Unit tests for all of the different kernels.

tests/test_kernels.py

@@ -0,0 +1,227 @@
+import parcels.application_kernels
+import plasticparcels as pp
+import parcels
+import numpy as np
+from datetime import datetime, timedelta
+import pytest
+
+
+def make_standard_simulation_settings():
+    simulation_settings = {'startdate': datetime.strptime('2020-01-04-00:00:00', '%Y-%m-%d-%H:%M:%S'),
+                                'runtime': timedelta(days=2),
+                                'outputdt': timedelta(hours=1),
+                                'dt': timedelta(minutes=20),
+                                }
+    return simulation_settings
+
+def make_standard_plastictype_settings():
+    #Use tiny wind percentage because test data set is not large and wind speeds are quick!
+    plastictype_settings = {'wind_coefficient' : 0.0001,  # Percentage of wind to apply to particles
+                                'plastic_diameter' : 0.001, # Plastic particle diameter (m)
+                                'plastic_density' : 1030.,  # Plastic particle density (kg/m^3)
+                                }
+    return plastictype_settings
+
+def make_standard_particleset(fieldset, settings):
+    # Generate a particleset that has particles in the test domain
+    settings['release'] = {'initialisation_type': 'fisheries', 'country': 'Malta'}
+    pset = pp.constructors.create_particleset_from_map(fieldset, settings)
+
+    # Only keep particles in the test domain
+    keep_particles = (pset.lon >17) & (pset.lon <20) & (pset.lat < 36) & (pset.lat > 34) 
+    pset.remove_booleanvector(~keep_particles)
+
+    return pset
+
+@pytest.mark.parametrize('use_3D', [True, False])
+def test_advection_only(use_3D):
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
+
+    settings['simulation'] = make_standard_simulation_settings()
+    settings['plastictype'] = make_standard_plastictype_settings()
+
+    # Turn on/off 3D advection
+    settings['use_3D'] = use_3D
+
+    # Turn off all other processes
+    settings['use_biofouling'] = False
+    settings['use_stokes'] = False
+    settings['use_wind'] = False
+    settings['use_mixing'] = False
+
+    fieldset = pp.constructors.create_fieldset(settings)
+    if use_3D:
+        kernels = [parcels.application_kernels.AdvectionRK4_3D, pp.kernels.checkThroughBathymetry, pp.kernels.checkErrorThroughSurface, pp.kernels.deleteParticle]
+    else:
+        kernels = [parcels.application_kernels.AdvectionRK4, pp.kernels.deleteParticle]
+
+    pset = make_standard_particleset(fieldset, settings)
+
+    start_lons = pset.lon.copy()
+    start_lats = pset.lat.copy()
+
+    pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+
+    # Assert that the particles move from their initial location
+    assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.)
+
+def test_settling_velocity():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
+
+    settings['simulation'] = make_standard_simulation_settings()
+    settings['plastictype'] = make_standard_plastictype_settings()
+
+    # Turn on 3D advection
+    settings['use_3D'] = True
+
+    # Turn off all other processes
+    settings['use_biofouling'] = False
+    settings['use_stokes'] = False
+    settings['use_wind'] = False
+    settings['use_mixing'] = False
+
+    fieldset = pp.constructors.create_fieldset(settings)
+
+    kernels = pp.constructors.create_kernel(fieldset)
+
+    pset = make_standard_particleset(fieldset, settings)
+
+    start_lons = pset.lon.copy()
+    start_lats = pset.lat.copy()
+    start_depths = pset.depth.copy()
+
+    pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+
+    # Assert that the particles move from their initial location
+    assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.) & (np.sum(np.abs(pset.depth - start_depths)) > 0.)
+
+def test_biofouling():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
+
+    settings['simulation'] = make_standard_simulation_settings()
+    settings['plastictype'] = make_standard_plastictype_settings()
+
+    # Turn on biofouling
+    settings['use_biofouling'] = True
+
+    # Turn off all other processes
+    settings['use_3D'] = False
+    settings['use_stokes'] = False
+    settings['use_wind'] = False
+    settings['use_mixing'] = False
+
+    fieldset = pp.constructors.create_fieldset(settings)
+
+    kernels = [pp.kernels.PolyTEOS10_bsq, pp.kernels.Biofouling,
+               pp.kernels.checkThroughBathymetry, pp.kernels.checkErrorThroughSurface,
+               pp.kernels.deleteParticle]
+
+    pset = make_standard_particleset(fieldset, settings)
+
+    start_depths = pset.depth.copy()
+
+    pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+
+    # Assert that the particles move from their initial location
+    assert (np.sum(np.abs(pset.depth - start_depths)) > 0.)
+
+def test_Stokes():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
+
+    settings['simulation'] = make_standard_simulation_settings()
+    settings['plastictype'] = make_standard_plastictype_settings()
+
+    # Turn on Stokes Drift
+    settings['use_stokes'] = True
+
+    # Turn off all other processes
+    settings['use_3D'] = False
+    settings['use_biofouling'] = False
+    settings['use_wind'] = False
+    settings['use_mixing'] = False
+
+    fieldset = pp.constructors.create_fieldset(settings)
+
+    kernels = [pp.kernels.StokesDrift, pp.kernels.deleteParticle]
+
+    pset = make_standard_particleset(fieldset, settings)
+
+    start_lons = pset.lon.copy()
+    start_lats = pset.lat.copy()
+    print(pset[0].dt)
+    pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+
+    # Assert that the particles move from their initial location
+    assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.)
+
+def test_wind():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
+
+    settings['simulation'] = make_standard_simulation_settings()
+    settings['plastictype'] = make_standard_plastictype_settings()
+
+    # Turn on Stokes Drift
+    settings['use_wind'] = True
+
+    # Turn off all other processes
+    settings['use_3D'] = False
+    settings['use_biofouling'] = False
+    settings['use_stokes'] = False
+    settings['use_mixing'] = False
+
+    fieldset = pp.constructors.create_fieldset(settings)
+
+    kernels = [pp.kernels.WindageDrift, pp.kernels.unbeaching, pp.kernels.periodicBC, pp.kernels.deleteParticle]
+
+    pset = make_standard_particleset(fieldset, settings)
+
+    start_lons = pset.lon.copy()
+    start_lats = pset.lat.copy()
+
+    pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+
+    # Assert that the particles move from their initial location
+    assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.)
+
+def test_mixing():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
+
+    settings['simulation'] = make_standard_simulation_settings()
+    settings['plastictype'] = make_standard_plastictype_settings()
+
+    settings['use_3D'] = True
+    settings['use_mixing'] = True
+
+    # Turn off all other processes
+    settings['use_wind'] = False
+    settings['use_biofouling'] = False
+    settings['use_stokes'] = False
+
+    fieldset = pp.constructors.create_fieldset(settings)
+    kernels = [parcels.application_kernels.AdvectionRK4_3D, pp.kernels.checkThroughBathymetry,
+               pp.kernels.checkErrorThroughSurface, pp.kernels.deleteParticle]
+
+    kernels_mixing = [parcels.application_kernels.AdvectionRK4_3D, pp.kernels.VerticalMixing,
+               pp.kernels.checkThroughBathymetry, pp.kernels.checkErrorThroughSurface,
+               pp.kernels.deleteParticle]
+
+    pset = make_standard_particleset(fieldset, settings)
+    pset_mixing = make_standard_particleset(fieldset, settings)
+
+    pset.execute(kernels, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+    pset.execute(kernels_mixing, runtime=settings['simulation']['runtime'], dt=settings['simulation']['dt'])
+
+    # Assert that the particles move from their initial location
+    assert (np.sum(np.abs(pset.lon - pset_mixing.lon)) > 0.) & (np.sum(np.abs(pset.lat - pset_mixing.lat)) > 0.)