SCHISM native reader

14:20:51 INFO    opendrift:509: OpenDriftSimulation initialised (version 1.13.0 / v1.13.0-75-gd4c13d2)
14:20:51 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
14:20:51 INFO    opendrift.readers.reader_schism_native:115: Opening file with dataset
14:20:53 INFO    opendrift.models.basemodel.environment:206: Adding a dynamical landmask with max. priority based on assumed maximum speed of 2.0 m/s. Adding a customised landmask may be faster...
14:20:57 INFO    opendrift.models.basemodel.environment:233: Fallback values will be used for the following variables which have no readers:
14:20:57 INFO    opendrift.models.basemodel.environment:236:    x_wind: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    y_wind: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    ocean_vertical_diffusivity: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wave_significant_height: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wave_stokes_drift_x_velocity: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wave_stokes_drift_y_velocity: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wave_period_at_variance_spectral_density_maximum: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_swell_wave_to_direction: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_swell_wave_peak_period_from_variance_spectral_density: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_swell_wave_significant_height: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wind_wave_to_direction: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wind_wave_mean_period: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    sea_surface_wind_wave_significant_height: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    surface_downward_x_stress: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    surface_downward_y_stress: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    turbulent_kinetic_energy: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    turbulent_generic_length_scale: 0.000000
14:20:57 INFO    opendrift.models.basemodel.environment:236:    ocean_mixed_layer_thickness: 50.000000
14:20:57 WARNING opendrift:1860: Simulation end is not at an output time step. Extending duration from 2:24:00 to 2:30:00
14:20:57 INFO    opendrift:919: Using existing reader for land_binary_mask
14:20:57 INFO    opendrift:930: All points are in ocean
14:20:57 WARNING opendrift:713: 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.
14:20:57 INFO    opendrift:2056: 2008-01-01 00:30:00 - step 1 of 10 - 300 active elements (0 deactivated)
14:20:57 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:11 INFO    opendrift:2056: 2008-01-01 00:45:00 - step 2 of 10 - 300 active elements (0 deactivated)
14:21:11 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:25 INFO    opendrift:2056: 2008-01-01 01:00:00 - step 3 of 10 - 300 active elements (0 deactivated)
14:21:25 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:25 INFO    opendrift:2056: 2008-01-01 01:15:00 - step 4 of 10 - 300 active elements (0 deactivated)
14:21:25 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:39 INFO    opendrift:2056: 2008-01-01 01:30:00 - step 5 of 10 - 300 active elements (0 deactivated)
14:21:39 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:39 INFO    opendrift:2056: 2008-01-01 01:45:00 - step 6 of 10 - 300 active elements (0 deactivated)
14:21:39 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:52 INFO    opendrift:2056: 2008-01-01 02:00:00 - step 7 of 10 - 300 active elements (0 deactivated)
14:21:52 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:21:52 INFO    opendrift:2056: 2008-01-01 02:15:00 - step 8 of 10 - 300 active elements (0 deactivated)
14:21:52 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:22:05 INFO    opendrift:2056: 2008-01-01 02:30:00 - step 9 of 10 - 300 active elements (0 deactivated)
14:22:05 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
14:22:05 INFO    opendrift:2056: 2008-01-01 02:45:00 - step 10 of 10 - 300 active elements (0 deactivated)
14:22:05 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
 0:01:20.7  total
 0:00:17.7  preparing
 0:01:20.7  reading
 0:00:00.2  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:
 1:27.7 total time
    6.6 configuration
    0.0 preparing main loop
      0.0 moving elements to ocean
 1:21.0 main loop
      0.0 updating elements
    0.0 cleaning up
--------------------
===========================
Model:  OceanDrift     (OpenDrift version 1.13.0)
        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:
  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 03:00:00 UTC
        Calculation steps: 10 * 0:15:00 - total time: 2:30:00
        Output steps: 11 * 0:15:00
===========================

14:22:19 WARNING opendrift:2429: Plotting fast. This will make your plots less accurate.
14:22:36 INFO    opendrift:4600: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_0.gif...
14:22:43 INFO    opendrift:3036: Time to make animation: 0:00:23.394376
14:22:43 INFO    opendrift:4600: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_1.gif...
14:22:45 INFO    opendrift:3246: Time to make animation: 0:00:01.755205

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()