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SCHISM native reader

16:06:59 INFO opendrift:513: OpenDriftSimulation initialised (version 1.14.2 / v1.14.2-82-g86a40e4)
16:06:59 INFO opendrift.readers.reader_schism_native:109: Opening dataset: https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
16:06:59 INFO opendrift.readers.reader_schism_native:115: Opening file with dataset
16:07:02 INFO opendrift.models.basemodel.environment:206: Adding a global landmask from GSHHG
16:07:06 INFO opendrift.models.basemodel.environment:229: Fallback values will be used for the following variables which have no readers:
16:07:06 INFO opendrift.models.basemodel.environment:232: x_wind: 0.000000
16:07:06 INFO opendrift.models.basemodel.environment:232: y_wind: 0.000000
16:07:06 INFO opendrift.models.basemodel.environment:232: ocean_vertical_diffusivity: 0.000000
16:07:06 INFO opendrift.models.basemodel.environment:232: sea_surface_wave_significant_height: 0.000000
16:07:06 INFO opendrift.models.basemodel.environment:232: sea_surface_wave_stokes_drift_x_velocity: 0.000000
16:07:06 INFO opendrift.models.basemodel.environment:232: sea_surface_wave_stokes_drift_y_velocity: 0.000000
16:07:06 INFO opendrift.models.basemodel.environment:232: ocean_mixed_layer_thickness: 50.000000
16:07:06 INFO opendrift:1722: Skipping environment variable ocean_vertical_diffusivity because of condition ['drift:vertical_mixing', 'is', False]
16:07:06 INFO opendrift:1722: Skipping environment variable ocean_mixed_layer_thickness because of condition ['drift:vertical_mixing', 'is', False]
16:07:06 INFO opendrift:1732: Storing previous values of element property lon because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous']))
16:07:06 INFO opendrift:1732: Storing previous values of element property lat because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous']))
16:07:06 WARNING opendrift:1811: Simulation end is not at an output time step. Extending duration from 2:24:00 to 2:30:00
16:07:06 INFO opendrift:889: Using existing reader for land_binary_mask
16:07:06 INFO opendrift:918: All points are in ocean
16:07:06 INFO opendrift:2015: 2008-01-01 00:30:00 - step 1 of 10 - 300 active elements (0 deactivated)
16:07:06 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:19 INFO opendrift:2015: 2008-01-01 00:45:00 - step 2 of 10 - 300 active elements (0 deactivated)
16:07:19 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:32 INFO opendrift:2015: 2008-01-01 01:00:00 - step 3 of 10 - 300 active elements (0 deactivated)
16:07:32 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:32 INFO opendrift:2015: 2008-01-01 01:15:00 - step 4 of 10 - 300 active elements (0 deactivated)
16:07:32 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:44 INFO opendrift:2015: 2008-01-01 01:30:00 - step 5 of 10 - 300 active elements (0 deactivated)
16:07:44 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:44 INFO opendrift:2015: 2008-01-01 01:45:00 - step 6 of 10 - 300 active elements (0 deactivated)
16:07:44 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:57 INFO opendrift:2015: 2008-01-01 02:00:00 - step 7 of 10 - 300 active elements (0 deactivated)
16:07:57 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:07:57 INFO opendrift:2015: 2008-01-01 02:15:00 - step 8 of 10 - 300 active elements (0 deactivated)
16:07:57 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:08:09 INFO opendrift:2015: 2008-01-01 02:30:00 - step 9 of 10 - 300 active elements (0 deactivated)
16:08:09 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
16:08:09 INFO opendrift:2015: 2008-01-01 02:45:00 - step 10 of 10 - 300 active elements (0 deactivated)
16:08:09 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
===========================
--------------------
Reader performance:
--------------------
https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
0:01:14.7 total
0:00:17.5 preparing
0:01:14.7 reading
0:00:00.3 interpolation
0:00:00.0 interpolation_time
0:00:00.0 rotating vectors
0:00:00.0 masking
--------------------
global_landmask
0:00:00.0 total
0:00:00.0 preparing
0:00:00.0 reading
0:00:00.0 masking
--------------------
Performance:
1:22.5 total time
7.5 configuration
0.0 preparing main loop
0.0 moving elements to ocean
1:14.9 main loop
0.0 updating elements
0.0 cleaning up
--------------------
===========================
Model: OceanDrift (OpenDrift version 1.14.2)
300 active Lagrangian3DArray particles (0 deactivated, 0 scheduled)
-------------------
Environment variables:
-----
sea_floor_depth_below_sea_level
sea_surface_height
upward_sea_water_velocity
x_sea_water_velocity
y_sea_water_velocity
1) https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
-----
land_binary_mask
1) global_landmask
-----
Readers not added for the following variables:
sea_surface_wave_significant_height
sea_surface_wave_stokes_drift_x_velocity
sea_surface_wave_stokes_drift_y_velocity
x_wind
y_wind
Discarded readers:
Time:
Start: 2008-01-01 00:30:00 UTC
Present: 2008-01-01 03:00:00 UTC
Calculation steps: 10 * 0:15:00 - total time: 2:30:00
Output steps: 11 * 0:15:00
===========================
16:08:21 WARNING opendrift:2371: Plotting fast. This will make your plots less accurate.
16:08:33 INFO opendrift:4533: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_0.gif...
16:08:38 INFO opendrift:2974: Time to make animation: 0:00:15.404898
16:08:38 INFO opendrift:4533: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_1.gif...
16:08:40 INFO opendrift:3184: Time to make animation: 0:00:01.630411
import numpy as np
from datetime import timedelta, datetime
from opendrift.readers import reader_schism_native
from opendrift.readers import reader_global_landmask
from opendrift.models.oceandrift import OceanDrift
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
try:
# 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)
except:
print('Thredds server not available, cannot run example')
schism_native = None
if schism_native is not None:
o.add_reader([schism_native])
# 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, number=100,
z=np.linspace(0,-10, 100), time=schism_native.start_time)
o.seed_elements(lon=174.2940, lat=-41.0888, radius=20, number=100,
z=np.linspace(0,-10, 100), time=schism_native.start_time)
#%%
# Running model
o.run(time_step=900,
end_time = schism_native.start_time+timedelta(days=0.1))
# outfile='schism_native_output.nc')
# Print and plot results
print(o)
o.plot(fast=True)
o.animation()
o.animation_profile()
Total running time of the script: (1 minutes 46.975 seconds)