,
time=[datetime(2010, 1, 1),
datetime(2010, 1, 3)])
o.run(duration=timedelta(hours=20),
time_step=3600,
time_step_output=3600 * 3)
index_of_first, index_of_last = \
o.index_of_activation_and_deactivation()
assert o.num_elements_active() == len(index_of_first)
def test_buffer_length_stranding(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(
o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
landmask = reader_global_landmask.Reader(extent=[4.5, 6.0, 60.1, 60.4])
o1.add_reader([landmask])
o1.set_config('environment:fallback:x_sea_water_velocity',
0.8) # onshore drift
o1.seed_elements(4.8,
60.2,
radius=5000,
number=100,
time=norkyst.start_time)
o1.run(steps=100,
time_step=900,
time_step_output=3600,
export_buffer_length=10)
# Without buffer
o2 = OceanDrift(loglevel=30)
o2.add_reader([landmask])
o2.set_config('environment:fallback:x_sea_water_velocity',
0.8) # onshore drift
o2.seed_elements(4.8,
60.2,
radius=5000,
number=100,
time=norkyst.start_time)
o2.run(steps=100,
time_step=900,
time_step_output=3600,
outfile='test_buffer_length_stranding.nc')
self.assertIsNone(
np.testing.assert_array_equal(o1.history['lon'].compressed(),
o2.history['lon'].compressed()))
self.assertIsNone(
np.testing.assert_array_almost_equal(
o1.history['status'].compressed(),
o2.history['status'].compressed()))
os.remove('test_buffer_length_stranding.nc')
def test_output_time_step(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(
o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
landmask = reader_global_landmask.Reader(extent=[4.5, 5.2, 60.0, 60.5])
o1.add_reader([landmask, norkyst])
o1.seed_elements(4.96,
60.1,
radius=3000,
number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=30)
o2.add_reader([landmask, norkyst])
o2.seed_elements(4.96,
60.1,
radius=3000,
number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100, 25))
self.assertEqual(o2.history.shape, (100, 13))
# Check that start and end conditions (longitudes) are idential
self.assertIsNone(
np.testing.assert_array_equal(
o1.history['lon'][:, 24].compressed(),
o2.history['lon'][:, 12].compressed()))
self.assertIsNone(
np.testing.assert_array_equal(o1.history['lon'][:, 0].compressed(),
o2.history['lon'][:,
0].compressed()))
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertIsNone(
np.testing.assert_array_equal(
o2i.history['lon'][:, 12].compressed(),
o2.history['lon'][:, 12].compressed()))
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
def test_time_step_config(self):
# Default
o = OceanDrift(loglevel=50)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.run(steps=2)
self.assertEqual(o.time_step.total_seconds(), 3600)
self.assertEqual(o.time_step_output.total_seconds(), 3600)
# Setting time_step
o = OceanDrift(loglevel=50)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.run(steps=2, time_step=1800)
self.assertEqual(o.time_step.total_seconds(), 1800)
# Setting time_step and time_step_output
o = OceanDrift(loglevel=50)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.run(steps=2, time_step=1800, time_step_output=3600)
self.assertEqual(o.time_step.total_seconds(), 1800)
self.assertEqual(o.time_step_output.total_seconds(), 3600)
# time_step from config
o = OceanDrift(loglevel=50)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.set_config('general:time_step_minutes', 15)
o.run(steps=2)
self.assertEqual(o.time_step.total_seconds(), 900)
self.assertEqual(o.time_step_output.total_seconds(), 900)
# time_step and time_step_output from config
o = OceanDrift(loglevel=50)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.set_config('general:time_step_minutes', 15)
o.set_config('general:time_step_output_minutes', 120)
o.run(steps=2)
self.assertEqual(o.time_step.total_seconds(), 900)
self.assertEqual(o.time_step_output.total_seconds(), 7200)
def test_reader_boundary(self):
# Check that the element outside reader coverage is
# not deactivated if fallback value exist
o = OceanDrift()
nordic3d = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc'
)
lon = [12.0, 12.0]
lat = [70.0, 70.5]
o.add_reader(nordic3d)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon, lat, number=2, radius=0, time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 2)
self.assertEqual(o.num_elements_deactivated(), 0)
# Check that the outside element is deactivated,
# if no fallback value exists
o = OceanDrift()
o.set_config('environment:fallback:x_sea_water_velocity', None)
o.add_reader(nordic3d)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon, lat, number=2, radius=0, time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
def test_seed_seafloor(self):
o = OpenOil(loglevel=50)
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
# Adding reader as lazy, to test seafloor seeding
o.add_readers_from_list([
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc'
])
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:x_wind', 0)
o.set_config('environment:fallback:y_wind', 0)
#o.set_config('environment:fallback:x_sea_water_velocity', 0)
#o.set_config('environment:fallback:y_sea_water_velocity', 0)
lon = 4.5
lat = 62.0
o.set_config('seed:droplet_diameter_min_subsea', 0.0010) # s
o.set_config('seed:droplet_diameter_max_subsea', 0.0010) # s
o.seed_elements(lon,
lat,
z='seafloor',
time=reader_norkyst.start_time,
density=1000,
oiltype='GENERIC BUNKER C')
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0, 0], -147.3, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1, 0], -122.52, 1) # After some rising
def test_seed_above_seafloor(self):
o = OpenOil(loglevel=30)
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:x_wind', 0)
o.set_config('environment:fallback:y_wind', 0)
o.set_config('environment:fallback:x_sea_water_velocity', 0)
o.set_config('environment:fallback:y_sea_water_velocity', 0)
o.add_reader([reader_norkyst])
lon = 4.5
lat = 62.0
o.set_config('seed:droplet_diameter_min_subsea', 0.0010) # s
o.set_config('seed:droplet_diameter_max_subsea', 0.0010) # s
# Seed elements 50 meters above seafloor:
o.seed_elements(lon,
lat,
z='seafloor+50',
time=reader_norkyst.start_time,
density=1000,
oil_type='AASGARD A 2003')
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0, 0], -97.3, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1, 0], -72.0, 1) # After some rising
def test_seed_below_reader_coverage(self):
o = OpenOil(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:x_wind', 0)
o.set_config('environment:fallback:y_wind', 0)
o.add_reader([reader_norkyst])
lon = 5.0
lat = 64.0
o.set_config('seed:droplet_diameter_min_subsea', 0.0005)
o.set_config('seed:droplet_diameter_max_subsea', 0.005)
o.seed_elements(lon,
lat,
z=-350,
time=reader_norkyst.start_time,
density=1000,
oil_type='AASGARD A 2003')
#o.set_config('vertical_mixing:TSprofiles', True)
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[-1, 0], -134.0, 1) # After some rising
def test_seed_below_seafloor(self):
o = OpenOil(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader([reader_norkyst])
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:x_wind', 0)
o.set_config('environment:fallback:y_wind', 0)
o.set_config('environment:fallback:x_sea_water_velocity', 0)
o.set_config('environment:fallback:y_sea_water_velocity', 0)
lon = 4.5
lat = 62.0
o.set_config('seed:droplet_diameter_min_subsea', 0.0005)
o.set_config('seed:droplet_diameter_max_subsea', 0.001)
o.seed_elements(lon,
lat,
z=-5000,
time=reader_norkyst.start_time,
density=1000,
oil_type='GENERIC BUNKER C')
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[0, 0], -147.3, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1, 0], -132.45, 1) # After some rising
def test_seed_below_seafloor_deactivating(self):
o = OpenOil(loglevel=50)
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader([reader_norkyst])
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:x_wind', 0)
o.set_config('environment:fallback:y_wind', 0)
o.set_config('environment:fallback:x_sea_water_velocity', 0)
o.set_config('environment:fallback:y_sea_water_velocity', 0)
lon = 4.5
lat = 62.0
o.set_config('seed:droplet_diameter_min_subsea', 0.0005)
o.set_config('seed:droplet_diameter_max_subsea', 0.001)
o.seed_elements(lon,
lat,
z=[-5000, -100],
time=reader_norkyst.start_time,
density=1000,
number=2,
oil_type='AASGARD A 2003')
o.set_config('general:seafloor_action',
'deactivate') # This time we deactivate
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertEqual(o.num_elements_total(), 2)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
self.assertAlmostEqual(z[0, 1], -100, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1, 1], -81.4, 1) # After some rising
def test_lift_above_seafloor(self):
# See an element at some depth, and progapate towards coast
# (shallower water) and check that it is not penetrating seafloor
o = OceanDrift(loglevel=50)
o.max_speed = 100
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
reader_norkyst.buffer = 200
o.add_reader([reader_norkyst],
variables='sea_floor_depth_below_sea_level')
o.set_config('environment:fallback:x_sea_water_velocity',
10) # Pure eastward motion
o.set_config('environment:fallback:y_sea_water_velocity', 0)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(3.9, 62.0, z=-200, time=reader_norkyst.start_time)
o.set_config('drift:vertical_mixing', False)
o.run(steps=12, time_step=300)
seafloor_depth, status = o.get_property(
'sea_floor_depth_below_sea_level')
z, status = o.get_property('z')
# Uncomment to plot
#import matplotlib.pyplot as plt
#plt.plot(-seafloor_depth, label='Seafloor depth')
#plt.plot(z, label='Element depth')
#plt.legend(loc='best')
#plt.show()
# Check that element has not penetrated seafloor
self.assertFalse(
o.elements.z < -o.environment.sea_floor_depth_below_sea_level)
self.assertIsNone(
np.testing.assert_array_almost_equal(o.elements.z, -134.5, 1))
def test_seed_on_land(self):
o = OceanDrift(loglevel=50)
o.seed_elements(lon=9, lat=60, time=datetime.now(), number=100)
outfile = 'out.nc'
with self.assertRaises(ValueError):
o.run(steps=4,
time_step=1800,
time_step_output=3600,
outfile=outfile)
os.remove(outfile)
#o.write_netcdf_density_map(outfile)
#os.remove(outfile)
def test_retirement(self):
o = OceanDrift(loglevel=0)
o.set_config('drift:max_age_seconds', 5000)
o.set_config('environment:fallback:x_sea_water_velocity', .5)
o.set_config('environment:fallback:y_sea_water_velocity', .3)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(
lon=0,
lat=60,
number=10,
time=[datetime.now(),
datetime.now() + timedelta(seconds=6000)])
o.run(time_step=1000, duration=timedelta(seconds=7000))
self.assertEqual(o.num_elements_deactivated(), 5)
def test_outside_domain(self):
o = OceanDrift(loglevel=50)
reader_osc_x = reader_oscillating.Reader('x_sea_water_velocity',
amplitude=1,
zero_time=datetime.now())
reader_osc_y = reader_oscillating.Reader('y_sea_water_velocity',
amplitude=1,
zero_time=datetime.now())
o.add_reader([reader_osc_x, reader_osc_y])
o.set_config('drift:deactivate_east_of', 2.1)
o.set_config('drift:deactivate_west_of', 1.9)
o.set_config('drift:deactivate_south_of', 59.9)
o.set_config('drift:deactivate_north_of', 60.1)
o.set_config('environment:fallback:land_binary_mask', 0)
o.seed_elements(lon=2,
lat=60,
number=1000,
time=datetime.now(),
radius=10000)
o.run(duration=timedelta(hours=5))
self.assertEqual(o.num_elements_deactivated(), 768)
self.assertEqual(o.num_elements_active(), 232)
def test_seed_time_backwards_run(self):
o = OceanDrift(loglevel=20)
o.set_config('drift:max_age_seconds', 2000)
o.set_config('environment:fallback:x_sea_water_velocity', .5)
o.set_config('environment:fallback:y_sea_water_velocity', .3)
o.set_config('environment:fallback:land_binary_mask', 0)
time = [datetime(2018, 1, 1, i) for i in range(10)]
o.seed_elements(lon=0, lat=60, time=time)
o.seed_elements(lon=1, lat=60, time=datetime(2018, 1, 1, 7))
o.run(end_time=datetime(2018, 1, 1, 2), time_step=-1800)
self.assertEqual(o.num_elements_scheduled(), 3)
self.assertEqual(o.num_elements_active(), 8)
self.assertEqual(o.steps_calculation, 14)
def test_oil_mixed_to_seafloor(self):
o = OpenOil(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader(norkyst)
o.set_config('processes:evaporation', False)
o.set_config('environment:fallback:x_wind', 25)
o.set_config('environment:fallback:y_wind', 0)
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:ocean_vertical_diffusivity', 0.9)
o.seed_elements(lon=5.38,
lat=62.77,
time=norkyst.start_time,
number=100,
radius=5000)
o.run(end_time=norkyst.end_time)
self.assertEqual(o.num_elements_active(), 100)
def test_unseeded_elements(self):
o = PlastDrift()
# Seeding elements for 12 hours, but running only 6
time = datetime(2019, 8, 30, 12)
o.seed_elements(lon=4.85,
lat=60,
number=10,
time=[time, time + timedelta(hours=6)],
origin_marker=7)
o.seed_elements(lon=4.75,
lat=60,
number=10,
time=[time, time + timedelta(hours=6)],
origin_marker=8)
o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('environment:fallback:y_sea_water_velocity', 1)
o.run(duration=timedelta(hours=3))
self.assertEqual(o.history.shape[0], 10)
self.assertEqual(o.history.shape[1], 4)
self.assertEqual(o.history['origin_marker'].min(), 7)
self.assertEqual(o.history['origin_marker'].max(), 8)
def test_no_active_but_still_unseeded_elements(self):
o = OceanDrift(loglevel=20)
# deactivate elements after 3 hours
o.set_config('drift:max_age_seconds', 3600 * 3)
norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader(norkyst)
# seed two elements at 6 hour interval
o.seed_elements(
number=2,
lon=4,
lat=62,
time=[norkyst.start_time, norkyst.start_time + timedelta(hours=6)])
o.set_config('environment:fallback:land_binary_mask', 0)
o.run(duration=timedelta(hours=8), outfile='test.nc')
os.remove('test.nc')
# Check that simulations has run until scheduled end
self.assertEqual(o.steps_calculation, 8)
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift() # Basic drift model suitable for passive tracers or drifters
#######################
# Preparing Readers
#######################
reader_current = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
reader_wind = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
o.add_reader([reader_current, reader_wind])
#######################
# Seeding elements
#######################
# Elements are moved with the ocean current, in addition to a fraction of
# the wind speed (wind_drift_factor). This factor depends on the properties
# of the elements. Typical empirical values are:
# - 0.035 (3.5 %) for oil and iSphere driftes
# - 0.01 (1 %) for CODE drifters partly submerged ~0.5 m
# As there are large uncertainties, it makes sence to provide a statistical
# distribution of wind_drift_factors
# Using a constant value for all elements:
#wind_drift_factor = 0.03
Example to illustrate stranding options using an artificial
east-west oscillating current field
Knut-Frode Dagestad, Feb 2017
"""
from datetime import datetime
from opendrift.readers import reader_oscillating
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
reader_osc = reader_oscillating.Reader('x_sea_water_velocity',
amplitude=1,
zero_time=datetime.now())
o.add_reader([reader_osc]) # Oscillating east-west current component
o.fallback_values['y_sea_water_velocity'] = .2 # Adding northwards drift
#%%
# Try different options: 'previous', 'stranding', 'none'
o.set_config('general:coastline_action', 'previous')
o.seed_elements(lon=12.2,
lat=67.7,
radius=5000,
number=25,
time=reader_osc.zero_time)
o.run(steps=36 * 4, time_step=900, time_step_output=1800)
================================================
"""
from datetime import timedelta
import numpy as np
from opendrift.readers.unstructured import shyfem
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
o.set_config('general:coastline_action', 'previous')
shyfem = shyfem.Reader(
'https://iws.ismar.cnr.it/thredds/dodsC/emerge/shyfem_unstructured_adriatic.nc'
)
o.add_reader(shyfem)
print(shyfem)
# Seed elements at defined positions, depth and time
N = 1000
z = -15 * np.random.uniform(0, 1, N)
o.seed_elements(lon=12.4,
lat=45.25,
radius=1000,
number=N,
z=z,
time=shyfem.start_time)
#%%
# Running model
o.run(time_step=1800, duration=timedelta(hours=12))
thredds_path_2 = 'http://thredds.moanaproject.org:8080/thredds/dodsC/moana/ocean/NZB/v1.9/raw_3D/nz5km_his_201708.nc?ntimes,dt,hc,grid,s_rho[5:1:12],Cs_r[5:1:12],h[0:1:466][0:1:396],lon_rho[0:1:466][0:1:396],lat_rho[0:1:466][0:1:396],lon_u[0:1:466][0:1:395],lat_u[0:1:466][0:1:395],lon_v[0:1:465][0:1:396],lat_v[0:1:465][0:1:396],lon_psi[0:1:465][0:1:395],angle[0:1:466][0:1:396],mask_rho[0:1:466][0:1:396],mask_u[0:1:466][0:1:395],mask_v[0:1:465][0:1:396],ocean_time[0:1:248],z_rho[0:1:248][5:1:12][0:1:466][0:1:396],u_eastward[0:1:248][5:1:12][0:1:466][0:1:396],v_northward[0:1:248][5:1:12][0:1:466][0:1:396]' # to finish the run in the previous month
reader_moana_v19_2 = reader_ROMS_native_MOANA.Reader([thredds_path_2]) #
reader_moana_v19_2.multiprocessing_fail = True
thredds_path_3 = 'http://thredds.moanaproject.org:8080/thredds/dodsC/moana/ocean/NZB/v1.9/raw_3D/nz5km_his_201707.nc?ntimes,dt,hc,grid,s_rho[5:1:12],Cs_r[5:1:12],h[0:1:466][0:1:396],lon_rho[0:1:466][0:1:396],lat_rho[0:1:466][0:1:396],lon_u[0:1:466][0:1:395],lat_u[0:1:466][0:1:395],lon_v[0:1:465][0:1:396],lat_v[0:1:465][0:1:396],lon_psi[0:1:465][0:1:395],angle[0:1:466][0:1:396],mask_rho[0:1:466][0:1:396],mask_u[0:1:466][0:1:395],mask_v[0:1:465][0:1:396],ocean_time[0:1:248],z_rho[0:1:248][5:1:12][0:1:466][0:1:396],u_eastward[0:1:248][5:1:12][0:1:466][0:1:396],v_northward[0:1:248][5:1:12][0:1:466][0:1:396]' # to finish the run in the previous month
reader_moana_v19_3 = reader_ROMS_native_MOANA.Reader([thredds_path_3]) #
reader_moana_v19_3.multiprocessing_fail = True
# Making customised landmask - not required here, using ROMS landmask
#reader_landmask = reader_global_landmask.Reader(
# llcrnrlon=171.0, llcrnrlat=184.5,
# urcrnrlon=-42.0, urcrnrlat=-32.0)# max is 185deg
# use native landmask of ROMS files
o.add_reader([reader_moana_v19_1, reader_moana_v19_2, reader_moana_v19_3])
#o.add_reader([reader_moana_v19])
o.set_config('general:use_auto_landmask', True) # dynamical landmask
###############################
# PARTICLE SEEDING
###############################
# Define the starting position of the particles on the Ninety miles beach: 200 random points along the beach, spreading 200m offshore.
nb_parts = 501 # number of particles released per point during the release interval
points = np.loadtxt(
'./Second_backtrack_input_files/Release_Ninety_miles_beach_backtrack2_high_dens_500mbuff.xyz',
delimiter='\t',
dtype=str)
plon = points[:, 0].astype(np.float)
from opendrift.readers import reader_basemap_landmask
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=4.0, llcrnrlat=59.9,
urcrnrlon=5.5, urcrnrlat=61.2,
resolution='h', projection='merc')
o.add_reader([reader_basemap, reader_norkyst])
# Seeding some particles
lons = np.linspace(4.4, 4.6, 10)
lats = np.linspace(60.0, 60.1, 10)
lons, lats = np.meshgrid(lons, lats)
lons = lons.ravel()
lats = lats.ravel()
# Seed oil elements on a grid at regular time interval
start_time = reader_norkyst.start_time
time_step = timedelta(hours=6)
num_steps = 10
for i in range(num_steps+1):
o.seed_elements(lons, lats, radius=0, number=100,
time=start_time + i*time_step)
from opendrift.readers import reader_telemac_selafin
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0)
filename = '{}Telemac_3D{}r3d_tide_open_drift.slf'.format(
o.test_data_folder(), sep)
#Lambert North
proj = "+proj=lcc +lat_1=49.50000000000001 +lat_0=49.50000000000001 +lon_0=0 \
+k_0=0.999877341 +x_0=600000 +y_0=200000 +a=6378249.2 +b=6356515 \
+units=m +no_defs"
start_time = datetime(2021, 1, 1, 00, 00)
selafin = reader_telemac_selafin.Reader(filename=filename,
proj4=proj,
start_time=start_time)
o.add_reader(selafin)
o.set_config('general:coastline_action', 'previous')
# start_time = selafin.start_time generally wrong
time_step = timedelta(seconds=selafin.slf.tags["times"][1])
length = timedelta(seconds=selafin.slf.tags["times"][-1])
num_steps = len(selafin.slf.tags["times"])
# center seeds in the middle
x,y = (selafin.x.max()-selafin.x.min())/2+selafin.x.min(),\
(selafin.y.max()-selafin.y.min())/2+selafin.y.min()
p = Proj(proj, preserve_units=False)
lon, lat = p(x, y, inverse=True)
o.seed_elements(lon=lon, lat=lat, radius=20000, number= 200, z= 0, \
time= start_time)
o.run(time_step=time_step / 10, duration=length)
o.plot(fast=True)
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
# Arome
reader_arome = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
#reader_arome = reader_netCDF_CF_generic.Reader('https://thredds.met.no/thredds/dodsC/mepslatest/meps_lagged_6_h_latest_2_5km_latest.nc')
# Norkyst
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
#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])
#%%
# Seeding some particles
lon = 4.2
lat = 60.0
# Outside Bergen
time = [reader_arome.start_time, reader_arome.start_time + timedelta(hours=30)]
#%%
# Seed oil elements at defined position and time
o.seed_elements(lon, lat, radius=50, number=5000, time=time)
#%%
# Using windspeed relative to moving ocean (current)
o.set_config('drift:relative_wind', False)
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=4.0,
llcrnrlat=59.9,
urcrnrlon=5.5,
urcrnrlat=61.2,
resolution='h',
projection='merc')
o.add_reader([reader_basemap, reader_norkyst])
# Seeding some particles
lons = np.linspace(4.4, 4.6, 10)
lats = np.linspace(60.0, 60.1, 10)
lons, lats = np.meshgrid(lons, lats)
lons = lons.ravel()
lats = lats.ravel()
# Seed oil elements on a grid at regular time interval
start_time = reader_norkyst.start_time
time_step = timedelta(hours=6)
num_steps = 10
for i in range(num_steps + 1):
o.seed_elements(lons,
lats,
reader_current = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
reader_wind = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=4,
llcrnrlat=59.8,
urcrnrlon=6,
urcrnrlat=61,
resolution='h',
projection='merc')
o.add_reader([reader_basemap, reader_current, reader_wind])
#######################
# Seeding elements
#######################
# Elements are moved with the ocean current, in addition to a fraction of
# the wind speed (wind_drift_factor). This factor depends on the properties
# of the elements. Typical empirical values are:
# - 0.035 (3.5 %) for oil and iSphere driftes
# - 0.01 (1 %) for CODE drifters partly submerged ~0.5 m
# As there are large uncertainties, it makes sence to provide a statistical
# distribution of wind_drift_factors
# Using a constant value for all elements:
#wind_drift_factor = 0.03
from opendrift.readers import reader_ROMS_native
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Nordic 4km
nordic_native = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=11.0, llcrnrlat=67.5,
urcrnrlon=16.0, urcrnrlat=69.0,
resolution='h', projection='merc')
o.add_reader([reader_basemap, nordic_native])
# Seeding some particles
time = nordic_native.start_time
lon = 12.0; lat = 68.3;
# Seed oil elements at defined position and time
o.seed_elements(lon, lat, radius=0, number=10, z=np.linspace(0, -150, 10), time=time)
print o
# Running model
o.run(time_step=3600)
# Print and plot results
print o
import numpy as np
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
# Norkyst
reader_norkyst = reader_netCDF_CF_generic.Reader(
'https://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
# Nordic4
reader_nordic4 = reader_netCDF_CF_generic.Reader(
'https://thredds.met.no/thredds/dodsC/sea/nordic4km/zdepths1h/aggregate_be'
)
o.add_reader([reader_norkyst, reader_nordic4])
o.set_config('environment:fallback:land_binary_mask', 0)
#%%
# Seeding some particles
lons = np.linspace(10.2, 12.2, 50)
lats = np.linspace(69.8, 70.8, 50)
lons, lats = np.meshgrid(lons, lats)
#%%
# Seed oil elements at defined position and time
o.seed_elements(lons,
lats,
radius=0,
number=2500,
time=reader_norkyst.start_time)
import numpy as np
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.readers import reader_ROMS_native
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
o.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'
)
#reader_current = reader_ROMS_native.Reader(o.test_data_folder() +
# '2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader([reader_current])
o.set_config('general:coastline_action', 'previous')
#%%
# Seeding elements on a grid
lons = np.linspace(12, 14.5, 30)
lats = np.linspace(67.5, 68.5, 30)
lons, lats = np.meshgrid(lons, lats)
lon = lons.ravel()
lat = lats.ravel()
time = reader_current.start_time
o.seed_elements(lon, lat, radius=0, number=30 * 30, time=time)
o.run(steps=24 * 2, time_step=3600)
# SCHISM reader
reader_landmask = reader_global_landmask.Reader(llcrnrlon=171.5,
llcrnrlat=-43.5,
urcrnrlon=177.0,
urcrnrlat=-38.0)
# NZTM proj4 string found at https://spatialreference.org/ref/epsg/nzgd2000-new-zealand-transverse-mercator-2000/
proj4str_nztm = '+proj=tmerc +lat_0=0 +lon_0=173 +k=0.9996 +x_0=1600000 +y_0=10000000 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs'
schism_native = reader_schism_native.Reader(
filename=
'https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc',
proj4=proj4str_nztm,
use_3d=True)
# schism_native.plot_mesh(variable = ['sea_floor_depth_below_sea_level']) # check reader was correctly loaded
o.add_reader([reader_landmask, schism_native])
o.set_config(
'general:use_auto_landmask', False
) # prevent opendrift from making a new dynamical landmask with global_landmask
# Seed elements at defined positions, depth and time
o.seed_elements(lon=174.046669,
lat=-40.928116,
radius=20,
number=100,
z=np.linspace(0, -10, 100),
time=schism_native.start_time)
o.seed_elements(lon=173.8839,
lat=-40.9160,
radius=20,
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Norkyst
reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
# Nordic4
reader_nordic4 = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/nordic4km/zdepths1h/aggregate_be')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=9.5, llcrnrlat=68.8,
urcrnrlon=19.0, urcrnrlat=71.2,
resolution='h', projection='merc')
o.add_reader([reader_basemap, reader_norkyst, reader_nordic4])
#o.add_reader([reader_basemap, reader_norkyst])
# Seeding some particles
lons = np.linspace(10.2, 12.2, 50)
lats = np.linspace(69.8, 70.8, 50)
lons, lats = np.meshgrid(lons, lats)
lons = lons.ravel()
lats = lats.ravel()
# Seed oil elements at defined position and time
o.seed_elements(lons, lats, radius=0, number=2500,
time=reader_nordic4.start_time)
# Running model (until end of driver data)
o.run(steps=16*4, time_step=900)
reader_norkyst = reader_netCDF_CF_generic.Reader(
'http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
# Nordic4
reader_nordic4 = reader_netCDF_CF_generic.Reader(
'http://thredds.met.no/thredds/dodsC/sea/nordic4km/zdepths1h/aggregate_be')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(llcrnrlon=9.5,
llcrnrlat=68.8,
urcrnrlon=19.0,
urcrnrlat=71.2,
resolution='h',
projection='merc')
o.add_reader([reader_basemap, reader_norkyst, reader_nordic4])
#o.add_reader([reader_basemap, reader_norkyst])
# Seeding some particles
lons = np.linspace(10.2, 12.2, 50)
lats = np.linspace(69.8, 70.8, 50)
lons, lats = np.meshgrid(lons, lats)
lons = lons.ravel()
lats = lats.ravel()
# Seed oil elements at defined position and time
o.seed_elements(lons,
lats,
radius=0,
number=2500,
time=reader_nordic4.start_time)
60.013670, 60.013412, 60.013240, 60.013068, 60.013154, 60.013412,
60.013584, 60.013842, 60.014186, 60.014616, 60.015218, 60.015820,
60.016594, 60.017454, 60.018400, 60.019346, 60.020464, 60.021410,
60.022442, 60.023474, 60.024678, 60.025882, 60.026914
]
drifterlats = drifterlats[::-1]
drifterlons = drifterlons[::-1]
driftertimes = [
datetime(2015, 6, 10, 5, 50) + timedelta(minutes=10) * i
for i in range(len(drifterlons))
]
r = reader_current_from_drifter.Reader(lons=drifterlons,
lats=drifterlats,
times=driftertimes)
o.add_reader(r)
#%%
# We seed elements within polygon, as could have been extracted
# from remote sensing imagery
lons = [2.39, 2.391, 2.392, 2.393, 2.394, 2.393, 2.392, 2.391, 2.39]
lats = [60.02, 60.02, 60.019, 60.02, 60.021, 60.022, 60.021, 60.021, 60.02]
o.seed_within_polygon(lons=lons, lats=lats, number=1000, time=r.start_time)
#%%
# Finally running simulation
o.run(end_time=r.end_time, time_step=r.time_step)
o.animation(buffer=.01, fast=True)
#%%
reader_custom = reader_landmask_custom.Reader(
polygon_file=
'/home/simon/Documents/GitHub/opendrift/examples/schism_marl_edit.shore')
# reader_custom.plot() # check reader was correctly loaded, close figure to continue
# NZTM proj4 string found at https://spatialreference.org/ref/epsg/nzgd2000-new-zealand-transverse-mercator-2000/
proj4str_nztm = '+proj=tmerc +lat_0=0 +lon_0=173 +k=0.9996 +x_0=1600000 +y_0=10000000 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs'
schism_native = reader_schism_native.Reader(
filename=
'https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc',
proj4=proj4str_nztm,
use_3d=True)
# schism_native.plot_mesh(variable = 'sea_floor_depth_below_sea_level') # check reader was correctly loaded, close figure to continue
o.add_reader([reader_custom, schism_native])
o.set_config(
'general:use_auto_landmask', False
) # prevent opendrift from making a new dynamical landmask with global_landmask
# Seed elements at defined positions, depth and time
o.seed_elements(lon=174.046669,
lat=-40.928116,
radius=20,
number=100,
z=np.linspace(0, -10, 100),
time=schism_native.start_time)
o.seed_elements(lon=173.8839,
lat=-40.9160,
radius=20,
def test_output_time_step(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(
o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
landmask = reader_global_landmask.Reader(extent=[4.5, 5.2, 60.0, 60.5])
o1.add_reader([landmask, norkyst])
o1.seed_elements(4.96,
60.1,
radius=3000,
number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=30)
o2.add_reader([landmask, norkyst])
o2.seed_elements(4.96,
60.1,
radius=3000,
number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100, 25))
self.assertEqual(o2.history.shape, (100, 13))
# Check that start and end conditions (longitudes) are idential
self.assertIsNone(
np.testing.assert_array_equal(
o1.history['lon'][:, 24].compressed(),
o2.history['lon'][:, 12].compressed()))
self.assertIsNone(
np.testing.assert_array_equal(o1.history['lon'][:, 0].compressed(),
o2.history['lon'][:,
0].compressed()))
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertIsNone(
np.testing.assert_array_equal(
o2i.history['lon'][:, 12].compressed(),
o2.history['lon'][:, 12].compressed()))
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
from opendrift.models.oceandrift import OceanDrift
lon = 4.5; lat = 60.0; # Outside Bergen
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Arome atmospheric model
reader_arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
# Norkyst ocean model
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# Uncomment to use live data from thredds
#reader_arome = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/meps25files/meps_det_extracted_2_5km_latest.nc')
#reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
o.set_config('general:basemap_resolution', 'i')
o.add_reader([reader_norkyst, reader_arome])
time = reader_arome.start_time
o.seed_elements(lon, lat, radius=500, number=2000, time=time)
o.set_config('drift:current_uncertainty', 0) # 0 is default
o.run(duration=timedelta(hours=24))
# Second run, identical, except for added diffusion
o2 = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
o2.set_config('general:basemap_resolution', 'i')
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.run(duration=timedelta(hours=24))
# Comparing
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.run(duration=timedelta(hours=24),
time_step=900,
time_step_output=1800,
outfile=outfile)
#%%
# Opening the output file lazily with Xarray.
# This will work even if the file is too large to fit in memory, as it
# will read and process data chuck-by-chunk directly from file using Dask.
# Note that the analysis file will be re-used if existing. Thus this file should be deleted after making any changes to the simulation above.
o = opendrift.open_xarray(outfile, analysis_file='simulation_density.nc')
#%%
# Making two animations, for each of the two seedings / origin_markers.
import numpy as np
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.readers import reader_ROMS_native
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
o.max_speed = 3
# This example works better using hourly input from Thredds than the daily data from test folder
reader_nordic = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/nordic4km/zdepths1h/aggregate_be')
#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('general:basemap_resolution', 'h')
o.set_config('general:coastline_action', 'previous')
# Seeding elements on a grid
lons = np.linspace(12, 14.5, 30)
lats = np.linspace(67.5, 68.5, 30)
lons, lats = np.meshgrid(lons, lats)
lon = lons.ravel()
lat = lats.ravel()
time = reader_nordic.start_time
o.seed_elements(lon, lat, radius=0, number=30*30, time=time)
o.run(steps=24*2, time_step=3600)
# By intialisation, only an XML-file with the contents is downloaded.
# The netCDF file with data is downloaded later, after the simulation is started,
# when necessary coverage (time/space) is known ( <reader>.prepare() )
cmems = reader_cmems.Reader(
dataset='global-analysis-forecast-phy-001-024-hourly-merged-uv',
variable_mapping={ # Overriding the mapping in reader_cmems.py
'utotal': 'x_sea_water_velocity',
'vtotal': 'y_sea_water_velocity',
'utide': 'sea_ice_x_velocity', # Fake mapping, as standard_name
'vtide': 'sea_ice_y_velocity'
}) # must be unique for a reader
o = OceanDrift()
o.add_reader(cmems)
# Alternatively, use OPeNDAP directly:
# https://help.marine.copernicus.eu/en/articles/5182598-how-to-consume-the-opendap-api-and-cas-sso-using-python
#o.add_readers_from_list(['https://nrt-dev.cmems-du.eu/thredds/dodsC/global-analysis-forecast-phy-001-024-hourly-merged-uv'])
o.seed_elements(lon=lon, lat=lat, number=5000, radius=1000, time=time)
o.run(duration=duration)
# Although total current (SMOC) has been used as forcing, we plot the tidal current as background field, disguised as ice velocity
o.animation(fast=True,
clabel='Tidal current [m/s]',
skip=1,
scale=20,
background=['sea_ice_x_velocity', 'sea_ice_y_velocity'])
#%%
time_step = timedelta(seconds=.5)
time_step_output = timedelta(seconds=.5)
delta = .01 # spatial resolution
steps = int(duration.total_seconds() / time_step_output.total_seconds() + 1)
o = OceanDrift(loglevel=20)
o.fallback_values['land_binary_mask'] = 0
#%%
# Note that Runge-Kutta here makes a difference to Euler scheme
o.set_config('drift:scheme', 'runge-kutta4')
double_gyre = reader_double_gyre.Reader(epsilon=.25, omega=0.628, A=0.1)
print(double_gyre)
o.add_reader(double_gyre)
#%%
# Calculate Lyapunov exponents
times = [double_gyre.initial_time + n * time_step_output for n in range(steps)]
lcs = o.calculate_ftle(time=times,
time_step=time_step,
duration=duration,
delta=delta,
RLCS=False)
#%%
# Make run with particles for the same period
o.reset()
x = [.9]
y = [.5]
lon, lat = double_gyre.xy2lonlat(x, y)
import numpy as np
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.readers import reader_ROMS_native
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
o.max_speed = 3
# This example works better using hourly input from Thredds than the daily data from test folder
reader_nordic = reader_netCDF_CF_generic.Reader(
'https://thredds.met.no/thredds/dodsC/sea/nordic4km/zdepths1h/aggregate_be'
)
#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('general:coastline_action', 'previous')
#%%
# Seeding elements on a grid
lons = np.linspace(12, 14.5, 30)
lats = np.linspace(67.5, 68.5, 30)
lons, lats = np.meshgrid(lons, lats)
lon = lons.ravel()
lat = lats.ravel()
time = reader_nordic.start_time
o.seed_elements(lon, lat, radius=0, number=30 * 30, time=time)
o.run(steps=24 * 2, time_step=3600)
class TestRun(unittest.TestCase):
"""Tests for (non-scalar) LagrangianArray"""
def make_OceanDrift_object(self):
self.o = OceanDrift(loglevel=20)
self.fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
self.o.use_block = False
self.reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=-1.5, llcrnrlat=59,
urcrnrlon=7, urcrnrlat=64, resolution='i')
self.o.add_reader([self.fake_eddy, self.reader_basemap])
def test_seed(self):
"""Test seeding"""
o = OceanDrift(loglevel=20)
number = 3
lonvec = np.linspace(2, 5, number)
latvec = np.linspace(60, 61, number)
o.seed_elements(lonvec, latvec, number=number,
time=datetime(2015, 1, 1, 12, 5, 17))
#time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.num_elements_active(), 0)
self.assertEqual(o.num_elements_activated(), 0)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), number)
def test_seed_outside_coverage(self):
"""Test seeding"""
o = OpenOil3D(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=60, urcrnrlon=6, urcrnrlat=64,
resolution='c', projection='merc')
o.add_reader([basemap, norkyst])
o.seed_elements(5, 63, number=5,
time=norkyst.start_time - 24*timedelta(hours=24))
o.run(steps=3, time_step=timedelta(minutes=15))
def test_runge_kutta(self):
number = 50
# With Euler
o = OceanDrift3D(loglevel=20, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.add_reader([norkyst])
z=-40*np.random.rand(number)
o.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o.run(steps=4*3, time_step=timedelta(minutes=15))
# With Runge-Kutta
o2 = OceanDrift3D(loglevel=20, seed=0)
o2.fallback_values['land_binary_mask'] = 0
o2.add_reader([norkyst])
z=-40*np.random.rand(number)
o2.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o2.set_config('drift:scheme', 'runge-kutta')
o2.run(steps=4*3, time_step=timedelta(minutes=15))
# And finally repeating the initial run to check that indetical
o3 = OceanDrift3D(loglevel=20, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o3.fallback_values['land_binary_mask'] = 0
o3.add_reader([norkyst])
z=-40*np.random.rand(number)
o3.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o3.run(steps=4*3, time_step=timedelta(minutes=15))
# Check that we get some difference with Runge-Kutta:
self.assertAlmostEqual((o2.elements.lon-o.elements.lon).max(),
0.0015, 3)
# Check that runs with Euler are identical
self.assertEqual((o3.elements.lon-o.elements.lon).max(), 0)
def test_seed_polygon(self):
o = OceanDrift(loglevel=20)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time=datetime(2015, 1, 1, 12, 5, 17)
o.seed_within_polygon(lonvec, latvec, number=number, time=time,
wind_drift_factor=.09)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time)
self.assertAlmostEqual(o.elements_scheduled.wind_drift_factor, .09)
def test_seed_polygon_timespan(self):
o = OceanDrift(loglevel=20)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time=[datetime(2015, 1, 1, 12, 5, 17),
datetime(2015, 1, 1, 18, 5, 17)]
o.seed_within_polygon(lonvec, latvec, number=number, time=time)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time[0])
self.assertEqual(o.elements_scheduled_time[-1], time[-1])
@unittest.skipIf(has_ogr is False,
'OGR library needed to read shapefiles')
def test_seed_shapefile(self):
o = OceanDrift(loglevel=20)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=100, layername=None,
featurenum=[2, 4], time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 100)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=300, layername=None,
featurenum=None, time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 400)
#@unittest.skipIf(has_ogr is False,
# 'GDAL library needed to read shapefiles')
#def test_write_geotiff(self):
# o = OceanDrift(loglevel=20)
# o.seed_elements(lon=4, lat=60, time=datetime(2016, 1, 1))
# o.run(steps=3)
# o.write_geotiff('geotiff.tif')
def test1_seed_single_point_over_time(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements(2.0, 61.0, radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 5)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
def test2_seed_elementss(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements([2.0, 4.5, 3.0], [61.0, 60.0, 62.0],
radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 9)
def test3_run_import(self):
"""Import output file from previous test, and check elements"""
self.o = OceanDrift(loglevel=20)
self.o.io_import_file('unittest.nc')
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 5)
def test4_cleaning(self):
"""Cleaning up"""
os.remove('unittest.nc')
def test_temporal_seed(self):
self.o = OceanDrift(loglevel=20)
self.o.fallback_values['x_sea_water_velocity'] = 1
self.o.fallback_values['land_binary_mask'] = 0
# Seed elements on a grid at regular time interval
start_time = datetime(2016,9,16)
time_step = timedelta(hours=6)
num_steps = 10
lon = 4.4
lat = 60.0
for i in range(num_steps+1):
self.o.seed_elements(lon, lat, radius=0, number=2,
time=start_time + i*time_step)
# Running model
self.o.run(steps=20, time_step=3600, outfile='temporal_seed.nc')
self.o = OceanDrift(loglevel=20)
# Check that data imported is properly masked
self.o.io_import_file('temporal_seed.nc')
self.assertTrue(self.o.history['lon'].max() < 1000)
self.assertTrue(self.o.history['lon'].min() > -1000)
self.assertTrue(self.o.history['lon'].mask[5,5])
self.assertFalse(self.o.history['lon'].mask[1,1])
os.remove('temporal_seed.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.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_export_step_interval(self):
# Export to file only at end
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o1.add_reader(norkyst)
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o1.run(steps=40)
# Export to file during simulation
o2 = OceanDrift(loglevel=20)
o2.add_reader(norkyst)
o2.fallback_values['land_binary_mask'] = 0
o2.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o2.run(steps=40, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertItemsEqual(o1.history['lon'].compressed(),
o2.history['lon'].compressed())
# Finally check when steps is multiple of export_buffer_length
o3 = OceanDrift(loglevel=20)
o3.add_reader(norkyst)
o3.fallback_values['land_binary_mask'] = 0
o3.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o3.run(steps=42)
# Export to file during simulation
o4 = OceanDrift(loglevel=20)
o4.add_reader(norkyst)
o4.fallback_values['land_binary_mask'] = 0
o4.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o4.run(steps=42, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertItemsEqual(o3.history['lon'].compressed(),
o4.history['lon'].compressed())
os.remove('export_step_interval.nc')
def test_buffer_length_stranding(self):
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=1, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='i', projection='merc')
o1.add_reader([basemap])
o1.fallback_values['x_sea_water_velocity'] = 1.0 # onshore drift
o1.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o1.run(steps=100,
time_step=900,
time_step_output=3600,
export_buffer_length=10)
# Without buffer
o2 = OceanDrift(loglevel=20)
o2.add_reader([basemap])
o2.fallback_values['x_sea_water_velocity'] = 1.0 # onshore drift
o2.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o2.run(steps=100,
time_step=900,
time_step_output=3600,
outfile='test_buffer_length_stranding.nc')
self.assertItemsEqual(o1.history['lon'].compressed(),
o2.history['lon'].compressed())
self.assertItemsEqual(o1.history['status'].compressed(),
o2.history['status'].compressed())
os.remove('test_buffer_length_stranding.nc')
def test_output_time_step(self):
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='i', projection='merc')
o1.add_reader([basemap, norkyst])
o1.seed_elements(4.95, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=20)
o2.add_reader([basemap, norkyst])
o2.seed_elements(4.95, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100,25))
self.assertEqual(o2.history.shape, (100,13))
# Check that start and end conditions (longitudes) are idential
self.assertItemsEqual(o1.history['lon'][:,24].compressed(),
o2.history['lon'][:,12].compressed())
self.assertItemsEqual(o1.history['lon'][:,0].compressed(),
o2.history['lon'][:,0].compressed())
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertItemsEqual(o2i.history['lon'][:,12].compressed(),
o2.history['lon'][:,12].compressed())
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
def test_reader_boundary(self):
# Check that the element outside reader coverage is
# not deactivated if fallback value exist
o = OceanDrift()
nordic3d = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
lon = [12.0, 12.0]
lat = [70.0, 70.5]
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 2)
self.assertEqual(o.num_elements_deactivated(), 0)
# Check that the outside element is deactivated,
# if no fallback value exists
o = OceanDrift()
del o.fallback_values['x_sea_water_velocity']
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
def test_reader_order(self):
# Check that we get the same output indepenently of reader order
o = OceanDrift(loglevel=50)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=2, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='c', projection='merc')
lon=4.; lat=60.
# First run
o.add_reader([basemap, norkyst, arome])
o.seed_elements(lon, lat, time=norkyst.start_time)
o.run(steps=30)
# Second run
# Check that we get almost identical results with other projection
o1 = OceanDrift(loglevel=50)
o1.add_reader([norkyst, arome, basemap])
o1.seed_elements(lon, lat, time=norkyst.start_time)
o1.run(steps=30)
self.assertAlmostEqual(o.elements.lon, o1.elements.lon, 2)
self.assertAlmostEqual(o.elements.lat, o1.elements.lat, 2)
# Third run
# Check that this is identical to run 1 if projection set equal
o2 = OceanDrift(loglevel=50)
o2.add_reader([norkyst, arome, basemap])
o2.seed_elements(lon, lat, time=norkyst.start_time)
o2.set_projection(basemap.proj4)
o2.run(steps=30)
self.assertEqual(o.elements.lon, o2.elements.lon)
def test_seed_seafloor(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.add_reader([reader_norkyst])
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z='seafloor', time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -151.2, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -106.0, 2) # After some rising
def test_seed_below_reader_coverage(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.add_reader([reader_norkyst])
lon = 5.0; lat = 64.0
o.seed_elements(lon, lat, z=-350, time=reader_norkyst.start_time,
density=1000)
#o.set_config('turbulentmixing:TSprofiles', True)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[-1,0], -305.0, 2) # After some rising
def test_seed_below_seafloor(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader([reader_norkyst])
o.fallback_values['land_binary_mask'] = 0
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z=-5000, time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -151.2, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -106.0, 2) # After some rising
def test_lift_above_seafloor(self):
# See an element at some depth, and progapate towards coast
# (shallower water) and check that it is not penetrating seafloor
o = OceanDrift3D(loglevel=20, proj4='+proj=merc')
o.max_speed = 100
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
reader_norkyst.buffer = 200
o.add_reader([reader_norkyst],
variables='sea_floor_depth_below_sea_level')
o.fallback_values['x_sea_water_velocity'] = 100 # Pure eastward motion
o.fallback_values['y_sea_water_velocity'] = 0
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(3.0, 62.0, z=-200, time=reader_norkyst.start_time)
o.set_config('processes:turbulentmixing', False)
o.run(steps=26, time_step=30)
seafloor_depth, status = o.get_property('sea_floor_depth_below_sea_level')
z, status = o.get_property('z')
# Uncomment to plot
#import matplotlib.pyplot as plt
#plt.plot(-seafloor_depth, label='Seafloor depth')
#plt.plot(z, label='Element depth')
#plt.legend(loc='best')
#plt.show()
# Check that element has not penetrated seafloor
self.assertFalse(o.elements.z <
-o.environment.sea_floor_depth_below_sea_level)
self.assertAlmostEqual(o.elements.z, -159.6, 1)
def test_seed_on_land(self):
o = OceanDrift(loglevel=50)
o.set_config('general:basemap_resolution', 'c')
o.seed_elements(lon=9, lat=60, time=datetime.now(), number=100)
outfile='out.nc'
o.run(steps=4, time_step=1800, time_step_output=3600,
outfile=outfile)
os.remove(outfile)
o.write_netcdf_density_map(outfile)
os.remove(outfile)
class TestRun(unittest.TestCase):
"""Tests for (non-scalar) LagrangianArray"""
def make_OceanDrift_object(self):
self.o = OceanDrift(loglevel=30)
self.fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
self.o.use_block = False
self.reader_landmask = reader_global_landmask.Reader(
extent = [-1.5, 59, 7, 64])
self.o.add_reader([self.fake_eddy, self.reader_landmask])
def test_seed(self):
"""Test seeding"""
o = OceanDrift(loglevel=20)
number = 3
lonvec = np.linspace(2, 5, number)
latvec = np.linspace(60, 61, number)
o.seed_elements(lonvec, latvec, number=number,
time=datetime(2015, 1, 1, 12, 5, 17))
#time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.num_elements_active(), 0)
self.assertEqual(o.num_elements_activated(), 0)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), number)
def test_seed_cone(self):
o = OceanDrift(loglevel=20)
o.seed_elements(time=[datetime.now(),
datetime.now() + timedelta(hours=3)],
number=100, cone=True,
lat=[60.5, 60.6], lon=[4.4, 4.5])
self.assertAlmostEqual(o.elements_scheduled.lon[50], 4.450, 2)
def test_seed_outside_coverage(self):
"""Test seeding"""
o = OpenOil3D(loglevel=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
landmask = reader_global_landmask.Reader(
llcrnrlon=4, llcrnrlat=60, urcrnrlon=6, urcrnrlat=64)
o.add_reader([landmask, norkyst])
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.set_config('seed:oil_type', 'SNORRE B')
o.seed_elements(5, 63, number=5,
time=norkyst.start_time - 24*timedelta(hours=24))
# Check that the oiltype is taken from config
self.assertEqual(o.oil_name, o.get_config('seed:oil_type'))
self.assertEqual(o.oil_name, 'SNORRE B')
with self.assertRaises(ValueError):
o.run(steps=3, time_step=timedelta(minutes=15))
def test_runge_kutta(self):
number = 50
# With Euler
o = OceanDrift3D(loglevel=30, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.add_reader([norkyst])
z=-40*np.random.rand(number)
o.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o.run(steps=4*3, time_step=timedelta(minutes=15))
# With Runge-Kutta
o2 = OceanDrift3D(loglevel=30, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o2.fallback_values['land_binary_mask'] = 0
o2.add_reader([norkyst])
z=-40*np.random.rand(number)
o2.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o2.set_config('drift:scheme', 'runge-kutta')
o2.run(steps=4*3, time_step=timedelta(minutes=15))
# And finally repeating the initial run to check that indetical
o3 = OceanDrift3D(loglevel=30, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o3.fallback_values['land_binary_mask'] = 0
o3.add_reader([norkyst])
z=-40*np.random.rand(number)
o3.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o3.run(steps=4*3, time_step=timedelta(minutes=15))
# Check that we get some difference with Runge-Kutta:
self.assertIsNone(np.testing.assert_array_almost_equal(
(o2.elements.lon-o.elements.lon).max(), 0.0015, 3))
#(o2.elements.lon-o.elements.lon).max(), 0.013, 3))
# Check that runs with Euler are identical
self.assertIsNone(np.testing.assert_array_almost_equal(
(o3.elements.lon-o.elements.lon).max(), 0))
def test_seed_polygon(self):
o = OpenOil3D(loglevel=0)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time=datetime(2015, 1, 1, 12, 5, 17)
o.set_config('seed:oil_type', 'HEIDRUN')
o.seed_within_polygon(lonvec, latvec, number=number,
time=time, wind_drift_factor=.09)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time)
self.assertAlmostEqual(o.elements_scheduled.wind_drift_factor, .09)
# Check that oil type is taken fom config
self.assertEqual(o.oil_name, 'HEIDRUN')
def test_seed_polygon_timespan(self):
o = OceanDrift(loglevel=20)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time=[datetime(2015, 1, 1, 12, 5, 17),
datetime(2015, 1, 1, 18, 5, 17)]
o.seed_within_polygon(lonvec, latvec, number=number, time=time)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time[0])
self.assertEqual(o.elements_scheduled_time[-1], time[-1])
@unittest.skipIf(has_ogr is False,
'OGR library needed to parse WKT')
def test_seed_wkt(self):
wkt = 'MULTIPOLYGON(((7.784889 64.353442,7.777561 64.353842,7.774236 64.354707,7.770215 64.355829,7.774269 64.356015,7.776829 64.356863,7.779107 64.3578,7.782827 64.358355,7.786346 64.359615,7.787109 64.361975,7.790125 64.361132,7.794584 64.359908,7.798455 64.359624,7.797258 64.358193,7.79978 64.356904,7.795957 64.356494,7.792955 64.355335,7.789134 64.355339,7.784889 64.353442)))'
o = OceanDrift(loglevel=20)
o.seed_from_wkt(wkt, time=datetime.now(), number=100)
wkt_multi = 'MULTIPOLYGON(((2.458058 59.178919,2.456276 59.179283,2.454867 59.180692,2.45277 59.182852,2.452521 59.183759,2.452675 59.184726,2.451365 59.18534,2.451436 59.186609,2.450835 59.188138,2.449576 59.189435,2.447393 59.190818,2.447211 59.191915,2.446273 59.193573,2.445551 59.19423,2.446597 59.195015,2.44838 59.194651,2.450277 59.193,2.452377 59.191919,2.453315 59.19026,2.45457 59.187885,2.455473 59.186131,2.457033 59.18461,2.458774 59.181992,2.458971 59.180403,2.459775 59.179444,2.459606 59.178969,2.458058 59.178919)),((2.442682 59.197444,2.440531 59.198922,2.439575 59.199994,2.440874 59.200951,2.439596 59.20166,2.436232 59.202958,2.433255 59.203728,2.42982 59.203756,2.428 59.202946,2.425857 59.200693,2.42454 59.199149,2.422418 59.198563,2.419404 59.198158,2.417332 59.197175,2.41514 59.19532,2.412395 59.194596,2.410072 59.194519,2.409481 59.193397,2.408199 59.191947,2.405959 59.190489,2.403129 59.188988,2.401292 59.18759,2.398331 59.187867,2.395639 59.187825,2.393585 59.187428,2.389665 59.187697,2.38736 59.188208,2.386923 59.189132,2.390625 59.188785,2.392191 59.189424,2.395825 59.188887,2.398602 59.188627,2.402104 59.189869,2.403773 59.191871,2.407276 59.193113,2.407648 59.194158,2.407751 59.195522,2.410008 59.196488,2.411979 59.197187,2.41439 59.19912,2.415839 59.199965,2.417946 59.201043,2.417796 59.202235,2.414886 59.203195,2.411923 59.203473,2.40923 59.203431,2.409753 59.204363,2.412549 59.20469,2.415342 59.203937,2.41891 59.20321,2.420325 59.203961,2.420463 59.20542,2.419357 59.207683,2.4218 59.208631,2.420303 59.209262,2.418925 59.210766,2.421401 59.21073,2.424984 59.20951,2.425201 59.208508,2.425939 59.207359,2.428832 59.205812,2.431004 59.206001,2.433124 59.205507,2.436926 59.204365,2.439568 59.203724,2.441518 59.202755,2.442879 59.201744,2.443246 59.20063,2.443311 59.199741,2.444589 59.199032,2.445428 59.198168,2.445088 59.197218,2.442682 59.197444)))'
o.seed_from_wkt(wkt_multi, time=datetime.now(), number=200)
self.assertEqual(len(o.elements_scheduled), 300)
self.assertAlmostEqual(
o.elements_scheduled.lat.max(), 64.36, 2)
self.assertAlmostEqual(
o.elements_scheduled.lat.min(), 59.18, 2)
@unittest.skipIf(has_ogr is False,
'OGR library needed to read shapefiles')
def test_seed_shapefile(self):
o = OceanDrift(loglevel=20)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=100, layername=None,
featurenum=[2, 4], time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 100)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=300, layername=None,
featurenum=None, time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 400)
#@unittest.skipIf(has_ogr is False,
# 'GDAL library needed to read shapefiles')
#def test_write_geotiff(self):
# o = OceanDrift(loglevel=20)
# o.seed_elements(lon=4, lat=60, time=datetime(2016, 1, 1))
# o.run(steps=3)
# o.write_geotiff('geotiff.tif')
def test1_seed_single_point_over_time(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements(2.0, 61.0, radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 5)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
def test2_seed_elements(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements([2.0, 5.0, 3.0], [61.0, 60.0, 62.0],
radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 9)
def test3_run_import(self):
"""Import output file from previous test, and check elements"""
self.o = OceanDrift(loglevel=20)
self.o.io_import_file('unittest.nc')
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 5)
def test4_cleaning(self):
"""Cleaning up"""
os.remove('unittest.nc')
def test_temporal_seed(self):
self.o = OceanDrift(loglevel=20)
self.o.fallback_values['x_sea_water_velocity'] = 1
self.o.fallback_values['land_binary_mask'] = 0
# Seed elements on a grid at regular time interval
start_time = datetime(2016,9,16)
time_step = timedelta(hours=6)
num_steps = 10
lon = 4.4
lat = 60.0
for i in range(num_steps+1):
self.o.seed_elements(lon, lat, radius=0, number=2,
time=start_time + i*time_step)
# Running model
self.o.run(steps=20, time_step=3600, outfile='temporal_seed.nc')
self.o = OceanDrift(loglevel=20)
# Check that data imported is properly masked
self.o.io_import_file('temporal_seed.nc')
self.assertTrue(self.o.history['lon'].max() < 1000)
self.assertTrue(self.o.history['lon'].min() > -1000)
self.assertTrue(self.o.history['lon'].mask[5,5])
self.assertFalse(self.o.history['lon'].mask[1,1])
os.remove('temporal_seed.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_export_step_interval(self):
# Export to file only at end
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o1.add_reader(norkyst)
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o1.run(steps=40)
# Export to file during simulation
o2 = OceanDrift(loglevel=20)
o2.add_reader(norkyst)
o2.fallback_values['land_binary_mask'] = 0
o2.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o2.run(steps=40, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertIsNone(np.testing.assert_array_equal(
o1.history['lon'].compressed(),
o2.history['lon'].compressed()))
# Finally check when steps is multiple of export_buffer_length
o3 = OceanDrift(loglevel=20)
o3.add_reader(norkyst)
o3.fallback_values['land_binary_mask'] = 0
o3.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o3.run(steps=42)
# Export to file during simulation
o4 = OceanDrift(loglevel=20)
o4.add_reader(norkyst)
o4.fallback_values['land_binary_mask'] = 0
o4.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o4.run(steps=42, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertIsNone(np.testing.assert_array_equal(
o3.history['lon'].compressed(),
o4.history['lon'].compressed()))
os.remove('export_step_interval.nc')
def test_buffer_length_stranding(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
landmask = reader_global_landmask.Reader(
llcrnrlon=4.5, llcrnrlat=60.1,
urcrnrlon=6.0, urcrnrlat=60.4)
o1.add_reader([landmask])
o1.fallback_values['x_sea_water_velocity'] = 0.8 # onshore drift
o1.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o1.run(steps=100,
time_step=900,
time_step_output=3600,
export_buffer_length=10)
# Without buffer
o2 = OceanDrift(loglevel=30)
o2.add_reader([landmask])
o2.fallback_values['x_sea_water_velocity'] = 0.8 # onshore drift
o2.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o2.run(steps=100,
time_step=900,
time_step_output=3600,
outfile='test_buffer_length_stranding.nc')
self.assertIsNone(np.testing.assert_array_equal(
o1.history['lon'].compressed(),
o2.history['lon'].compressed()))
self.assertIsNone(np.testing.assert_array_almost_equal(
o1.history['status'].compressed(),
o2.history['status'].compressed()))
os.remove('test_buffer_length_stranding.nc')
def test_output_time_step(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
landmask = reader_global_landmask.Reader(
llcrnrlon=4.5, llcrnrlat=60.0,
urcrnrlon=5.2, urcrnrlat=60.5)
o1.add_reader([landmask, norkyst])
o1.seed_elements(4.96, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=30)
o2.add_reader([landmask, norkyst])
o2.seed_elements(4.96, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100,25))
self.assertEqual(o2.history.shape, (100,13))
# Check that start and end conditions (longitudes) are idential
self.assertIsNone(np.testing.assert_array_equal(
o1.history['lon'][:,24].compressed(),
o2.history['lon'][:,12].compressed()))
self.assertIsNone(np.testing.assert_array_equal(
o1.history['lon'][:,0].compressed(),
o2.history['lon'][:,0].compressed()))
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertIsNone(np.testing.assert_array_equal(
o2i.history['lon'][:,12].compressed(),
o2.history['lon'][:,12].compressed()))
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
def test_time_step_config(self):
# Default
o = OceanDrift(loglevel=50)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.run(steps=2)
self.assertEqual(o.time_step.total_seconds(), 3600)
self.assertEqual(o.time_step_output.total_seconds(), 3600)
# Setting time_step
o = OceanDrift(loglevel=50)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.run(steps=2, time_step=1800)
self.assertEqual(o.time_step.total_seconds(), 1800)
# Setting time_step and time_step_output
o = OceanDrift(loglevel=50)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.run(steps=2, time_step=1800, time_step_output=3600)
self.assertEqual(o.time_step.total_seconds(), 1800)
self.assertEqual(o.time_step_output.total_seconds(), 3600)
# time_step from config
o = OceanDrift(loglevel=50)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.set_config('general:time_step_minutes', 15)
o.run(steps=2)
self.assertEqual(o.time_step.total_seconds(), 900)
self.assertEqual(o.time_step_output.total_seconds(), 900)
# time_step and time_step_output from config
o = OceanDrift(loglevel=50)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=4, lat=60, time=datetime.now())
o.set_config('general:time_step_minutes', 15)
o.set_config('general:time_step_output_minutes', 120)
o.run(steps=2)
self.assertEqual(o.time_step.total_seconds(), 900)
self.assertEqual(o.time_step_output.total_seconds(), 7200)
def test_reader_boundary(self):
# Check that the element outside reader coverage is
# not deactivated if fallback value exist
o = OceanDrift()
nordic3d = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
lon = [12.0, 12.0]
lat = [70.0, 70.5]
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 2)
self.assertEqual(o.num_elements_deactivated(), 0)
# Check that the outside element is deactivated,
# if no fallback value exists
o = OceanDrift()
del o.fallback_values['x_sea_water_velocity']
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
@pytest.mark.slow
def test_reader_order(self):
# Check that we get the same output indepenently of reader order
o = OceanDrift(loglevel=50)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
landmask = reader_global_landmask.Reader(extent = [2, 59.8, 6, 61])
lon=4.; lat=60.
# First run
o.add_reader([landmask, norkyst, arome])
o.seed_elements(lon, lat, time=norkyst.start_time)
o.run(steps=30)
# Second run
# Check that we get almost identical results with other projection
o1 = OceanDrift(loglevel=50)
o1.add_reader([norkyst, arome, landmask])
o1.seed_elements(lon, lat, time=norkyst.start_time)
o1.run(steps=30)
np.testing.assert_array_almost_equal(
o.elements.lon, o1.elements.lon, 2)
np.testing.assert_array_almost_equal(
o.elements.lat, o1.elements.lat, 2)
# Third run
# Check that this is identical to run 1 if projection set equal
o2 = OceanDrift(loglevel=50)
o2.add_reader([norkyst, arome, landmask])
o2.seed_elements(lon, lat, time=norkyst.start_time)
o2.set_projection(landmask.proj4)
o2.run(steps=30)
np.testing.assert_array_almost_equal(
o.elements.lon, o2.elements.lon, decimal=3)
def test_seed_seafloor(self):
o = OpenOil3D(loglevel=30)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
# Adding reader as lazy, to test seafloor seeding
o.add_readers_from_list([o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc'])
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z='seafloor', time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -151.7, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -94.0, 1) # After some rising
def test_seed_above_seafloor(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
o.add_reader([reader_norkyst])
lon = 4.5; lat = 62.0
# Seed elements 50 meters above seafloor:
o.seed_elements(lon, lat, z='seafloor+50', time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -101.7, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -44.3, 1) # After some rising
def test_seed_below_reader_coverage(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.add_reader([reader_norkyst])
lon = 5.0; lat = 64.0
o.seed_elements(lon, lat, z=-350, time=reader_norkyst.start_time,
density=1000)
#o.set_config('turbulentmixing:TSprofiles', True)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[-1,0], -291.7, 1) # After some rising
def test_seed_below_seafloor(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader([reader_norkyst])
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z=-5000, time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -151.7, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -94.0, 1) # After some rising
def test_seed_below_seafloor_deactivating(self):
o = OpenOil3D(loglevel=50)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader([reader_norkyst])
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z=[-5000, -100], time=reader_norkyst.start_time,
density=1000, number=2)
o.set_config('drift:lift_to_seafloor', False) # This time we deactivate
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertEqual(o.num_elements_total(), 2)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
self.assertAlmostEqual(z[0,1], -100, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,1], -35.7, 1) # After some rising
def test_lift_above_seafloor(self):
# See an element at some depth, and progapate towards coast
# (shallower water) and check that it is not penetrating seafloor
o = OceanDrift3D(loglevel=30, proj4='+proj=merc')
o.max_speed = 100
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
reader_norkyst.buffer = 200
o.add_reader([reader_norkyst],
variables='sea_floor_depth_below_sea_level')
o.fallback_values['x_sea_water_velocity'] = 100 # Pure eastward motion
o.fallback_values['y_sea_water_velocity'] = 0
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(3.0, 62.0, z=-200, time=reader_norkyst.start_time)
o.set_config('processes:turbulentmixing', False)
o.run(steps=26, time_step=30)
seafloor_depth, status = o.get_property('sea_floor_depth_below_sea_level')
z, status = o.get_property('z')
# Uncomment to plot
#import matplotlib.pyplot as plt
#plt.plot(-seafloor_depth, label='Seafloor depth')
#plt.plot(z, label='Element depth')
#plt.legend(loc='best')
#plt.show()
# Check that element has not penetrated seafloor
self.assertFalse(o.elements.z <
-o.environment.sea_floor_depth_below_sea_level)
self.assertIsNone(np.testing.assert_array_almost_equal(
o.elements.z, -160.06, 1))
def test_seed_on_land(self):
o = OceanDrift(loglevel=0)
o.seed_elements(lon=9, lat=60, time=datetime.now(), number=100)
outfile='out.nc'
with self.assertRaises(ValueError):
o.run(steps=4, time_step=1800, time_step_output=3600,
outfile=outfile)
os.remove(outfile)
#o.write_netcdf_density_map(outfile)
#os.remove(outfile)
def test_retirement(self):
o = OceanDrift(loglevel=0)
o.set_config('drift:max_age_seconds', 5000)
o.fallback_values['x_sea_water_velocity'] = .5
o.fallback_values['y_sea_water_velocity'] = .3
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=0, lat=60, number=10,
time=[datetime.now(),
datetime.now() + timedelta(seconds=6000)])
o.run(time_step=1000, duration=timedelta(seconds=7000))
self.assertEqual(o.num_elements_deactivated(), 5)
def test_outside_domain(self):
o = OceanDrift(loglevel=50)
reader_osc_x = reader_oscillating.Reader(
'x_sea_water_velocity', amplitude=1,
zero_time=datetime.now())
reader_osc_y = reader_oscillating.Reader(
'y_sea_water_velocity', amplitude=1,
zero_time=datetime.now())
o.add_reader([reader_osc_x, reader_osc_y])
o.set_config('drift:deactivate_east_of', 2.1)
o.set_config('drift:deactivate_west_of', 1.9)
o.set_config('drift:deactivate_south_of', 59.9)
o.set_config('drift:deactivate_north_of', 60.1)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon=2, lat=60, number=1000,
time=datetime.now(), radius=10000)
o.run(duration=timedelta(hours=5))
self.assertEqual(o.num_elements_deactivated(), 768)
self.assertEqual(o.num_elements_active(), 232)
def test_seed_time_backwards_run(self):
o = OceanDrift(loglevel=20)
o.set_config('drift:max_age_seconds', 2000)
o.fallback_values['x_sea_water_velocity'] = .5
o.fallback_values['y_sea_water_velocity'] = .3
o.fallback_values['land_binary_mask'] = 0
time = [datetime(2018,1,1,i) for i in range(10)]
o.seed_elements(lon=0, lat=60, time=time)
o.seed_elements(lon=1, lat=60, time=datetime(2018,1,1,7))
o.run(end_time=datetime(2018,1,1,2), time_step=-1800)
self.assertEqual(o.num_elements_scheduled(), 3)
self.assertEqual(o.num_elements_active(), 8)
self.assertEqual(o.steps_calculation, 14)
def test_oil_mixed_to_seafloor(self):
o = OpenOil3D(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader(norkyst)
o.set_config('processes:evaporation', False)
o.fallback_values['x_wind'] = 25
o.fallback_values['y_wind'] = 0
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['ocean_vertical_diffusivity'] = 0.9
o.seed_elements(lon=5.38, lat=62.77, time=norkyst.start_time,
number=100, radius=5000)
o.run(end_time=norkyst.end_time)
self.assertEqual(o.num_elements_active(), 100)
def test_unseeded_elements(self):
o = PlastDrift()
# Seeding elements for 12 hours, but running only 6
time = datetime(2019, 8, 30, 12)
o.seed_elements(lon=4.85, lat=60, number=10,
time=[time, time + timedelta(hours=6)],
origin_marker=7)
o.seed_elements(lon=4.75, lat=60, number=10,
time=[time, time + timedelta(hours=6)],
origin_marker=8)
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['y_sea_water_velocity'] = 1
o.run(duration=timedelta(hours=3))
self.assertEqual(o.history.shape[0], 10)
self.assertEqual(o.history.shape[1], 4)
self.assertEqual(o.history['origin_marker'].min(), 7)
self.assertEqual(o.history['origin_marker'].max(), 8)
from opendrift.readers import reader_basemap_landmask
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
time = reader_norkyst.start_time
reader_norkyst.interpolation = 'linearND'
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=59.9,
urcrnrlon=5.5, urcrnrlat=61.5, resolution='h')
o.add_reader([reader_norkyst, reader_basemap])
lon = 4.5; lat = 60.0;
# First run, with Euler scheme:
o.set_config('drift:scheme', 'euler')
o.seed_elements(lon, lat, radius=0, number=1, time=time)
o.run(steps=66*2, time_step=1800)
# Second run, with Runge-Kutta scheme:
o2 = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
o2.add_reader([reader_norkyst, reader_basemap])
o2.set_config('drift:scheme', 'runge-kutta')
o2.seed_elements(lon, lat, radius=0, number=1, time=time)
o2.run(steps=66*2, time_step=1800)
# Animate and compare the two runs
from opendrift.readers import reader_ROMS_native
from opendrift.readers import reader_oscillating
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=0) # Set loglevel to 0 for debug information
# Adding nordic reader for coastline
reader_nordic = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
reader_nordic.variables = ['land_binary_mask']
reader_osc = reader_oscillating.Reader('x_sea_water_velocity', amplitude=1,
zero_time=reader_nordic.start_time)
o.add_reader([reader_osc]) # Oscillating east-west current component
o.fallback_values['y_sea_water_velocity'] = .2 # Adding northwards drift
o.set_config('general:basemap_resolution', 'i')
##########################################################
# Try different options: 'previous', 'stranding', 'none'
o.set_config('general:coastline_action', 'previous')
##########################################################
time = reader_osc.zero_time
lon = 12.2; lat = 67.7
o.seed_elements(lon, lat, radius=5000, number=15, time=time)
o.run(steps=36*4, time_step=900)
# Demonstrating how the spatial resolution of # fields from a reader mey be reduced from datetime import datetime, timedelta import matplotlib.pyplot as plt from opendrift.readers import reader_netCDF_CF_generic from opendrift.models.oceandrift import OceanDrift lon = 4.9; lat = 60.0 o = OceanDrift() reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc') time = reader_norkyst.start_time o.add_reader([reader_norkyst]) o.seed_elements(lon, lat, radius=1000, number=1000, time=time) o.run(steps=20) # Store final field of x-component of current original_current = reader_norkyst.var_block_after["['y_sea_water_velocity', 'x_sea_water_velocity']"].data_dict['x_sea_water_velocity'].copy() # For the second run, the NorKyst currents are convolved with a kernel, # effectively lowering the spatial resolution. # <reader>.convolve may also be given as an array (kernel) directly N = 10 # Convolusion kernel size reader_norkyst.convolve = N # Using convolution kernel for second run o2 = OceanDrift() o2.add_reader([reader_norkyst]) o2.seed_elements(lon, lat, radius=1000, number=1000, time=time) o2.run(steps=20)
#!/usr/bin/env python
"""
Advection schemes
=================
Illustrating the difference between Euler and Runge-Kutta propagation
schemes, using an idealised (analytical) eddy current field.
"""
from datetime import datetime, timedelta
from opendrift.readers import reader_ArtificialOceanEddy
from opendrift.models.oceandrift import OceanDrift
fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
runs = []
leg = []
for scheme in ['euler', 'runge-kutta', 'runge-kutta4']:
for time_step in [1800, 3600 * 3]:
leg.append(scheme + ', T=%.1fh' % (time_step / 3600.))
print(leg[-1])
o = OceanDrift(loglevel=50)
o.fallback_values['land_binary_mask'] = 0
o.set_config('drift:scheme', scheme)
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)
runs[0].plot(compare=runs[1:], legend=leg, fast=True, buffer=.3)
def test_plot(tmpdir):
anifile = os.path.join(tmpdir, 'anim.mp4')
plotfile = os.path.join(tmpdir, 'plot.png')
#anifile = None
#plotfile = None
o = OceanDrift(loglevel=30)
rn = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o.add_reader(rn)
o.seed_elements(lon=4.8,
lat=60.0,
number=10,
radius=1000,
time=rn.start_time)
o.run(steps=5)
# Making figures/animations
o.plot(filename=plotfile,
fast=True,
background=['x_sea_water_velocity', 'y_sea_water_velocity'])
o.animation(color='lat',
filename=anifile,
show_trajectories=True,
fast=True)
o.animation(density=True,
filename=anifile,
show_trajectories=True,
fast=True)
o.animation(filename=anifile, show_trajectories=True, fast=True)
o.animation(filename=anifile,
fast=True,
background=['x_sea_water_velocity', 'y_sea_water_velocity'])
o.plot(filename=plotfile, fast=True, linecolor='lat')
o.plot(filename=plotfile, fast=False)
# Second run for comparison
o2 = OceanDrift(loglevel=30)
o2.add_reader(rn)
o2.fallback_values['x_wind'] = 15 # Adding wind
o2.fallback_values['y_wind'] = 0
o2.seed_elements(lon=4.8,
lat=60.0,
number=10,
radius=1000,
time=rn.start_time)
o2.run(steps=5)
o.animation(filename=anifile,
compare=o2,
fast=True,
legend=['No wind', '10 m/s wind'])
o.plot(filename=plotfile,
compare=o2,
fast=True,
legend=['No wind', '10 m/s wind'])
# Check that files have been written
assert os.path.exists(anifile)
assert os.path.exists(plotfile)
ROMS native reader
==================================
"""
import numpy as np
from opendrift.readers import reader_ROMS_native
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
#%%
# Creating and adding reader for Nordic 4km current dataset
nordic_native = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader(nordic_native)
#%%
# Seed elements at defined positions, depth and time
o.seed_elements(lon=12.0,
lat=68.3,
radius=0,
number=10,
z=np.linspace(0, -150, 10),
time=nordic_native.start_time)
#%%
# Running model
o.run(time_step=3600)
#%%
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
# Norkyst
#reader_norkyst = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/sea/norkyst800m/1h/aggregate_be')
reader_norkyst = reader_netCDF_CF_generic.Reader(
o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
#reader_norkyst = reader_netCDF_CF_generic.Reader('test_data/16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# Landmask
reader_landmask = reader_global_landmask.Reader(llcrnrlon=3.5,
llcrnrlat=59.9,
urcrnrlon=5.5,
urcrnrlat=61.2)
o.add_reader([reader_landmask, reader_norkyst])
# Seeding particles in a checkerboard pattern
di = 5 # Horizontal number of particles per square
dj = 5 # Vertical number of particles per square
lons = np.linspace(3.5, 5.0, 100)
lats = np.linspace(60, 61, 100)
ii = np.arange(len(lons)) // di
jj = np.arange(len(lats)) // dj
ii, jj = np.meshgrid(ii, jj)
board = (ii + jj) % 2 > 0
lons, lats = np.meshgrid(lons, lats)
lons = lons[board].ravel()
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift() # Basic drift model suitable for passive tracers or drifters
#######################
# Preparing Readers
#######################
reader_current = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
reader_wind = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
o.add_reader([reader_current, reader_wind])
#######################
# Seeding elements
#######################
# Elements are moved with the ocean current, in addition to a fraction of
# the wind speed (wind_drift_factor). This factor depends on the properties
# of the elements. Typical empirical values are:
# - 0.035 (3.5 %) for oil and iSphere driftes
# - 0.01 (1 %) for CODE drifters partly submerged ~0.5 m
# As there are large uncertainties, it makes sence to provide a statistical
# distribution of wind_drift_factors
# Using a constant value for all elements:
#wind_drift_factor = 0.03
class TestRun(unittest.TestCase):
"""Tests for (non-scalar) LagrangianArray"""
def make_OceanDrift_object(self):
self.o = OceanDrift(loglevel=30)
self.fake_eddy = reader_ArtificialOceanEddy.Reader(2, 62)
self.o.use_block = False
self.reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=-1.5, llcrnrlat=59,
urcrnrlon=7, urcrnrlat=64, resolution='c')
self.o.add_reader([self.fake_eddy, self.reader_basemap])
def test_seed(self):
"""Test seeding"""
o = OceanDrift(loglevel=20)
number = 3
lonvec = np.linspace(2, 5, number)
latvec = np.linspace(60, 61, number)
o.seed_elements(lonvec, latvec, number=number,
time=datetime(2015, 1, 1, 12, 5, 17))
#time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.num_elements_active(), 0)
self.assertEqual(o.num_elements_activated(), 0)
self.assertEqual(o.num_elements_deactivated(), 0)
self.assertEqual(o.num_elements_total(), number)
def test_seed_outside_coverage(self):
"""Test seeding"""
o = OpenOil3D(loglevel=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=60, urcrnrlon=6, urcrnrlat=64,
resolution='c', projection='merc')
o.add_reader([basemap, norkyst])
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.seed_elements(5, 63, number=5,
time=norkyst.start_time - 24*timedelta(hours=24))
with self.assertRaises(ValueError):
o.run(steps=3, time_step=timedelta(minutes=15))
def test_runge_kutta(self):
number = 50
# With Euler
o = OceanDrift3D(loglevel=20, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.add_reader([norkyst])
z=-40*np.random.rand(number)
o.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o.run(steps=4*3, time_step=timedelta(minutes=15))
# With Runge-Kutta
o2 = OceanDrift3D(loglevel=20, seed=0)
o2.fallback_values['land_binary_mask'] = 0
o2.add_reader([norkyst])
z=-40*np.random.rand(number)
o2.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o2.set_config('drift:scheme', 'runge-kutta')
o2.run(steps=4*3, time_step=timedelta(minutes=15))
# And finally repeating the initial run to check that indetical
o3 = OceanDrift3D(loglevel=20, seed=0)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o3.fallback_values['land_binary_mask'] = 0
o3.add_reader([norkyst])
z=-40*np.random.rand(number)
o3.seed_elements(5, 62.5, number=number, radius=5000, z=z,
time=norkyst.start_time)
o3.run(steps=4*3, time_step=timedelta(minutes=15))
# Check that we get some difference with Runge-Kutta:
self.assertAlmostEqual((o2.elements.lon-o.elements.lon).max(),
0.0015, 3)
# Check that runs with Euler are identical
self.assertEqual((o3.elements.lon-o.elements.lon).max(), 0)
def test_seed_polygon(self):
o = OceanDrift(loglevel=20)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time=datetime(2015, 1, 1, 12, 5, 17)
o.seed_within_polygon(lonvec, latvec, number=number, time=time,
wind_drift_factor=.09)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time)
self.assertAlmostEqual(o.elements_scheduled.wind_drift_factor, .09)
def test_seed_polygon_timespan(self):
o = OceanDrift(loglevel=20)
number = 10
lonvec = np.array([2, 3, 3, 2])
latvec = np.array([60, 60, 61, 61])
time=[datetime(2015, 1, 1, 12, 5, 17),
datetime(2015, 1, 1, 18, 5, 17)]
o.seed_within_polygon(lonvec, latvec, number=number, time=time)
self.assertEqual(o.num_elements_scheduled(), number)
self.assertEqual(o.elements_scheduled_time[0], time[0])
self.assertEqual(o.elements_scheduled_time[-1], time[-1])
@unittest.skipIf(has_ogr is False,
'OGR library needed to read shapefiles')
def test_seed_shapefile(self):
o = OceanDrift(loglevel=20)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=100, layername=None,
featurenum=[2, 4], time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 100)
o.seed_from_shapefile(o.test_data_folder() +
'shapefile_spawning_areas/Torsk.shp',
number=300, layername=None,
featurenum=None, time=datetime.now())
self.assertEqual(len(o.elements_scheduled), 400)
#@unittest.skipIf(has_ogr is False,
# 'GDAL library needed to read shapefiles')
#def test_write_geotiff(self):
# o = OceanDrift(loglevel=20)
# o.seed_elements(lon=4, lat=60, time=datetime(2016, 1, 1))
# o.run(steps=3)
# o.write_geotiff('geotiff.tif')
def test1_seed_single_point_over_time(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements(2.0, 61.0, radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 5)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
def test2_seed_elements(self):
"""Test a model run"""
self.make_OceanDrift_object()
self.o.seed_elements([2.0, 5.0, 3.0], [61.0, 60.0, 62.0],
radius=0, number=9,
time=[datetime(2015, 1, 1), datetime(2015, 1, 3)])
# Check that 6 elements are scheduled, but none seeded
self.assertEqual(self.o.num_elements_scheduled(), 9)
self.assertEqual(self.o.num_elements_active(), 0)
self.assertEqual(self.o.num_elements_activated(), 0)
self.assertEqual(self.o.num_elements_deactivated(), 0)
self.assertEqual(self.o.num_elements_total(), 9)
# Run simulation
self.o.run(steps=30, outfile='unittest.nc')
# Check that 1 element is deactivated (stranded),
# 1 yet not seeded and 4 active
self.assertEqual(self.o.num_elements_scheduled(), 4)
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 9)
def test3_run_import(self):
"""Import output file from previous test, and check elements"""
self.o = OceanDrift(loglevel=20)
self.o.io_import_file('unittest.nc')
self.assertEqual(self.o.num_elements_active(), 4)
self.assertEqual(self.o.num_elements_activated(), 5)
self.assertEqual(self.o.num_elements_deactivated(), 1)
self.assertEqual(self.o.num_elements_total(), 5)
def test4_cleaning(self):
"""Cleaning up"""
os.remove('unittest.nc')
def test_temporal_seed(self):
self.o = OceanDrift(loglevel=20)
self.o.fallback_values['x_sea_water_velocity'] = 1
self.o.fallback_values['land_binary_mask'] = 0
# Seed elements on a grid at regular time interval
start_time = datetime(2016,9,16)
time_step = timedelta(hours=6)
num_steps = 10
lon = 4.4
lat = 60.0
for i in range(num_steps+1):
self.o.seed_elements(lon, lat, radius=0, number=2,
time=start_time + i*time_step)
# Running model
self.o.run(steps=20, time_step=3600, outfile='temporal_seed.nc')
self.o = OceanDrift(loglevel=20)
# Check that data imported is properly masked
self.o.io_import_file('temporal_seed.nc')
self.assertTrue(self.o.history['lon'].max() < 1000)
self.assertTrue(self.o.history['lon'].min() > -1000)
self.assertTrue(self.o.history['lon'].mask[5,5])
self.assertFalse(self.o.history['lon'].mask[1,1])
os.remove('temporal_seed.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.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(), -31.9, 1)
self.assertAlmostEqual(o1.history['z'].max(), 0.0, 1)
os.remove('verticalmixing.nc')
def test_export_step_interval(self):
# Export to file only at end
o1 = OceanDrift(loglevel=20)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
o1.add_reader(norkyst)
o1.fallback_values['land_binary_mask'] = 0
o1.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o1.run(steps=40)
# Export to file during simulation
o2 = OceanDrift(loglevel=20)
o2.add_reader(norkyst)
o2.fallback_values['land_binary_mask'] = 0
o2.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o2.run(steps=40, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertItemsEqual(o1.history['lon'].compressed(),
o2.history['lon'].compressed())
# Finally check when steps is multiple of export_buffer_length
o3 = OceanDrift(loglevel=20)
o3.add_reader(norkyst)
o3.fallback_values['land_binary_mask'] = 0
o3.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o3.run(steps=42)
# Export to file during simulation
o4 = OceanDrift(loglevel=20)
o4.add_reader(norkyst)
o4.fallback_values['land_binary_mask'] = 0
o4.seed_elements(4.25, 60.2, radius=1000, number=10,
time=norkyst.start_time)
o4.run(steps=42, export_buffer_length=6,
outfile='export_step_interval.nc')
self.assertItemsEqual(o3.history['lon'].compressed(),
o4.history['lon'].compressed())
os.remove('export_step_interval.nc')
def test_buffer_length_stranding(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4.5, llcrnrlat=60.1,
urcrnrlon=6.0, urcrnrlat=60.4,
resolution='c', projection='merc')
o1.add_reader([basemap])
o1.fallback_values['x_sea_water_velocity'] = 0.8 # onshore drift
o1.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o1.run(steps=100,
time_step=900,
time_step_output=3600,
export_buffer_length=10)
# Without buffer
o2 = OceanDrift(loglevel=30)
o2.add_reader([basemap])
o2.fallback_values['x_sea_water_velocity'] = 0.8 # onshore drift
o2.seed_elements(4.8, 60.2, radius=5000, number=100,
time=norkyst.start_time)
o2.run(steps=100,
time_step=900,
time_step_output=3600,
outfile='test_buffer_length_stranding.nc')
self.assertItemsEqual(o1.history['lon'].compressed(),
o2.history['lon'].compressed())
self.assertItemsEqual(o1.history['status'].compressed(),
o2.history['status'].compressed())
os.remove('test_buffer_length_stranding.nc')
def test_output_time_step(self):
o1 = OceanDrift(loglevel=30)
norkyst = reader_netCDF_CF_generic.Reader(o1.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=4.5, llcrnrlat=60.0,
urcrnrlon=5.2, urcrnrlat=60.5,
resolution='i', projection='merc')
o1.add_reader([basemap, norkyst])
o1.seed_elements(4.96, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o1.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=30),
outfile='test_time_step30.nc')
# Check length of time array and output array
time = o1.get_time_array()[0]
self.assertEqual(o1.history.shape[1], len(time))
self.assertEqual(o1.start_time, time[0])
self.assertEqual(o1.time, time[-1])
# Second run, with larger output time step
o2 = OceanDrift(loglevel=30)
o2.add_reader([basemap, norkyst])
o2.seed_elements(4.96, 60.1, radius=3000, number=100,
time=norkyst.start_time)
o2.run(duration=timedelta(hours=12),
time_step=timedelta(minutes=30),
time_step_output=timedelta(minutes=60),
outfile='test_time_step60.nc')
self.assertEqual(o1.history.shape, (100,25))
self.assertEqual(o2.history.shape, (100,13))
# Check that start and end conditions (longitudes) are idential
self.assertItemsEqual(o1.history['lon'][:,24].compressed(),
o2.history['lon'][:,12].compressed())
self.assertItemsEqual(o1.history['lon'][:,0].compressed(),
o2.history['lon'][:,0].compressed())
# Check that also run imported from file is identical
o1i = OceanDrift(loglevel=20)
o1i.io_import_file('test_time_step30.nc')
o2i = OceanDrift(loglevel=20)
o2i.io_import_file('test_time_step60.nc')
os.remove('test_time_step30.nc')
os.remove('test_time_step60.nc')
self.assertItemsEqual(o2i.history['lon'][:,12].compressed(),
o2.history['lon'][:,12].compressed())
# Check number of activated elements
self.assertEqual(o1.num_elements_total(), o2.num_elements_total())
self.assertEqual(o1.num_elements_total(), o1i.num_elements_total())
self.assertEqual(o1.num_elements_total(), o2i.num_elements_total())
# Check number of deactivated elements
self.assertEqual(o1.num_elements_deactivated(),
o2.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o1i.num_elements_deactivated())
self.assertEqual(o1.num_elements_deactivated(),
o2i.num_elements_deactivated())
def test_reader_boundary(self):
# Check that the element outside reader coverage is
# not deactivated if fallback value exist
o = OceanDrift()
nordic3d = reader_ROMS_native.Reader(o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
lon = [12.0, 12.0]
lat = [70.0, 70.5]
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 2)
self.assertEqual(o.num_elements_deactivated(), 0)
# Check that the outside element is deactivated,
# if no fallback value exists
o = OceanDrift()
del o.fallback_values['x_sea_water_velocity']
o.add_reader(nordic3d)
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(lon, lat, number=2, radius=0,
time=nordic3d.start_time)
o.run(steps=2, time_step=3600)
self.assertEqual(o.num_elements_active(), 1)
self.assertEqual(o.num_elements_deactivated(), 1)
def test_reader_order(self):
# Check that we get the same output indepenently of reader order
o = OceanDrift(loglevel=50)
norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
basemap = reader_basemap_landmask.Reader(
llcrnrlon=2, llcrnrlat=59.8, urcrnrlon=6, urcrnrlat=61,
resolution='c', projection='merc')
lon=4.; lat=60.
# First run
o.add_reader([basemap, norkyst, arome])
o.seed_elements(lon, lat, time=norkyst.start_time)
o.run(steps=30)
# Second run
# Check that we get almost identical results with other projection
o1 = OceanDrift(loglevel=50)
o1.add_reader([norkyst, arome, basemap])
o1.seed_elements(lon, lat, time=norkyst.start_time)
o1.run(steps=30)
self.assertAlmostEqual(o.elements.lon, o1.elements.lon, 2)
self.assertAlmostEqual(o.elements.lat, o1.elements.lat, 2)
# Third run
# Check that this is identical to run 1 if projection set equal
o2 = OceanDrift(loglevel=50)
o2.add_reader([norkyst, arome, basemap])
o2.seed_elements(lon, lat, time=norkyst.start_time)
o2.set_projection(basemap.proj4)
o2.run(steps=30)
self.assertEqual(o.elements.lon, o2.elements.lon)
def test_seed_seafloor(self):
o = OpenOil3D(loglevel=30)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
o.add_reader([reader_norkyst])
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z='seafloor', time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -151.7, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -91.3, 1) # After some rising
def test_seed_above_seafloor(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
o.add_reader([reader_norkyst])
lon = 4.5; lat = 62.0
# Seed elements 50 meters above seafloor:
o.seed_elements(lon, lat, z='seafloor+50', time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.run(steps=3, time_step=300, time_step_output=300)
#o.plot_property('z')
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -101.7, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -41.7, 1) # After some rising
def test_seed_below_reader_coverage(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.add_reader([reader_norkyst])
lon = 5.0; lat = 64.0
o.seed_elements(lon, lat, z=-350, time=reader_norkyst.start_time,
density=1000)
#o.set_config('turbulentmixing:TSprofiles', True)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[-1,0], -289.2, 1) # After some rising
def test_seed_below_seafloor(self):
o = OpenOil3D(loglevel=20)
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
o.add_reader([reader_norkyst])
o.fallback_values['land_binary_mask'] = 0
o.fallback_values['x_wind'] = 0
o.fallback_values['y_wind'] = 0
o.fallback_values['x_sea_water_velocity'] = 0
o.fallback_values['y_sea_water_velocity'] = 0
lon = 4.5; lat = 62.0
o.seed_elements(lon, lat, z=-5000, time=reader_norkyst.start_time,
density=1000)
o.set_config('processes:turbulentmixing', True)
o.set_config('turbulentmixing:verticalresolution', 1) # m
o.set_config('turbulentmixing:timestep', 1) # s
o.set_config('input:spill:droplet_diameter_min_subsea', 0.005)
o.set_config('input:spill:droplet_diameter_max_subsea', 0.005)
o.run(steps=3, time_step=300, time_step_output=300)
z, status = o.get_property('z')
self.assertAlmostEqual(z[0,0], -151.7, 1) # Seeded at seafloor depth
self.assertAlmostEqual(z[-1,0], -91.3, 1) # After some rising
def test_lift_above_seafloor(self):
# See an element at some depth, and progapate towards coast
# (shallower water) and check that it is not penetrating seafloor
o = OceanDrift3D(loglevel=30, proj4='+proj=merc')
o.max_speed = 100
reader_norkyst = reader_netCDF_CF_generic.Reader(o.test_data_folder() + '14Jan2016_NorKyst_z_3d/NorKyst-800m_ZDEPTHS_his_00_3Dsubset.nc')
reader_norkyst.buffer = 200
o.add_reader([reader_norkyst],
variables='sea_floor_depth_below_sea_level')
o.fallback_values['x_sea_water_velocity'] = 100 # Pure eastward motion
o.fallback_values['y_sea_water_velocity'] = 0
o.fallback_values['land_binary_mask'] = 0
o.seed_elements(3.0, 62.0, z=-200, time=reader_norkyst.start_time)
o.set_config('processes:turbulentmixing', False)
o.run(steps=26, time_step=30)
seafloor_depth, status = o.get_property('sea_floor_depth_below_sea_level')
z, status = o.get_property('z')
# Uncomment to plot
#import matplotlib.pyplot as plt
#plt.plot(-seafloor_depth, label='Seafloor depth')
#plt.plot(z, label='Element depth')
#plt.legend(loc='best')
#plt.show()
# Check that element has not penetrated seafloor
self.assertFalse(o.elements.z <
-o.environment.sea_floor_depth_below_sea_level)
self.assertAlmostEqual(o.elements.z, -160.06, 1)
def test_seed_on_land(self):
o = OceanDrift(loglevel=0)
o.set_config('general:basemap_resolution', 'c')
o.seed_elements(lon=9, lat=60, time=datetime.now(), number=100)
outfile='out.nc'
with self.assertRaises(ValueError):
o.run(steps=4, time_step=1800, time_step_output=3600,
outfile=outfile)
os.remove(outfile)
#######################
# Preparing Readers
#######################
reader_current = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
reader_wind = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
'16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
# Landmask (Basemap)
reader_basemap = reader_basemap_landmask.Reader(
llcrnrlon=4, llcrnrlat=59.8,
urcrnrlon=6, urcrnrlat=61,
resolution='h', projection='merc')
o.add_reader([reader_basemap, reader_current, reader_wind])
#######################
# Seeding elements
#######################
# Elements are moved with the ocean current, in addition to a fraction of
# the wind speed (wind_drift_factor). This factor depends on the properties
# of the elements. Typical empirical values are:
# - 0.035 (3.5 %) for oil and iSphere driftes
# - 0.01 (1 %) for CODE drifters partly submerged ~0.5 m
# As there are large uncertainties, it makes sence to provide a statistical
# distribution of wind_drift_factors
# Using a constant value for all elements:
#wind_drift_factor = 0.03
#!/usr/bin/env python
from datetime import timedelta
import numpy as np
from opendrift.models.oceandrift import OceanDrift
from opendrift.readers import reader_netCDF_CF_generic
# Drift simulation using 10 member ensemble wind data
# from MEPS model of MET Norway
o = OceanDrift()
r = reader_netCDF_CF_generic.Reader('http://thredds.met.no/thredds/dodsC/meps25files/meps_allmembers_extracted_2_5km_latest.nc')
o.add_reader(r)
#o.set_config('general:basemap_resolution', 'c')
o.seed_elements(lat=60, lon=4.8, time=r.start_time,
radius=1000, number=10000)
o.run(duration=timedelta(hours=50), time_step=3600)
# Ensemble members are recycled among the 10000 particles
ensemble_number = np.remainder(o.history['ID'], 10) + 1
o.animation(filename='wind_drift_ensemble.mp4',
color=ensemble_number, clabel='Ensemble number')
