Broadening the unit tests

.gitignore

@@ -2,7 +2,6 @@ input_data/
 **.code-workspace*
 **.DS_store**
 **.pyc**
-**.nc
 **.zarr
 docs/_build/*
 docs/_downloads

docs/examples/example_Croatian_fisheries_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

docs/examples/example_Greece_coast_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

docs/examples/example_Italy_coast_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

docs/examples/example_add_your_own_kernel_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

tests/test_constructors.py

@@ -0,0 +1,156 @@
+import parcels.application_kernels
+import plasticparcels as pp
+import parcels
+from datetime import datetime, timedelta
+import pytest
+
+
+def make_simple_fieldset():
+    fieldset = parcels.FieldSet.from_data({'U': 0, 'V': 0},
+                                          {'lon': 0, 'lat': 0},
+                                          mesh='spherical')
+    return fieldset
+
+
+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():
+    plastictype_settings = {'wind_coefficient': 0.01,    # Percentage of wind to apply to particles
+                            'plastic_diameter': 0.01,    # Plastic particle diameter (m)
+                            'plastic_density': 1030.,    # Plastic particle density (kg/m^3)
+                            }
+    return plastictype_settings
+
+
+# Test the create_hydrodynamic_fieldset() function
+def test_create_hydrodynamic_fieldset():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings['simulation'] = make_standard_simulation_settings()
+
+    fieldset = pp.constructors.create_hydrodynamic_fieldset(settings)
+
+    assert isinstance(fieldset, parcels.FieldSet)
+
+
+# Test the create_fieldset() function
+@pytest.mark.parametrize('use_3D', [True, False])
+@pytest.mark.parametrize('use_biofouling', [True, False])
+@pytest.mark.parametrize('use_stokes', [True, False])
+@pytest.mark.parametrize('use_wind', [True, False])
+@pytest.mark.parametrize('use_mixing', [True, False])
+def test_create_fieldset(use_3D, use_biofouling, use_stokes, use_wind, use_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['use_3D'] = use_3D
+    settings['use_biofouling'] = use_biofouling
+    settings['use_stokes'] = use_stokes
+    settings['use_wind'] = use_wind
+    settings['use_mixing'] = use_mixing
+
+    fieldset = pp.constructors.create_fieldset(settings)
+
+    assert isinstance(fieldset, parcels.FieldSet)
+
+
+# Test three different initialisation maps
+@pytest.mark.parametrize('initialisation_map', ['coastal', 'fisheries', 'rivers'])
+def test_create_particleset_from_map(initialisation_map):
+    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['release'] = {'initialisation_type': initialisation_map,
+                           'country': 'Italy',
+                           }
+
+    fieldset = make_simple_fieldset()
+    pset = pp.constructors.create_particleset_from_map(fieldset, settings)
+
+    assert isinstance(pset, parcels.ParticleSet)
+
+
+# Test the two global concentration release map types
+@pytest.mark.parametrize('concentration_type', ['Beach', 'Ocean'])
+def test_create_particleset_from_map_concentrations(concentration_type):
+    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['release'] = {'initialisation_type': 'global_concentrations',
+                           'concentration_type': concentration_type,
+                           }
+
+    fieldset = make_simple_fieldset()
+    pset = pp.constructors.create_particleset_from_map(fieldset, settings)
+
+    assert isinstance(pset, parcels.ParticleSet)
+
+
+# Test three different initialisation maps
+@pytest.mark.parametrize('use_3D', [True, False])
+@pytest.mark.parametrize('use_biofouling', [True, False])
+@pytest.mark.parametrize('use_stokes', [True, False])
+@pytest.mark.parametrize('use_wind', [True, False])
+@pytest.mark.parametrize('use_mixing', [True, False])
+def test_create_kernel(use_3D, use_biofouling, use_stokes, use_wind, use_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['use_3D'] = use_3D
+    settings['use_biofouling'] = use_biofouling
+    settings['use_stokes'] = use_stokes
+    settings['use_wind'] = use_wind
+    settings['use_mixing'] = use_mixing
+
+    fieldset = pp.constructors.create_fieldset(settings)
+    kernels = pp.constructors.create_kernel(fieldset)
+
+    if use_3D:
+        assert parcels.application_kernels.AdvectionRK4_3D in kernels
+        assert pp.kernels.checkThroughBathymetry in kernels
+        assert pp.kernels.checkErrorThroughSurface in kernels
+    else:
+        assert parcels.application_kernels.AdvectionRK4 in kernels
+
+    if use_3D and use_biofouling:
+        assert pp.kernels.Biofouling in kernels
+    elif use_3D and not use_biofouling:
+        assert pp.kernels.SettlingVelocity in kernels
+
+    if use_mixing:
+        assert pp.kernels.VerticalMixing in kernels
+
+    if use_stokes:
+        assert pp.kernels.StokesDrift in kernels
+        assert pp.kernels.unbeaching in kernels
+
+    if use_wind:
+        assert pp.kernels.WindageDrift in kernels
+        assert pp.kernels.unbeaching in kernels
+
+    assert pp.kernels.deleteParticle in kernels
+    assert pp.kernels.periodicBC in kernels
+    assert pp.kernels.PolyTEOS10_bsq in kernels

tests/test_data/test_settings.json

@@ -0,0 +1,167 @@
+{
+    "use_3D": true,
+    "allow_time_extrapolation": true,
+    "verbose_delete": false,
+    "use_mixing": true,
+    "use_biofouling": true,
+    "use_stokes": true,
+    "use_wind": true,
+    "ocean": {
+        "modelname": "NEMO0083",
+        "directory": "tests/test_data/",
+        "filename_style": "test_",
+        "ocean_mesh": "test_ocean_mesh_hgr.nc",
+        "bathymetry_mesh": "test_bathymetry_mesh_zgr.nc",
+        "variables": {
+            "U": "vozocrtx",
+            "V": "vomecrty",
+            "W": "vovecrtz",
+            "conservative_temperature": "votemper",
+            "absolute_salinity": "vosaline"
+        },
+        "dimensions": {
+            "U": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "V": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "W": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "conservative_temperature": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "absolute_salinity": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            }
+        },
+        "indices": {},
+        "bathymetry_variables": {
+            "bathymetry": "mbathy"
+        },
+        "bathymetry_dimensions": {
+            "lon": "nav_lon",
+            "lat": "nav_lat"
+        },
+        "vertical_mixing_variables": {
+            "mixing_kz": "votkeavt"
+        },
+        "vertical_mixing_dimensions": {
+            "lon": "glamf",
+            "lat": "gphif",
+            "depth": "depthw",
+            "time": "time_counter"
+        }
+    },
+    "bgc": {
+        "directory": "tests/test_data/",
+        "filename_style": "test_",
+        "bgc_mesh": "test_bgc_mesh_hgr.nc",
+        "variables": {
+            "pp_phyto": "nppv",
+            "bio_nanophy": "phy",
+            "bio_diatom": "phy2"
+        },
+        "dimensions": {
+            "pp_phyto": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "bio_nanophy": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "bio_diatom": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            }
+        },
+        "indices": {},
+        "constants": {
+            "biofilm_density": 1388.0,
+            "algae_cell_volume": 2e-16,
+            "K": 1.3805834190672156e-23,
+            "R20": 1.1574074074074074e-06,
+            "Q10": 2.13,
+            "Gamma": 2.0,
+            "carbon_molecular_weight": 12.0,
+            "collision_probability": 1.0,
+            "algae_mortality_rate": 1.0,
+            "algae_respiration_f": 1.0
+        }
+    },
+    "stokes": {
+        "directory": "tests/test_data/",
+        "filename_style": "test_waves_",
+        "variables": {
+            "Stokes_U": "ust",
+            "Stokes_V": "vst",
+            "wave_Tp": "pp1d"
+        },
+        "dimensions": {
+            "lat": "latitude",
+            "lon": "longitude",
+            "time": "time"
+        },
+        "indices": {}
+    },
+    "wind": {
+        "directory": "tests/test_data/",
+        "filename_style": "test_wind_",
+        "variables": {
+            "Wind_U": "u10",
+            "Wind_V": "v10"
+        },
+        "dimensions": {
+            "lat": "latitude",
+            "lon": "longitude",
+            "time": "time"
+        },
+        "indices": {}
+    },
+    "unbeaching": {
+        "filename": "input_data/NEMO0083/land_current_NEMO0083.nc",
+        "variables": {
+            "unbeach_U": "land_current_u",
+            "unbeach_V": "land_current_v"
+        },
+        "dimensions": {
+            "lat": "lat",
+            "lon": "lon"
+        }
+    },
+    "simulation": {
+        "start_date": null,
+        "runtime": null,
+        "dt_write": null,
+        "dt_timestep": null
+    },
+    "release_maps": {
+        "coastal": "input_data/NEMO0083/coastal_population_MPW_NEMO0083.csv",
+        "rivers": "input_data/NEMO0083/river_emissions_NEMO0083.csv",
+        "fisheries": "input_data/NEMO0083/agg_data_fisheries_info_NEMO0083.csv",
+        "global_concentrations": "input_data/NEMO0083/global_concentrations_NEMO0083.csv"
+    }
+}