SCHISM native reader

17:15:52 INFO    opendrift:513: OpenDriftSimulation initialised (version 1.14.2 / v1.14.2-88-gf09b7bd)
17:15:52 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
17:15:52 INFO    opendrift.readers.reader_schism_native:115: Opening file with dataset
17:15:55 INFO    opendrift.models.basemodel.environment:206: Adding a global landmask from GSHHG
17:16:00 INFO    opendrift.models.basemodel.environment:229: Fallback values will be used for the following variables which have no readers:
17:16:00 INFO    opendrift.models.basemodel.environment:232:    x_wind: 0.000000
17:16:00 INFO    opendrift.models.basemodel.environment:232:    y_wind: 0.000000
17:16:00 INFO    opendrift.models.basemodel.environment:232:    ocean_vertical_diffusivity: 0.000000
17:16:00 INFO    opendrift.models.basemodel.environment:232:    sea_surface_wave_significant_height: 0.000000
17:16:00 INFO    opendrift.models.basemodel.environment:232:    sea_surface_wave_stokes_drift_x_velocity: 0.000000
17:16:00 INFO    opendrift.models.basemodel.environment:232:    sea_surface_wave_stokes_drift_y_velocity: 0.000000
17:16:00 INFO    opendrift.models.basemodel.environment:232:    ocean_mixed_layer_thickness: 50.000000
17:16:00 INFO    opendrift:1732: Skipping environment variable ocean_vertical_diffusivity because of condition ['drift:vertical_mixing', 'is', False]
17:16:00 INFO    opendrift:1732: Skipping environment variable ocean_mixed_layer_thickness because of condition ['drift:vertical_mixing', 'is', False]
17:16:00 INFO    opendrift:1743: Storing previous values of element property lon because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous']))
17:16:00 INFO    opendrift:1743: Storing previous values of element property lat because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous']))
17:16:00 INFO    opendrift:1751: Storing previous values of environment variable sea_surface_height because of condition ['drift:vertical_advection', 'is', True]
17:16:00 WARNING opendrift:1831: Simulation end is not at an output time step. Extending duration from 2:24:00 to 2:30:00
17:16:00 INFO    opendrift:899: Using existing reader for land_binary_mask
17:16:00 INFO    opendrift:928: All points are in ocean
17:16:00 INFO    opendrift:2035: 2008-01-01 00:30:00 - step 1 of 10 - 300 active elements (0 deactivated)
17:16:00 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:18 INFO    opendrift:2035: 2008-01-01 00:45:00 - step 2 of 10 - 300 active elements (0 deactivated)
17:16:18 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:32 INFO    opendrift:2035: 2008-01-01 01:00:00 - step 3 of 10 - 300 active elements (0 deactivated)
17:16:32 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:32 INFO    opendrift:2035: 2008-01-01 01:15:00 - step 4 of 10 - 300 active elements (0 deactivated)
17:16:32 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:45 INFO    opendrift:2035: 2008-01-01 01:30:00 - step 5 of 10 - 300 active elements (0 deactivated)
17:16:45 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:45 INFO    opendrift:2035: 2008-01-01 01:45:00 - step 6 of 10 - 300 active elements (0 deactivated)
17:16:45 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:58 INFO    opendrift:2035: 2008-01-01 02:00:00 - step 7 of 10 - 300 active elements (0 deactivated)
17:16:58 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:16:58 INFO    opendrift:2035: 2008-01-01 02:15:00 - step 8 of 10 - 300 active elements (0 deactivated)
17:16:58 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:17:10 INFO    opendrift:2035: 2008-01-01 02:30:00 - step 9 of 10 - 300 active elements (0 deactivated)
17:17:10 WARNING opendrift.readers.basereader.unstructured:141: z-coordinates are not bounds-checked
17:17:10 INFO    opendrift:2035: 2008-01-01 02:45:00 - step 10 of 10 - 300 active elements (0 deactivated)
17:17:10 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
 0:01:28.0  total
 0:00:29.2  preparing
 0:01:28.0  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:
 1:36.7 total time
    8.4 configuration
    0.0 preparing main loop
      0.0 moving elements to ocean
 1:28.2 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
===========================

17:17:29 WARNING opendrift:2391: Plotting fast. This will make your plots less accurate.
17:17:41 INFO    opendrift:4553: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_0.gif...
17:17:47 INFO    opendrift:2994: Time to make animation: 0:00:16.845689
17:17:47 INFO    opendrift:4553: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_1.gif...
17:17:49 INFO    opendrift:3204: Time to make animation: 0:00:01.761850

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()