No advection when using LarvalFish and FVCOM inputs

[tiagoams]

Hi,

I am trying to run a toy problem using FVCOM output on the THREDDS server and the LarvalFish model.
I get the following error:

  ERROR   opendrift.models.basemodel.environment:663: missing variables requested
  Traceback (most recent call last):
    File "C:\Users\TAMS00\temp\git\opendrift\opendrift\models\basemodel\environment.py", line 637, in get_environment
      reader.get_variables_interpolated(
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
          variable_group, profiles = profiles_from_reader,
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          profiles_depth = profiles_depth, time = time,
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          lon=lon[missing_indices], lat=lat[missing_indices],
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          z=z[missing_indices], rotate_to_proj=self.proj_latlon)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\variables.py", line 913, in get_variables_interpolated
      env, env_profiles = self.get_variables_interpolated_xy(

It seems that some of the variables required by the model LarvalFish are not present and as a result the reader is reset and zeros read. I tried to circumvent this by adding a constant reader and setting all extra variable required by LarvalFish to 0, but with no success. The output shows advection in the 1st time step and then the reader is still reading 0s.

Thanks!

    from datetime import timedelta
    import urllib.request as urllib_request
    import numpy as np
    from opendrift.readers import reader_netCDF_CF_unstructured
    from opendrift.readers import reader_global_landmask
    from opendrift.models.larvalfish import LarvalFish
    
    # Input
    fvcompath = 'AkvaplanNiva_sample_lonlat_fixed.nc'
    #fvcompath = 'https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/AkvaplanNiva_sample_lonlat_fixed.nc'
    
    
    proj = "+proj=utm +zone=33 +north +ellps=WGS84 +datum=WGS84 +units=m +no_defs"
    fvcom = reader_netCDF_CF_unstructured.Reader(filename = fvcompath, proj4 = proj)
    
    # add constant reader to keep reader from being discarded when
    #  some of the required variables are not found 
    from opendrift.readers.reader_constant import Reader as ConstantReader
    
    o = LarvalFish(loglevel=20)
    
    o.add_reader(fvcom)
    
    # Supply the missing pieces that LarvalFish asks for
    const = ConstantReader({
        'x_wind': 0,
        'y_wind': 0,
        'sea_surface_wave_significant_height': 0,
        'sea_surface_wave_stokes_drift_x_velocity': 0,
        'sea_surface_wave_stokes_drift_y_velocity': 0,
        'ocean_vertical_diffusivity': 0.01,      # or a more realistic profile if you have it
        'ocean_mixed_layer_thickness': 50,
        'land_binary_mask': {'fallback': None},
        'sea_floor_depth_below_sea_level': {'fallback': 100},
        'sea_water_temperature': {'fallback': 10, 'profiles': True},
        'sea_water_salinity': {'fallback': 34, 'profiles': True},
        'sea_surface_wave_stokes_drift_x_velocity': {'fallback': 0},
        'sea_surface_wave_stokes_drift_y_velocity': {'fallback': 0},
    })
    o.add_reader(const)
    
    o.set_config('drift:vertical_mixing', True)
 
    # Seed elements at defined positions, depth and time
    N = 10
    z = np.linspace(-20, -2, N)
    o.seed_elements(lon=18.0, lat=69.8, radius=0, number=N,
                    z=z, time=fvcom.start_time)
    
    #%%
    # Running model
    o.run(time_step=300, duration=timedelta(hours=24))
    
    #%%
    # Print and plot results
    print(o)
    o.plot_property('lon')
    o.plot_property('z')

[knutfrode]

Hi,

There is no need to add a Constant reader like this, as these variables have fallback (default values) already specified in the LarvalFish model.
What is the error message you get if you remove this Constant reader?
A Reader will be discarded (not reset) if not covering any relevant variables or the elements in space and time.

[tiagoams]

Thanks Knut,

Sorry, I did jump ahead to my second solution. By commenting out the o.add_reader(const) this is what I am getting. I also forgot to state the version: '1.14.9':

    08:22:24 INFO    opendrift:568: OpenDriftSimulation initialised (version 1.14.9 / v1.14.9-43-g22dbf7d)
    08:22:24 INFO    opendrift.models.basemodel.environment:203: Adding a global landmask from GSHHG
    08:22:26 INFO    opendrift.models.basemodel.environment:227: Fallback values will be used for the following variables which have no readers: 
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	sea_surface_height: 0.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	sea_surface_wave_significant_height: 0.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	x_wind: 0.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	y_wind: 0.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	sea_floor_depth_below_sea_level: 100.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	ocean_vertical_diffusivity: 0.010000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	ocean_mixed_layer_thickness: 50.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	sea_surface_wave_stokes_drift_x_velocity: 0.000000
    08:22:26 INFO    opendrift.models.basemodel.environment:230: 	sea_surface_wave_stokes_drift_y_velocity: 0.000000
    08:22:26 INFO    opendrift:1905: Storing previous values of element property lon because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous']))
    08:22:26 INFO    opendrift:1905: Storing previous values of element property lat because of condition (('general:coastline_action', 'in', ['stranding', 'previous']), 'or', ('general:seafloor_action', 'in', ['previous']))
    08:22:26 INFO    opendrift:947: Using existing reader for land_binary_mask to move elements to ocean
    08:22:26 INFO    opendrift:978: All points are in ocean
    08:22:26 INFO    opendrift:2202: 2018-04-30 01:01:52 - step 1 of 288 - 10 active elements (0 deactivated)
    08:22:26 INFO    opendrift.models.basemodel.environment:662: ========================
    08:22:26 ERROR   opendrift.models.basemodel.environment:663: missing variables requested
    Traceback (most recent call last):
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\models\basemodel\environment.py", line 637, in get_environment
        reader.get_variables_interpolated(
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variable_group, profiles = profiles_from_reader,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...
    08:22:30 INFO    opendrift:2202: 2018-05-01 00:46:52 - step 286 of 288 - 10 active elements (0 deactivated)
    08:22:30 INFO    opendrift:2202: 2018-05-01 00:51:52 - step 287 of 288 - 10 active elements (0 deactivated)
    08:22:30 INFO    opendrift:2202: 2018-05-01 00:56:52 - step 288 of 288 - 10 active elements (0 deactivated)
    08:22:30 WARNING opendrift:2565: Plotting fast. This will make your plots less accurate.
    Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?e3355850-8dd0-4519-afd8-b1fdfa00625d) or open in a [text editor](command:workbench.action.openLargeOutput?e3355850-8dd0-4519-afd8-b1fdfa00625d). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...
    ===========================
    --------------------
    Reader performance:
    --------------------
    global_landmask
     0:00:00.0  total
     0:00:00.0  preparing
     0:00:00.0  reading
     0:00:00.0  masking
    --------------------
    Performance:
        6.2 total time
        2.5 configuration
        0.0 preparing main loop
          0.0 moving elements to ocean
        3.6 main loop
          0.3 updating elements
            0.2 vertical mixing
        0.0 cleaning up
    --------------------
    ===========================
    Model:	LarvalFish     (OpenDrift version 1.14.9)
        10 active LarvalFishElement particles  (0 deactivated, 0 scheduled)
    -------------------
    Environment variables:
    ...
        Calculation steps: 288 * 0:05:00 - total time: 1 day, 0:00:00
        Output steps: 289 * 0:05:00
    ===========================

[tiagoams]

Adding DEBUG output with (loglevel=10) for the error section:

    [32m08:51:03�[0m �[1;35mERROR  �[0m �[34mopendrift.models.basemodel.environment:663:�[0m �[31mmissing variables requested�[0m
    Traceback (most recent call last):
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\models\basemodel\environment.py", line 637, in get_environment
        reader.get_variables_interpolated(
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variable_group, profiles = profiles_from_reader,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            profiles_depth = profiles_depth, time = time,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            lon=lon[missing_indices], lat=lat[missing_indices],
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            z=z[missing_indices], rotate_to_proj=self.proj_latlon)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\variables.py", line 913, in get_variables_interpolated
        env, env_profiles = self.get_variables_interpolated_xy(
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variables, profiles, profiles_depth, time, x, y, z, rotate_to_proj)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\variables.py", line 779, in get_variables_interpolated_xy
        env, env_profiles = self._get_variables_interpolated_(
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variables, profiles, profiles_depth, time, x, y, z)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\unstructured.py", line 61, in _get_variables_interpolated_
        env = self.get_variables(variables, time, reader_x, reader_y, z)
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\reader_netCDF_CF_unstructured.py", line 273, in get_variables
        assert (len(node_variables) + len(face_variables)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                ) == len(requested_variables), "missing variables requested"
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    AssertionError: missing variables requested
    �[32m08:51:03�[0m �[1;35mDEBUG  �[0m �[34mopendrift.models.basemodel.environment:664:�[0m �[32mTraceback (most recent call last):
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\models\basemodel\environment.py", line 637, in get_environment
        reader.get_variables_interpolated(
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variable_group, profiles = profiles_from_reader,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            profiles_depth = profiles_depth, time = time,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            lon=lon[missing_indices], lat=lat[missing_indices],
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            z=z[missing_indices], rotate_to_proj=self.proj_latlon)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\variables.py", line 913, in get_variables_interpolated
        env, env_profiles = self.get_variables_interpolated_xy(
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variables, profiles, profiles_depth, time, x, y, z, rotate_to_proj)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\variables.py", line 779, in get_variables_interpolated_xy
        env, env_profiles = self._get_variables_interpolated_(
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            variables, profiles, profiles_depth, time, x, y, z)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\basereader\unstructured.py", line 61, in _get_variables_interpolated_
        env = self.get_variables(variables, time, reader_x, reader_y, z)
      File "C:\Users\TAMS00\temp\git\opendrift\opendrift\readers\reader_netCDF_CF_unstructured.py", line 273, in get_variables
        assert (len(node_variables) + len(face_variables)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                ) == len(requested_variables), "missing variables requested"
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    AssertionError: missing variables requested
    �[0m
    �[32m08:51:03�[0m �[1;35mINFO   �[0m �[34mopendrift.models.basemodel.environment:665:�[0m ========================