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=0)  # Set loglevel to 0 for debug information

Out:

12:27 DEBUG   opendrift.models.basemodel: Adding 17 config items from basemodel
12:27 DEBUG   opendrift.models.basemodel: Adding 4 config items from basemodel
12:27 DEBUG   opendrift.models.basemodel: Adding 36 config items from basemodel
12:27 INFO    opendrift.models.basemodel: OpenDriftSimulation initialised (version 1.7.1 / v1.7.1-145-gdf95ed3)
12:27 DEBUG   opendrift.models.basemodel: Adding 14 config items from oceandrift
12:27 DEBUG   opendrift.models.basemodel:   Overwriting config item seed:z

READERS

Creating and adding reader using a native SCHISM netcdf output file SCHISM reader

reader_landmask = reader_global_landmask.Reader(
                    llcrnrlon=171.5, llcrnrlat=-43.5,
                    urcrnrlon=177.0, urcrnrlat=-38.0)

# 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

# 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)

o.disable_vertical_motion()  #Deactivate any vertical processes/advection"""

Out:

12:27 DEBUG   opendrift.readers.basereader: Variable mapping: ['sea_floor_depth_below_sea_level'] -> ['land_binary_mask'] is not activated
12:27 DEBUG   opendrift_landmask_data.mask: memmapping mask..
12:30 INFO    opendrift.readers.reader_schism_native: Opening dataset: https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:30 INFO    opendrift.readers.reader_schism_native: Opening file with dataset
12:30 DEBUG   opendrift.readers.reader_schism_native: Finding coordinate variables.
12:31 DEBUG   opendrift.readers.basereader: Variable mapping: ['sea_floor_depth_below_sea_level'] -> ['land_binary_mask'] is not activated
12:31 DEBUG   opendrift.readers.reader_schism_native: Building CKDtree of static 2D nodes for nearest-neighbor search
12:31 DEBUG   opendrift.readers.reader_schism_native: Building convex hull of nodes for particles in-mesh checks
12:31 DEBUG   opendrift.models.basemodel: Added reader global_landmask
12:31 DEBUG   opendrift.models.basemodel: Added reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:31 INFO    opendrift.models.oceandrift: Setting config: drift:vertical_advection -> False
12:31 INFO    opendrift.models.oceandrift: Setting config: drift:vertical_mixing -> False

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()

OpenDrift - OceanDrift 2008-01-01 00:30 to 2008-01-01 02:45 UTC (10 steps)

Out:

12:32 DEBUG   opendrift.models.basemodel:
------------------------------------------------------
Software and hardware:
  OpenDrift version 1.7.1
  Platform: Linux, 4.15.0-1110-aws
69182968139648 GB memory
processors ()
  NumPy version 1.21.2
  SciPy version 1.7.1
  Matplotlib version 3.4.3
  NetCDF4 version 1.5.6
  Xarray version 0.19.0
  OilLibrary version 1.1.3
  Python version 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:46) [GCC 9.4.0]
------------------------------------------------------

12:32 DEBUG   opendrift.models.basemodel: No output file is specified, neglecting export_buffer_length
12:32 INFO    opendrift.models.basemodel: Fallback values will be used for the following variables which have no readers:
12:32 INFO    opendrift.models.basemodel:    x_wind: 0.000000
12:32 INFO    opendrift.models.basemodel:    y_wind: 0.000000
12:32 INFO    opendrift.models.basemodel:    ocean_vertical_diffusivity: 0.000000
12:32 INFO    opendrift.models.basemodel:    sea_surface_wave_significant_height: 0.000000
12:32 INFO    opendrift.models.basemodel:    sea_surface_wave_stokes_drift_x_velocity: 0.000000
12:32 INFO    opendrift.models.basemodel:    sea_surface_wave_stokes_drift_y_velocity: 0.000000
12:32 INFO    opendrift.models.basemodel:    sea_surface_wave_period_at_variance_spectral_density_maximum: 0.000000
12:32 INFO    opendrift.models.basemodel:    sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0.000000
12:32 INFO    opendrift.models.basemodel:    surface_downward_x_stress: 0.000000
12:32 INFO    opendrift.models.basemodel:    surface_downward_y_stress: 0.000000
12:32 INFO    opendrift.models.basemodel:    turbulent_kinetic_energy: 0.000000
12:32 INFO    opendrift.models.basemodel:    turbulent_generic_length_scale: 0.000000
12:32 INFO    opendrift.models.basemodel:    ocean_mixed_layer_thickness: 50.000000
12:32 DEBUG   opendrift.models.basemodel: Preparing readers for simulation coverage ([173.78658236004176, -41.16232081232844, 174.39130460284886, -40.842619220630546]) and time (2008-01-01 00:30:00 to 2008-01-01 02:45:00)
12:32 DEBUG   opendrift.models.basemodel:    Preparing global_landmask
12:32 DEBUG   opendrift.readers.basereader: Nothing more to prepare for global_landmask
12:32 DEBUG   opendrift.models.basemodel:    Preparing https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:32 DEBUG   opendrift.readers.basereader: Nothing more to prepare for https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:32 INFO    opendrift.models.basemodel: Using existing reader for land_binary_mask
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
12:32 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
12:32 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
12:32 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
12:32 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
12:32 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
12:32 DEBUG   opendrift.models.basemodel: ---------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
12:32 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
12:32 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
12:32 DEBUG   opendrift.models.basemodel: ---------------------------------
12:32 DEBUG   opendrift.models.basemodel:            0 active elements
12:32 INFO    opendrift.models.basemodel: All points are in ocean
12:32 DEBUG   opendrift.models.basemodel: to be seeded: 300, already seeded 0
12:32 DEBUG   opendrift.models.basemodel: Released 300 new elements.
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level']
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
12:32 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
12:32 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:32 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 00:30:00 (before)
                2008-01-01 01:00:00 (after)
12:32 DEBUG   opendrift.readers.reader_schism_native: reading constant data from unstructured reader sea_floor_depth_below_sea_level
12:32 DEBUG   opendrift.readers.reader_schism_native: initialize ReaderBlockUnstruct var_block_before
12:32 DEBUG   opendrift.readers.reader_schism_native: saving readers 2D (horizontal) KDtree to ReaderBlockUnstruct
12:32 DEBUG   opendrift.readers.reader_schism_native: Fetched env-block (size 149233x149233x149233) for time before (2008-01-01 00:30:00)
12:32 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 00:30:00) in space  (linearNDFast)
12:32 DEBUG   opendrift.readers.reader_schism_native: No time interpolation needed - right on time.
12:32 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
12:32 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
12:32 DEBUG   opendrift.models.basemodel: ---------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
12:32 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
12:32 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 15.0017 (min) 74.046 (max)
12:32 DEBUG   opendrift.models.basemodel: ---------------------------------
12:32 DEBUG   opendrift.models.basemodel:            300 active elements
12:32 DEBUG   opendrift.models.basemodel:            -41.089348 <- latitude  -> -40.915592
12:32 DEBUG   opendrift.models.basemodel:            173.88324 <- longitude -> 174.29465
12:32 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
12:32 DEBUG   opendrift.models.basemodel: ---------------------------------
12:32 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
12:32 DEBUG   opendrift.models.basemodel: ======================================================================
12:32 INFO    opendrift.models.basemodel: 2008-01-01 00:30:00 - step 1 of 9 - 300 active elements (0 deactivated)
12:32 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
12:32 DEBUG   opendrift.models.basemodel: ======================================================================
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
12:32 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
12:32 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
12:32 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
12:32 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
12:32 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:32 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:32 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
12:32 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
12:32 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:32 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 00:30:00 (before)
                2008-01-01 01:00:00 (after)
12:32 DEBUG   opendrift.readers.reader_schism_native: reading constant data from unstructured reader sea_floor_depth_below_sea_level
12:32 DEBUG   opendrift.readers.reader_schism_native: reading 3D data from unstructured reader upward_sea_water_velocity
12:38 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader x_sea_water_velocity
12:44 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader y_sea_water_velocity
12:50 DEBUG   opendrift.readers.reader_schism_native: initialize ReaderBlockUnstruct var_block_before
12:50 DEBUG   opendrift.readers.reader_schism_native: saving readers 2D (horizontal) KDtree to ReaderBlockUnstruct
12:50 DEBUG   opendrift.readers.reader_schism_native: Compute time-varying KDtree for 3D nearest-neighbor search (i.e using zcor)
12:51 DEBUG   opendrift.readers.reader_schism_native: Fetched env-block (size 149233x149233x149233) for time before (2008-01-01 00:30:00)
12:51 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 00:30:00) in space  (linearNDFast)
12:51 DEBUG   opendrift.readers.reader_schism_native: No time interpolation needed - right on time.
12:51 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
12:51 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
12:51 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
12:51 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8509596907996719 and -0.578507548367259 degrees.
12:51 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
12:51 DEBUG   opendrift.models.basemodel: ---------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
12:51 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
12:51 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
12:51 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
12:51 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.30496 (min) 0.0345555 (max)
12:51 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.149951 (min) 0.107663 (max)
12:51 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.000698592 (min) 0.0035493 (max)
12:51 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
12:51 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 15.0017 (min) 74.046 (max)
12:51 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
12:51 DEBUG   opendrift.models.basemodel: ---------------------------------
12:51 DEBUG   opendrift.models.basemodel:            300 active elements
12:51 DEBUG   opendrift.models.basemodel:            -41.089348 <- latitude  -> -40.915592
12:51 DEBUG   opendrift.models.basemodel:            173.88324 <- longitude -> 174.29465
12:51 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
12:51 DEBUG   opendrift.models.basemodel: ---------------------------------
12:51 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
12:51 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
12:51 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
12:51 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
12:51 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
12:51 DEBUG   opendrift.models.basemodel: No elements to deactivate
12:51 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
12:51 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
12:51 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
12:51 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
12:51 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
12:51 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
12:51 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
12:51 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
12:51 DEBUG   opendrift.models.basemodel: ======================================================================
12:51 INFO    opendrift.models.basemodel: 2008-01-01 00:45:00 - step 2 of 9 - 300 active elements (0 deactivated)
12:51 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
12:51 DEBUG   opendrift.models.basemodel: ======================================================================
12:51 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
12:51 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
12:51 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
12:51 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
12:51 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
12:51 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
12:51 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
12:51 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
12:51 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
12:51 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:51 DEBUG   opendrift.models.basemodel: ----------------------------------------
12:51 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
12:51 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
12:51 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
12:51 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 00:30:00 (before)
                2008-01-01 01:00:00 (after)
12:51 DEBUG   opendrift.readers.reader_schism_native: reading constant data from unstructured reader sea_floor_depth_below_sea_level
12:51 DEBUG   opendrift.readers.reader_schism_native: reading 3D data from unstructured reader upward_sea_water_velocity
12:57 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader x_sea_water_velocity
13:04 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader y_sea_water_velocity
13:10 DEBUG   opendrift.readers.reader_schism_native: initialize ReaderBlockUnstruct var_block_after
13:10 DEBUG   opendrift.readers.reader_schism_native: saving readers 2D (horizontal) KDtree to ReaderBlockUnstruct
13:10 DEBUG   opendrift.readers.reader_schism_native: Compute time-varying KDtree for 3D nearest-neighbor search (i.e using zcor)
13:14 DEBUG   opendrift.readers.reader_schism_native: Fetched env-block (size 149233x149233x149233) for time after (2008-01-01 01:00:00)
13:14 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 00:30:00) in space  (linearNDFast)
13:14 DEBUG   opendrift.readers.reader_schism_native: Interpolating after (2008-01-01 01:00:00) in space  (linearNDFast)
13:14 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 00:30:00, weight 0.50) and
                      after (2008-01-01 01:00:00, weight 0.50) in time
13:14 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8511387193191574 and -0.5777240434517761 degrees.
13:14 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:14 DEBUG   opendrift.models.basemodel: ---------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
13:14 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
13:14 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
13:14 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
13:14 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.286947 (min) 0.0479919 (max)
13:14 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.131052 (min) 0.126287 (max)
13:14 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.000621651 (min) 0.00194884 (max)
13:14 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 15.0126 (min) 70.6919 (max)
13:14 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel: ---------------------------------
13:14 DEBUG   opendrift.models.basemodel:            300 active elements
13:14 DEBUG   opendrift.models.basemodel:            -41.0893291027404 <- latitude  -> -40.91640122024551
13:14 DEBUG   opendrift.models.basemodel:            173.88203002866666 <- longitude -> 174.29491999965848
13:14 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
13:14 DEBUG   opendrift.models.basemodel: ---------------------------------
13:14 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
13:14 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
13:14 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
13:14 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
13:14 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:14 DEBUG   opendrift.models.basemodel: No elements to deactivate
13:14 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
13:14 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
13:14 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
13:14 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
13:14 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
13:14 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
13:14 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
13:14 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:14 DEBUG   opendrift.models.basemodel: ======================================================================
13:14 INFO    opendrift.models.basemodel: 2008-01-01 01:00:00 - step 3 of 9 - 300 active elements (0 deactivated)
13:14 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
13:14 DEBUG   opendrift.models.basemodel: ======================================================================
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:14 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
13:14 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
13:14 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
13:14 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:14 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
13:14 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:14 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 01:00:00 (before)
                2008-01-01 01:30:00 (after)
13:14 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 01:00:00) in space  (linearNDFast)
13:14 DEBUG   opendrift.readers.reader_schism_native: No time interpolation needed - right on time.
13:14 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8514708067107853 and -0.5768643161861188 degrees.
13:14 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:14 DEBUG   opendrift.models.basemodel: ---------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
13:14 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
13:14 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
13:14 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
13:14 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.264079 (min) 0.0626803 (max)
13:14 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.114077 (min) 0.125723 (max)
13:14 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.000524679 (min) 0.00125092 (max)
13:14 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
13:14 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.9912 (min) 68.2496 (max)
13:14 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
13:14 DEBUG   opendrift.models.basemodel: ---------------------------------
13:14 DEBUG   opendrift.models.basemodel:            300 active elements
13:14 DEBUG   opendrift.models.basemodel:            -41.08940917782002 <- latitude  -> -40.91708668546262
13:14 DEBUG   opendrift.models.basemodel:            173.88068628252125 <- longitude -> 174.29542356560665
13:14 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
13:14 DEBUG   opendrift.models.basemodel: ---------------------------------
13:14 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
13:14 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
13:14 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
13:14 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
13:14 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:14 DEBUG   opendrift.models.basemodel: No elements to deactivate
13:14 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
13:14 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
13:14 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
13:14 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
13:14 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
13:14 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
13:14 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
13:14 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:14 DEBUG   opendrift.models.basemodel: ======================================================================
13:14 INFO    opendrift.models.basemodel: 2008-01-01 01:15:00 - step 4 of 9 - 300 active elements (0 deactivated)
13:14 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
13:14 DEBUG   opendrift.models.basemodel: ======================================================================
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:14 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
13:14 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
13:14 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
13:14 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
13:14 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:14 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:14 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:14 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
13:14 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:14 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 01:00:00 (before)
                2008-01-01 01:30:00 (after)
13:14 DEBUG   opendrift.readers.reader_schism_native: reading constant data from unstructured reader sea_floor_depth_below_sea_level
13:15 DEBUG   opendrift.readers.reader_schism_native: reading 3D data from unstructured reader upward_sea_water_velocity
13:21 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader x_sea_water_velocity
13:27 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader y_sea_water_velocity
13:34 DEBUG   opendrift.readers.reader_schism_native: initialize ReaderBlockUnstruct var_block_after
13:34 DEBUG   opendrift.readers.reader_schism_native: saving readers 2D (horizontal) KDtree to ReaderBlockUnstruct
13:34 DEBUG   opendrift.readers.reader_schism_native: Compute time-varying KDtree for 3D nearest-neighbor search (i.e using zcor)
13:34 DEBUG   opendrift.readers.reader_schism_native: Fetched env-block (size 149233x149233x149233) for time after (2008-01-01 01:30:00)
13:34 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 01:00:00) in space  (linearNDFast)
13:34 DEBUG   opendrift.readers.reader_schism_native: Interpolating after (2008-01-01 01:30:00) in space  (linearNDFast)
13:34 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 01:00:00, weight 0.50) and
                      after (2008-01-01 01:30:00, weight 0.50) in time
13:34 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8519146825983345 and -0.5759763404788042 degrees.
13:34 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:34 DEBUG   opendrift.models.basemodel: ---------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
13:34 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
13:34 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
13:34 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
13:34 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.211725 (min) 0.071528 (max)
13:34 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.11247 (min) 0.161214 (max)
13:34 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.001029 (min) 0.000646276 (max)
13:34 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.9725 (min) 66.3621 (max)
13:34 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel: ---------------------------------
13:34 DEBUG   opendrift.models.basemodel:            300 active elements
13:34 DEBUG   opendrift.models.basemodel:            -41.08958806250113 <- latitude  -> -40.917578675049306
13:34 DEBUG   opendrift.models.basemodel:            173.87931439648045 <- longitude -> 174.29609496475925
13:34 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
13:34 DEBUG   opendrift.models.basemodel: ---------------------------------
13:34 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
13:34 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
13:34 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
13:34 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
13:34 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:34 DEBUG   opendrift.models.basemodel: No elements to deactivate
13:34 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
13:34 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
13:34 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
13:34 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
13:34 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
13:34 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
13:34 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
13:34 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:34 DEBUG   opendrift.models.basemodel: ======================================================================
13:34 INFO    opendrift.models.basemodel: 2008-01-01 01:30:00 - step 5 of 9 - 300 active elements (0 deactivated)
13:34 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
13:34 DEBUG   opendrift.models.basemodel: ======================================================================
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:34 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
13:34 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
13:34 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
13:34 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:34 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
13:34 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:34 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 01:30:00 (before)
                2008-01-01 02:00:00 (after)
13:34 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 01:30:00) in space  (linearNDFast)
13:34 DEBUG   opendrift.readers.reader_schism_native: No time interpolation needed - right on time.
13:34 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8524118629393195 and -0.5751932745160425 degrees.
13:34 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:34 DEBUG   opendrift.models.basemodel: ---------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
13:34 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
13:34 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
13:34 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
13:34 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.164051 (min) 0.0801302 (max)
13:34 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.0929248 (min) 0.127591 (max)
13:34 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.00110893 (min) 0.00030505 (max)
13:34 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
13:34 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.9532 (min) 71.6028 (max)
13:34 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
13:34 DEBUG   opendrift.models.basemodel: ---------------------------------
13:34 DEBUG   opendrift.models.basemodel:            300 active elements
13:34 DEBUG   opendrift.models.basemodel:            -41.08992754869232 <- latitude  -> -40.91804962256336
13:34 DEBUG   opendrift.models.basemodel:            173.87810549750185 <- longitude -> 174.29684253481656
13:34 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
13:34 DEBUG   opendrift.models.basemodel: ---------------------------------
13:34 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
13:34 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
13:34 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
13:34 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
13:34 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:34 DEBUG   opendrift.models.basemodel: No elements to deactivate
13:34 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
13:34 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
13:34 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
13:34 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
13:34 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
13:34 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
13:34 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
13:34 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:34 DEBUG   opendrift.models.basemodel: ======================================================================
13:34 INFO    opendrift.models.basemodel: 2008-01-01 01:45:00 - step 6 of 9 - 300 active elements (0 deactivated)
13:34 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
13:34 DEBUG   opendrift.models.basemodel: ======================================================================
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:34 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
13:34 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
13:34 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
13:34 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
13:34 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:34 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:34 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:34 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
13:34 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:34 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 01:30:00 (before)
                2008-01-01 02:00:00 (after)
13:34 DEBUG   opendrift.readers.reader_schism_native: reading constant data from unstructured reader sea_floor_depth_below_sea_level
13:35 DEBUG   opendrift.readers.reader_schism_native: reading 3D data from unstructured reader upward_sea_water_velocity
13:41 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader x_sea_water_velocity
13:47 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader y_sea_water_velocity
13:54 DEBUG   opendrift.readers.reader_schism_native: initialize ReaderBlockUnstruct var_block_after
13:54 DEBUG   opendrift.readers.reader_schism_native: saving readers 2D (horizontal) KDtree to ReaderBlockUnstruct
13:54 DEBUG   opendrift.readers.reader_schism_native: Compute time-varying KDtree for 3D nearest-neighbor search (i.e using zcor)
13:54 DEBUG   opendrift.readers.reader_schism_native: Fetched env-block (size 149233x149233x149233) for time after (2008-01-01 02:00:00)
13:54 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 01:30:00) in space  (linearNDFast)
13:54 DEBUG   opendrift.readers.reader_schism_native: Interpolating after (2008-01-01 02:00:00) in space  (linearNDFast)
13:54 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 01:30:00, weight 0.50) and
                      after (2008-01-01 02:00:00, weight 0.50) in time
13:54 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8529280385061384 and -0.57450302971034 degrees.
13:54 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:54 DEBUG   opendrift.models.basemodel: ---------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
13:54 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
13:54 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
13:54 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
13:54 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.143503 (min) 0.0907263 (max)
13:54 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.106097 (min) 0.153984 (max)
13:54 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.00105162 (min) 0.00241269 (max)
13:54 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.9122 (min) 72.3233 (max)
13:54 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel: ---------------------------------
13:54 DEBUG   opendrift.models.basemodel:            300 active elements
13:54 DEBUG   opendrift.models.basemodel:            -41.09044269751982 <- latitude  -> -40.918310328410364
13:54 DEBUG   opendrift.models.basemodel:            173.87703861812966 <- longitude -> 174.29761509475745
13:54 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
13:54 DEBUG   opendrift.models.basemodel: ---------------------------------
13:54 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
13:54 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
13:54 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
13:54 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
13:54 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:54 DEBUG   opendrift.models.basemodel: No elements to deactivate
13:54 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
13:54 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
13:54 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
13:54 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
13:54 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
13:54 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
13:54 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
13:54 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:54 DEBUG   opendrift.models.basemodel: ======================================================================
13:54 INFO    opendrift.models.basemodel: 2008-01-01 02:00:00 - step 7 of 9 - 300 active elements (0 deactivated)
13:54 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
13:54 DEBUG   opendrift.models.basemodel: ======================================================================
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:54 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
13:54 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
13:54 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
13:54 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:54 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
13:54 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:54 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 02:00:00 (before)
                2008-01-01 02:30:00 (after)
13:54 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 02:00:00) in space  (linearNDFast)
13:54 DEBUG   opendrift.readers.reader_schism_native: No time interpolation needed - right on time.
13:54 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.853522802613444 and -0.5738990981743826 degrees.
13:54 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:54 DEBUG   opendrift.models.basemodel: ---------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
13:54 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
13:54 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
13:54 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
13:54 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.119909 (min) 0.101955 (max)
13:54 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.131457 (min) 0.195151 (max)
13:54 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.000943503 (min) 0.00290554 (max)
13:54 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
13:54 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.9098 (min) 72.3628 (max)
13:54 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
13:54 DEBUG   opendrift.models.basemodel: ---------------------------------
13:54 DEBUG   opendrift.models.basemodel:            300 active elements
13:54 DEBUG   opendrift.models.basemodel:            -41.091103212118504 <- latitude  -> -40.918543393973145
13:54 DEBUG   opendrift.models.basemodel:            173.87610457913843 <- longitude -> 174.29850223098953
13:54 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
13:54 DEBUG   opendrift.models.basemodel: ---------------------------------
13:54 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
13:54 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
13:54 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
13:54 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
13:54 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:54 DEBUG   opendrift.models.basemodel: No elements to deactivate
13:54 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
13:54 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
13:54 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
13:54 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
13:54 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
13:54 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
13:54 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
13:54 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
13:54 DEBUG   opendrift.models.basemodel: ======================================================================
13:54 INFO    opendrift.models.basemodel: 2008-01-01 02:15:00 - step 8 of 9 - 300 active elements (0 deactivated)
13:54 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
13:54 DEBUG   opendrift.models.basemodel: ======================================================================
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:54 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
13:54 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
13:54 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
13:54 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
13:54 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:54 DEBUG   opendrift.models.basemodel: ----------------------------------------
13:54 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
13:54 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
13:54 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
13:54 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 02:00:00 (before)
                2008-01-01 02:30:00 (after)
13:54 DEBUG   opendrift.readers.reader_schism_native: reading constant data from unstructured reader sea_floor_depth_below_sea_level
13:55 DEBUG   opendrift.readers.reader_schism_native: reading 3D data from unstructured reader upward_sea_water_velocity
14:01 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader x_sea_water_velocity
14:07 DEBUG   opendrift.readers.reader_schism_native: reading 3D velocity data from unstructured reader y_sea_water_velocity
14:14 DEBUG   opendrift.readers.reader_schism_native: initialize ReaderBlockUnstruct var_block_after
14:14 DEBUG   opendrift.readers.reader_schism_native: saving readers 2D (horizontal) KDtree to ReaderBlockUnstruct
14:14 DEBUG   opendrift.readers.reader_schism_native: Compute time-varying KDtree for 3D nearest-neighbor search (i.e using zcor)
14:15 DEBUG   opendrift.readers.reader_schism_native: Fetched env-block (size 149233x149233x149233) for time after (2008-01-01 02:30:00)
14:15 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 02:00:00) in space  (linearNDFast)
14:15 DEBUG   opendrift.readers.reader_schism_native: Interpolating after (2008-01-01 02:30:00) in space  (linearNDFast)
14:15 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 02:00:00, weight 0.50) and
                      after (2008-01-01 02:30:00, weight 0.50) in time
14:15 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8541717714466792 and -0.5734120040600208 degrees.
14:15 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
14:15 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
14:15 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
14:15 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
14:15 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.117142 (min) 0.119011 (max)
14:15 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.149542 (min) 0.1757 (max)
14:15 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.00042492 (min) 0.00331649 (max)
14:15 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.8292 (min) 72.2146 (max)
14:15 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------
14:15 DEBUG   opendrift.models.basemodel:            300 active elements
14:15 DEBUG   opendrift.models.basemodel:            -41.09208791422689 <- latitude  -> -40.91874902574774
14:15 DEBUG   opendrift.models.basemodel:            173.87535344147895 <- longitude -> 174.29946849110334
14:15 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------
14:15 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
14:15 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
14:15 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
14:15 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
14:15 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
14:15 DEBUG   opendrift.models.basemodel: No elements to deactivate
14:15 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
14:15 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
14:15 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
14:15 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
14:15 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
14:15 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
14:15 DEBUG   opendrift.models.basemodel: to be seeded: 0, already seeded 300
14:15 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
14:15 DEBUG   opendrift.models.basemodel: ======================================================================
14:15 INFO    opendrift.models.basemodel: 2008-01-01 02:30:00 - step 9 of 9 - 300 active elements (0 deactivated)
14:15 DEBUG   opendrift.models.basemodel: 0 elements scheduled.
14:15 DEBUG   opendrift.models.basemodel: ======================================================================
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
14:15 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
14:15 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
14:15 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
14:15 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Variable group ['sea_floor_depth_below_sea_level', 'upward_sea_water_velocity', 'x_sea_water_velocity', 'y_sea_water_velocity']
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Calling reader https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
14:15 WARNING opendrift.readers.basereader.unstructured: z-coordinates are not bounds-checked
14:15 DEBUG   opendrift.readers.basereader.variables: Fetching variables from https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
14:15 DEBUG   opendrift.readers.reader_schism_native: Reader time:
                2008-01-01 02:30:00 (before)
                2008-01-01 03:00:00 (after)
14:15 DEBUG   opendrift.readers.reader_schism_native: Interpolating before (2008-01-01 02:30:00) in space  (linearNDFast)
14:15 DEBUG   opendrift.readers.reader_schism_native: No time interpolation needed - right on time.
14:15 DEBUG   opendrift.readers.basereader.variables: Checking sea_floor_depth_below_sea_level for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Checking x_sea_water_velocity for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Checking y_sea_water_velocity for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Rotating vectors between -0.8550049634790596 and -0.5730335678231382 degrees.
14:15 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
14:15 DEBUG   opendrift.models.basemodel: Creating empty dictionary for profiles not profided by any reader: ['ocean_vertical_diffusivity']
14:15 DEBUG   opendrift.models.basemodel:       Using fallback value 0 for ocean_vertical_diffusivity for all profiles
14:15 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
14:15 DEBUG   opendrift.models.basemodel:     x_sea_water_velocity: -0.125804 (min) 0.137176 (max)
14:15 DEBUG   opendrift.models.basemodel:     y_sea_water_velocity: -0.169118 (min) 0.177556 (max)
14:15 DEBUG   opendrift.models.basemodel:     x_wind: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     y_wind: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     upward_sea_water_velocity: -0.00151108 (min) 0.0028862 (max)
14:15 DEBUG   opendrift.models.basemodel:     ocean_vertical_diffusivity: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_significant_height: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_x_velocity: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_stokes_drift_y_velocity: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_period_at_variance_spectral_density_maximum: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     surface_downward_x_stress: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     surface_downward_y_stress: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     turbulent_kinetic_energy: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     turbulent_generic_length_scale: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel:     ocean_mixed_layer_thickness: 50 (min) 50 (max)
14:15 DEBUG   opendrift.models.basemodel:     sea_floor_depth_below_sea_level: 14.8849 (min) 72.8428 (max)
14:15 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------
14:15 DEBUG   opendrift.models.basemodel:            300 active elements
14:15 DEBUG   opendrift.models.basemodel:            -41.09329728755135 <- latitude  -> -40.91826793641322
14:15 DEBUG   opendrift.models.basemodel:            173.87476933432094 <- longitude -> 174.30071037578372
14:15 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------
14:15 DEBUG   opendrift.models.physics_methods: Calculating Hs from wind, min: 0.000000, mean: 0.000000, max: 0.000000
14:15 DEBUG   opendrift.models.physics_methods: Calculating wave period Tm02 from wind
14:15 DEBUG   opendrift.models.physics_methods:    min: 1.256637, mean: 1.256637, max: 1.256637
14:15 DEBUG   opendrift.models.physics_methods: Calculating wave period from wind, min: 1.256637, mean: 1.256637, max: 1.256637
14:15 DEBUG   opendrift.models.basemodel: No elements hit seafloor.
14:15 DEBUG   opendrift.models.basemodel: No elements to deactivate
14:15 DEBUG   opendrift.models.basemodel: Calling OceanDrift.update()
14:15 DEBUG   opendrift.models.physics_methods: No wind for wind-sheared ocean drift
14:15 DEBUG   opendrift.models.physics_methods: No Stokes drift velocity available
14:15 DEBUG   opendrift.models.oceandrift: Vertical advection deactivated
14:15 DEBUG   opendrift.models.basemodel: Horizontal diffusivity is 0, no random walk.
14:15 DEBUG   opendrift.models.basemodel: 300 active elements (0 deactivated)
14:15 DEBUG   opendrift.models.basemodel: Cleaning up
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Variable group ['land_binary_mask']
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Calling reader global_landmask
14:15 DEBUG   opendrift.models.basemodel: ----------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Data needed for 300 elements
14:15 DEBUG   opendrift.readers.basereader.variables: Fetching variables from global_landmask
14:15 DEBUG   opendrift.readers.basereader.continuous: Fetched env-before
14:15 DEBUG   opendrift.readers.basereader.variables: Checking land_binary_mask for invalid values
14:15 DEBUG   opendrift.readers.basereader.variables: Reader projection is latlon - rotation of vectors is not needed.
14:15 DEBUG   opendrift.models.basemodel: Obtained data for all elements.
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------------
14:15 DEBUG   opendrift.models.basemodel: Finished processing all variable groups
14:15 DEBUG   opendrift.models.basemodel: ------------ SUMMARY -------------
14:15 DEBUG   opendrift.models.basemodel:     land_binary_mask: 0 (min) 0 (max)
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------
14:15 DEBUG   opendrift.models.basemodel:            300 active elements
14:15 DEBUG   opendrift.models.basemodel:            -41.09466096649841 <- latitude  -> -40.91682897288021
14:15 DEBUG   opendrift.models.basemodel:            173.87433607562917 <- longitude -> 174.30217983199773
14:15 DEBUG   opendrift.models.basemodel:            -10.0   <- z ->   0.0
14:15 DEBUG   opendrift.models.basemodel: ---------------------------------
===========================
--------------------
Reader performance:
--------------------
global_landmask
00:00.0  total
00:00.0  preparing
00:00.0  reading
00:00.0  masking
--------------------
https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
01:42.9  total
00:25.2  preparing
01:42.8  reading
00:00.1  interpolation
00:00.0  interpolation_time
00:00.0  masking
00:00.0  rotating vectors
--------------------
Performance:
47.6 total time
4 configuration
0 preparing main loop
0 moving elements to ocean
43.0 readers
        0.0 global_landmask
        0.0 postprocessing
43.0 main loop
42.9 https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc
0 updating elements
0 cleaning up
--------------------
===========================
Model:  OceanDrift     (OpenDrift version 1.7.1)
        300 active Lagrangian3DArray particles  (0 deactivated, 0 scheduled)
-------------------
Environment variables:
  -----
  land_binary_mask
     1) global_landmask
  -----
  sea_floor_depth_below_sea_level
  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_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
  surface_downward_x_stress
  surface_downward_y_stress
  turbulent_generic_length_scale
  turbulent_kinetic_energy
  x_wind
  y_wind

Time:
        Start: 2008-01-01 00:30:00
        Present: 2008-01-01 02:45:00
        Calculation steps: 9 * 0:15:00 - total time: 2:15:00
        Output steps: 10 * 0:15:00
===========================

14:15 WARNING opendrift.models.basemodel: Plotting fast. This will make your plots less accurate.
14:15 DEBUG   opendrift_landmask_data.mask: mask already memmapped
14:17 DEBUG   opendrift.readers.reader_global_landmask: Using existing GSHHS shapes..
14:17 DEBUG   opendrift_landmask_data.mask: mask already memmapped
14:20 INFO    opendrift.models.basemodel: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_0.gif...
14:20 INFO    opendrift.models.basemodel: Making animated gif...
MovieWriter imagemagick unavailable; using Pillow instead.
14:21 DEBUG   opendrift.models.basemodel: Time to make animation: 0:00:04.930873
14:21 INFO    opendrift.models.basemodel: Saving animation to /root/project/docs/source/gallery/animations/example_schism_native_1.gif...
14:21 INFO    opendrift.models.basemodel: Making animated gif...
MovieWriter imagemagick unavailable; using Pillow instead.

Total running time of the script: ( 1 minutes 55.475 seconds)

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