Note
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SCHISM native reader
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
MODEL
o = OceanDrift(loglevel=20) # Set loglevel to 0 for debug information
15:23:19 INFO opendrift.models.basemodel:533: OpenDriftSimulation initialised (version 1.11.2 / v1.11.2-34-g74f61eb)
READERS
Creating and adding reader using a native SCHISM netcdf output file SCHISM reader
reader_landmask = reader_global_landmask.Reader()
# 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
o.disable_vertical_motion() #Deactivate any vertical processes/advection"""
# 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)
15:23:24 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
15:23:24 INFO opendrift.readers.reader_schism_native:115: Opening file with dataset
15:23:26 INFO opendrift.models.oceandrift:377: Setting config: drift:vertical_advection -> False
15:23:26 INFO opendrift.models.oceandrift:377: Setting config: drift:vertical_mixing -> False
15:23:26 INFO opendrift.models.basemodel.environment:245: Fallback values will be used for the following variables which have no readers:
15:23:26 INFO opendrift.models.basemodel.environment:248: x_wind: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: y_wind: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: ocean_vertical_diffusivity: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_significant_height: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_stokes_drift_x_velocity: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_stokes_drift_y_velocity: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_period_at_variance_spectral_density_maximum: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_swell_wave_to_direction: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_swell_wave_peak_period_from_variance_spectral_density: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_swell_wave_significant_height: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wind_wave_to_direction: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wind_wave_mean_period: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: sea_surface_wind_wave_significant_height: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: surface_downward_x_stress: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: surface_downward_y_stress: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: turbulent_kinetic_energy: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: turbulent_generic_length_scale: 0.000000
15:23:26 INFO opendrift.models.basemodel.environment:248: ocean_mixed_layer_thickness: 50.000000
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()
15:23:26 INFO opendrift.models.basemodel:911: Using existing reader for land_binary_mask
15:23:26 INFO opendrift.models.basemodel:922: All points are in ocean
15:23:26 WARNING opendrift.models.basemodel:705: Seafloor check not being run because environment is missing. This will happen the first time the function is run but if it happens subsequently there is probably a problem.
15:23:26 INFO opendrift.models.basemodel:2011: 2008-01-01 00:30:00 - step 1 of 9 - 300 active elements (0 deactivated)
15:23:26 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:23:42 INFO opendrift.models.basemodel:2011: 2008-01-01 00:45:00 - step 2 of 9 - 300 active elements (0 deactivated)
15:23:42 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:23:55 INFO opendrift.models.basemodel:2011: 2008-01-01 01:00:00 - step 3 of 9 - 300 active elements (0 deactivated)
15:23:55 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:23:55 INFO opendrift.models.basemodel:2011: 2008-01-01 01:15:00 - step 4 of 9 - 300 active elements (0 deactivated)
15:23:55 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:24:09 INFO opendrift.models.basemodel:2011: 2008-01-01 01:30:00 - step 5 of 9 - 300 active elements (0 deactivated)
15:24:09 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:24:09 INFO opendrift.models.basemodel:2011: 2008-01-01 01:45:00 - step 6 of 9 - 300 active elements (0 deactivated)
15:24:09 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:24:23 INFO opendrift.models.basemodel:2011: 2008-01-01 02:00:00 - step 7 of 9 - 300 active elements (0 deactivated)
15:24:23 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:24:23 INFO opendrift.models.basemodel:2011: 2008-01-01 02:15:00 - step 8 of 9 - 300 active elements (0 deactivated)
15:24:23 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
15:24:38 INFO opendrift.models.basemodel:2011: 2008-01-01 02:30:00 - step 9 of 9 - 300 active elements (0 deactivated)
15:24:38 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
===========================
--------------------
Reader performance:
--------------------
global_landmask
0:00:00.0 total
0:00:00.0 preparing
0:00:00.0 reading
0:00:00.0 masking
--------------------
https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
0:01:11.7 total
0:00:18.5 preparing
0:01:11.7 reading
0:00:00.1 interpolation
0:00:00.0 interpolation_time
0:00:00.0 rotating vectors
0:00:00.0 masking
--------------------
Performance:
1:19.4 total time
7.5 configuration
0.0 preparing main loop
0.0 moving elements to ocean
1:11.8 main loop
0.0 updating elements
0.0 cleaning up
--------------------
===========================
Model: OceanDrift (OpenDrift version 1.11.2)
300 active Lagrangian3DArray particles (0 deactivated, 0 scheduled)
-------------------
Environment variables:
-----
land_binary_mask
1) global_landmask
-----
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
-----
Readers not added for the following variables:
ocean_mixed_layer_thickness
ocean_vertical_diffusivity
sea_surface_swell_wave_peak_period_from_variance_spectral_density
sea_surface_swell_wave_significant_height
sea_surface_swell_wave_to_direction
sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment
sea_surface_wave_period_at_variance_spectral_density_maximum
sea_surface_wave_significant_height
sea_surface_wave_stokes_drift_x_velocity
sea_surface_wave_stokes_drift_y_velocity
sea_surface_wind_wave_mean_period
sea_surface_wind_wave_significant_height
sea_surface_wind_wave_to_direction
surface_downward_x_stress
surface_downward_y_stress
turbulent_generic_length_scale
turbulent_kinetic_energy
x_wind
y_wind
Discarded readers:
Time:
Start: 2008-01-01 00:30:00 UTC
Present: 2008-01-01 02:45:00 UTC
Calculation steps: 9 * 0:15:00 - total time: 2:15:00
Output steps: 10 * 0:15:00
===========================
15:24:38 WARNING opendrift.models.basemodel:2379: Plotting fast. This will make your plots less accurate.
/opt/conda/envs/opendrift/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:1683: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
result = super().scatter(*args, **kwargs)
15:24:53 INFO opendrift.models.basemodel:4563: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_0.gif...
15:25:21 INFO opendrift.models.basemodel:3003: Time to make animation: 0:00:40.621567
/root/project/opendrift/models/basemodel/__init__.py:3122: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
points = ax.scatter([], [],
15:25:21 INFO opendrift.models.basemodel:4563: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_1.gif...
15:25:22 INFO opendrift.models.basemodel:3217: Time to make animation: 0:00:01.325774
Total running time of the script: (2 minutes 4.689 seconds)