# Vertical swimming
###############################
# Need a null terminal_velocity
o.set_config('drift:active_vertical_swimming', False) # Correlated random walk across the water column when advected away from coastal habitats
#o.set_config('drift:vertical_velocity', (0.001/10)) # Vertical swimming speed of the larvae: in meter/seconds
o.set_config('drift:maximum_depth', -50) # Maximum depth of larvae: negative in meters
#o.set_config('drift:persistence', 50) # Control the persistence (memory) of the vertical movement to create a correlated random walk and sample the water column
o.list_config()
# o.list_configspec()
###############################
# RUN
###############################
# Running model (until end of driver data)
o.run(stop_on_error=False,
time_step=timedelta(seconds = 900),
end_time = finish_time,
time_step_output=timedelta(minutes = 60*24),
outfile= 'test_development_Opendrift_using_moana.nc')
print("--- %s seconds ---" % (time.time() - start_time))
print(process.memory_info().rss) # in bytes
print(o)
o.plot(fast=True, color='z', corners=[163, 180, -52, -31])
o.animation(fast=True, color='z', corners=[163, 180, -52, -31])
o.animation_profile()
####################################################################################################################
# CONFIG
# Adjusting some configuration
o.set_config('general:coastline_action', 'previous')
o.set_config('drift:vertical_advection', True)
o.set_config('drift:vertical_mixing', True)
o.set_config('drift:min_settlement_age_seconds',
3600) # minimum age before settling can occur
o.set_config(
'vertical_mixing:diffusivitymodel',
'constant') # use eddy diffusivity from ocean model, or fallback value
o.set_config(
'vertical_mixing:timestep', 900.
) # seconds - # Vertical mixing requires fast time step (but for constant diffusivity, use same as model step)
####################################################################################################################
# Running model
o.run(end_time=nordic_native.start_time + timedelta(days=4.0), time_step=900)
# Print and plot results.
# At the end the wind vanishes, and eggs come to surface
print(o)
o.plot(fast=True)
o.animation(fast=True, color='z')
# Interactive slider (not working in browser)
o.plot_vertical_distribution()
o.set_config('drift:vertical_advection', False)
o.set_config('drift:vertical_mixing', True)
o.set_config('vertical_mixing:timestep', 90.0) # if some ocean_vertical_diffusivity!=0, turbulentmixing:timestep should be << 900 seconds
###############################
# Type of settlement
###############################
#o.set_config('general:coastline_action','previous') # option('none', 'stranding', 'previous', default='stranding')
o.set_config('drift:settlement_in_habitat', True)
o.set_config('drift:max_age_seconds', 30*24*3600) #
o.set_config('drift:min_settlement_age_seconds', 1*24*3600)
#o.disable_vertical_motion() #Deactivate any vertical processes/advection"""
o.list_config()
# o.list_configspec()
###############################
# RUN
###############################
# Running model (until end of driver data)
o.run(stop_on_error=False,
time_step=timedelta(seconds = 900),
end_time = finish_time,
time_step_output=timedelta(minutes = 120),
outfile= 'test_development_Opendrift_using_moana.nc')
print(o)
o.plot(fast=True, color='z')
o.animation(fast=True, color='z')
o.set_config('biology:settlement_in_habitat', True) # settlement restricted to suitable habitat only, specified by shapefile or txt file with nan-delimited polys
o.add_settlement_habitat('./habitat_moana/poly_habitat_taranaki_bivalve.txt') # Location of the files with the user-defined habitat polygons
# habitat files can be text file with simple nan-delimited polygon(s)
else:
o.set_config('biology:settlement_in_habitat', False) # particle will settle on coast or seafloor after it reached 'min_settlement_age_seconds'
o.list_config()
###############################
# RUN
###############################
# Running model (until end of driver data)
o.run(stop_on_error=False,
time_step=timedelta(seconds = 900),
end_time = reader_moana_v19.start_time + timedelta(days = 4.0),
time_step_output=timedelta(seconds = 3600 * 3))
import matplotlib.pyplot as plt
plt.ion()
o.plot(fast=True)#, corners=[163, 180, -52, -31])
if use_habitat ==1 :
# add habitat polygons
import cartopy.crs as ccrs
gcrs = ccrs.PlateCarree()
plt.plot(o.multiShp.exterior.xy[0][:],o.multiShp.exterior.xy[1][:], transform = gcrs)
import pdb;pdb.set_trace()
# o.animation(fast=True, color='status') #corners=[163, 180, -52, -31])
# o.animation_profile()
# o.plot(fast=True)
o.set_config('drift:max_age_seconds', 3600 * 24 * 35)
o.set_config('drift:min_settlement_age_seconds', 3600 * 24 * 21)
o.set_config('general:seafloor_action', 'lift_to_seafloor')
o.set_config('drift:vertical_mixing', False)
o.set_config('general:coastline_action', 'previous')
o.list_config()
###############################
#Run
###############################
lons_start = o.elements_scheduled.lon
lats_start = o.elements_scheduled.lat
o.plot()
o.run(stop_on_error=False,
end_time=reader2.end_time,
time_step=900,
time_step_output=86400.0,
export_variables=[])
index_of_first, index_of_last = o.index_of_activation_and_deactivation()
lons = o.get_property('lon')[0]
lats = o.get_property('lat')[0]
status = o.get_property('status')[0]
lons_end = lons[index_of_last, range(lons.shape[1])]
lats_end = lats[index_of_last, range(lons.shape[1])]
status_end = status[index_of_last, range(lons.shape[1])]
print(o.status_categories)
#SEED PARTICLES
##############################
#There's a bunch of different ways to seed particles, here's my go-to method
#give corners of a polygon to seed within
minlon = 173.2
maxlon = 173.3
minlat = -35.6
maxlat = -35.5
lons = [minlon, maxlon, maxlon, minlon]
lats = [maxlat, maxlat, minlat, minlat]
time0 = reader0.start_time
z = -5
number = 100
o.seed_within_polygon(lons, lats, number=number, z=z, time=time0)
##############################
#RUN
##############################
#a bunch of tricks you can do here to save only exactly what you want, but here's the basics
o.run(stop_on_error=False,
end_time=reader1.end_time,
time_step=3600,
time_step_output=3600.0,
outfile='path/outfile_name.nc')
o.plot(filename='path/figure_name.jpg')
o.animation(filename='path/anim_name.mp4')
