Merge pull request #1632 from knutfrode/dev

knutfrode · web-flow · commit 96f30bab2a65 · 2025-06-30T19:23:19.000+02:00
[run-ex] Dev
diff --git a/examples/example_codegg.py b/examples/example_codegg.py
@@ -25,7 +25,7 @@
 
 #%%
 # spawn NEA cod eggs at defined position and time
-time = datetime.utcnow()
+time = datetime.now()
 o.seed_elements(14. , 68.1, z=-40, radius=2000, number=500,
                 time=time, diameter=0.0014, neutral_buoyancy_salinity=31.25)
 o.seed_elements(12.5, 68., z=-40, radius=2000, number=500,
diff --git a/examples/example_depth.py b/examples/example_depth.py
@@ -23,7 +23,7 @@
 # Seed 1000 elements at random depths
 z = -np.random.rand(2000)*50
 o.seed_elements(lon=4.8, lat=60.0, z=z, radius=0, number=2000,
-                time=datetime.utcnow())
+                time=datetime.now())
 
 print(o)
 
diff --git a/examples/example_entrainment_rate_oil_types.py b/examples/example_entrainment_rate_oil_types.py
@@ -23,7 +23,7 @@
 o2.set_config('wave_entrainment:droplet_size_distribution', 'Johansen et al. (2015)')
 o2.set_config('processes:evaporation', False)
 o2.set_config('processes:dispersion', False)
-o2.seed_elements(lon=4, lat=60, time=datetime.utcnow(), number=1000,
+o2.seed_elements(lon=4, lat=60, time=datetime.now(), number=1000,
                 radius=100, z=0, oil_type='TIA JUANA HEAVY')
 o2.run(duration=timedelta(hours=12), time_step=900, time_step_output=3600)
 
@@ -39,7 +39,7 @@
 o3.set_config('wave_entrainment:droplet_size_distribution', 'Johansen et al. (2015)')
 o3.set_config('processes:evaporation', False)
 o3.set_config('processes:dispersion', False)
-o3.seed_elements(lon=4, lat=60, time=datetime.utcnow(), number=1000,
+o3.seed_elements(lon=4, lat=60, time=datetime.now(), number=1000,
                  radius=100, z=0, oil_type='TIA JUANA LIGHT') #'EKOFISK BLEND, STATOIL' similar ent.
 o3.run(duration=timedelta(hours=12), time_step=900, time_step_output=3600)
 
diff --git a/examples/example_long_vietnam.py b/examples/example_long_vietnam.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Vietnam
-==================================
+========
 """
 
 from datetime import datetime, timedelta
@@ -19,7 +19,7 @@
 # Seed some particles
 object_type = 26  # 26 = Life-raft, no ballast
 o.seed_elements(lon=107.8, lat=10.0, radius=1000, number=1000,
-                object_type=object_type, time=datetime.utcnow())
+                object_type=object_type, time=datetime.now())
 
 # Run model
 o.run(duration=timedelta(days=3),
diff --git a/examples/example_oil_ice.py b/examples/example_oil_ice.py
@@ -26,7 +26,7 @@
 #%%
 # Imaginary oil spill in Hinlopen strait
 o.seed_elements(lon=19.1909, lat=79.5986, radius=50,
-                number=3000, time=datetime.utcnow() - timedelta(days=7))
+                number=3000, time=datetime.now() - timedelta(days=7))
 
 #%%
 # Running model
diff --git a/examples/example_oil_thickness.py b/examples/example_oil_thickness.py
@@ -42,7 +42,7 @@
 o1.seed_elements(lon=4.5, lat=60, number=number,
                 mass_oil=mass_oil, radius=1000,
                 oil_type=oil_type,
-                time=datetime.utcnow())
+                time=datetime.now())
 o1.run(time_step=timestep, time_step_output=timestep_output,
        duration=duration)
 
@@ -78,7 +78,7 @@
 o2.seed_elements(lon=4.5, lat=60, number=number,
                 mass_oil=mass_oil, radius=1000,
                 oil_type=oil_type,
-                time=datetime.utcnow())
+                time=datetime.now())
 o2.run(time_step=timestep, time_step_output=timestep_output,
        duration=duration)
 
diff --git a/examples/example_sediments.py b/examples/example_sediments.py
@@ -31,7 +31,7 @@
 lat=59.169194
 lon=10.962920
 o.seed_elements(lon=lon, lat=lat, number=10000,
-                time=[datetime.utcnow(), datetime.utcnow()+timedelta(hours=48)],
+                time=[datetime.now(), datetime.now()+timedelta(hours=48)],
                 terminal_velocity=-.001)  # 1 mm/s settling speed
 
 o.run(time_step=600, time_step_output=1800, duration=timedelta(hours=36))
diff --git a/examples/example_sediments_resuspension.py b/examples/example_sediments_resuspension.py
@@ -11,9 +11,9 @@
 #%%
 # Constructing an artificial current field where x- and y-components are oscilating with different amplitude and period
 reader_oscx = reader_oscillating.Reader('x_sea_water_velocity',
-    amplitude=0.6, zero_time=datetime.utcnow())
+    amplitude=0.6, zero_time=datetime.now())
 reader_oscy = reader_oscillating.Reader('y_sea_water_velocity',
-    amplitude=.3, period_seconds=3600*5, zero_time=datetime.utcnow())
+    amplitude=.3, period_seconds=3600*5, zero_time=datetime.now())
 
 o = SedimentDrift(loglevel=50)  # 0 for debug output
 
@@ -39,7 +39,7 @@
 #%%
 # Seeding sediments
 o.seed_elements(lon=4.65, lat=60, number=10000, 
-                time=[datetime.utcnow(), datetime.utcnow()+timedelta(hours=6)],
+                time=[datetime.now(), datetime.now()+timedelta(hours=6)],
                 terminal_velocity=-.01)  # 1 cm/s settling speed
 
 o.run(time_step=1800, time_step_output=1800, duration=timedelta(hours=72))
diff --git a/examples/example_seed_from_shapefile.py b/examples/example_seed_from_shapefile.py
@@ -16,13 +16,13 @@
 # Seed particles within all polygons from shapefile
 o.seed_from_shapefile(test_data_folder +
                       'shapefile_spawning_areas/Torsk.shp',
-                      number=1000, time=datetime.utcnow())
+                      number=1000, time=datetime.now())
 
 
 #%%
 # Alternative by using GeoPandas and selecting a subset of two polygons
 gdf = gpd.read_file(test_data_folder + 'shapefile_spawning_areas/Torsk.shp')
 gdf = gdf.iloc[[1, 5]]
-o.seed_from_geopandas(gdf, number=2000, time=datetime.utcnow())
+o.seed_from_geopandas(gdf, number=2000, time=datetime.now())
 
 o.plot(fast=True)
diff --git a/examples/example_shipdrift.py b/examples/example_shipdrift.py
@@ -19,7 +19,7 @@
 # Seed ship elements at defined position and time
 # Note: beam/length ratio is larger than allowed, but is then clipped internally
 o.seed_elements(lon=5.0, lat=63.0, radius=1000, number=1000,
-                time=datetime.utcnow(),
+                time=datetime.now(),
                 length=80.0, beam=20.0, height=9.0, draft=4.0)
 
 #%%
diff --git a/opendrift/config.py b/opendrift/config.py
@@ -20,7 +20,7 @@ def get_config(self, key, default='raise'):
                 raise ValueError('No config setting named %s' % key)
             else:
                 return default
-        return (self._config[key]['value'])
+        return self._config[key]['value']
 
     def list_config(self, prefix=''):
         """List all possible configuration settings with values"""
diff --git a/opendrift/elements/elements.py b/opendrift/elements/elements.py
@@ -15,6 +15,7 @@
 # Copyright 2015, Knut-Frode Dagestad, MET Norway
 
 import logging; logger = logging.getLogger(__name__)
+import copy
 from collections import OrderedDict
 import numpy as np
 
@@ -99,6 +100,8 @@ def __init__(self, **kwargs):
             An empty object may be created by giving no input.
         """
 
+        self.variables = copy.deepcopy(self.variables)  # Make self.variables dictionary immutable
+
         # Collect default values in separate dict, for easier access
         default_values = {variable: self.variables[variable]['dtype'](
                           self.variables[variable]['default'])
diff --git a/opendrift/export/io_netcdf.py b/opendrift/export/io_netcdf.py
@@ -17,7 +17,7 @@
 
 def datetime_from_datetime64(dt64):
     t = (dt64 - np.datetime64('1970-01-01T00:00:00')) / np.timedelta64(1, 's')
-    return datetime.utcfromtimestamp(float(t))
+    return datetime.fromtimestamp(float(t))
 
 def init(self, filename):
 
diff --git a/opendrift/models/basemodel/__init__.py b/opendrift/models/basemodel/__init__.py
@@ -266,6 +266,8 @@ def __init__(self,
         self.elements = self.ElementType()  # Empty array
         self._elements_previous = None
         self._environment_previous = None
+        self.elements_previous = None
+        self.environment_previous = None
 
         # Set up logging
         logformat = '%(asctime)s %(levelname)-7s %(name)s:%(lineno)d: %(message)s'
@@ -1794,7 +1796,6 @@ def run(self,
 
         if self.num_elements_scheduled() == 0:
             raise ValueError('Please seed elements before starting a run.')
-        self.elements = self.ElementType()
 
         # Export seed_geojson as FeatureCollection string
         self.add_metadata('seed_geojson',
@@ -2041,9 +2042,7 @@ def run(self,
             self.timer_end('preparing main loop:moving elements to ocean')
 
         # TODO: adjust store_previous according to config, later with upcming conditional mechanism
-        if self.get_config('general:coastline_action') in ['previous', 'stranding'] or (
-                'general:coastline_action' in self._config and
-                self.get_config('general:coastline_action') == 'previous'):
+        if self.get_config('general:coastline_action', None) in ['stranding', 'previous']:
             logger.info('Storing previous position of elements for coastline interaction')
             self.elements.variables['lon']['store_previous'] = True
             self.elements.variables['lat']['store_previous'] = True
diff --git a/opendrift/models/eulerdrift/simulation.py b/opendrift/models/eulerdrift/simulation.py
@@ -75,7 +75,7 @@ class Simulation:
     def __init__(self, grid):
         self.grid = grid
         self.readers = []
-        self.t0 = datetime.utcnow()
+        self.t0 = datetime.now()
 
     @classmethod
     def new(cls, lon0 = 10., lat0 = 65., res = 10., shape=(100, 100)):
diff --git a/opendrift/models/openoil/openoil.py b/opendrift/models/openoil/openoil.py
@@ -1321,7 +1321,7 @@ def plot_oil_budget(self,
 
         b = self.get_oil_budget()
 
-        oil_budget = np.row_stack(
+        oil_budget = np.vstack(
             (b['mass_dispersed'], b['mass_submerged'], b['mass_surface'],
              b['mass_stranded'], b['mass_evaporated'], b['mass_biodegraded']))
         oil_density = b['oil_density']
diff --git a/opendrift/readers/basereader/variables.py b/opendrift/readers/basereader/variables.py
@@ -111,6 +111,9 @@ def rotate_vectors(self, reader_x, reader_y, u_component, v_component,
     def xy2lonlat(self, x, y):
         """Calculate x,y in own projection from given lon,lat (scalars/arrays).
         """
+        #if hasattr(x, '__len__') and len(x) == 1:
+        #    x = x.copy().item()
+        #    y = y.copy().item()
         if self.proj.crs.is_geographic:
             if 'ob_tran' in str(self.proj4):
                 logger.debug('NB: Converting degrees to radians ' +
@@ -127,10 +130,9 @@ def lonlat2xy(self, lon, lat):
         """
         Calculate lon,lat from given x,y (scalars/arrays) in own projection.
         """
-        if hasattr(lon, '__len__'):
-            if len(lon) == 1:
-                lon = lon[0]
-                lat = lat[0]
+        #if hasattr(lon, '__len__') and len(lon) == 1:
+        #    lon = lon.copy().item()
+        #    lat = lat.copy().item()
         if 'ob_tran' in str(self.proj4):
             x, y = self.proj(lon, lat, inverse=False)
             return np.degrees(x), np.degrees(y)
@@ -381,7 +383,7 @@ def check_arguments(self, variables, time, x, y, z):
             lon, lat = self.xy2lonlat(x, y)
             raise OutsideSpatialCoverageError(('Argcheck: all %s particles (%.2f-%.2fE, ' +
                     '%.2f-%.2fN) are outside domain of %s (%s)') %
-                    (len(lon), lon.min(), lon.max(), lat.min(),
+                    (np.size(x), lon.min(), lon.max(), lat.min(),
                      lat.max(), self.name, self.coverage_string()))
 
         return variables, time, x, y, z, outside
diff --git a/opendrift/readers/reader_grib2.py b/opendrift/readers/reader_grib2.py
@@ -54,7 +54,7 @@ def __init__(self, filename, proj4=None, engine='cfgrib'):
         # convert to python datetime
         assert '[ns]' in self.times.dtype.str, "datetime is not in nanoseconds"
         self.times = np.array([
-            datetime.utcfromtimestamp(d.astype('int') / 1e9)
+            datetime.fromtimestamp(d.astype('int') / 1e9)
             for d in self.times
         ])
 
diff --git a/opendrift/readers/reader_shape.py b/opendrift/readers/reader_shape.py
@@ -105,9 +105,9 @@ def __init__(self, shapes, proj4_str = '+proj=lonlat +ellps=WGS84', invert=False
 
     def __on_land__(self, x, y):
         if self.invert is False:
-            return shapely.vectorized.contains(self.land, x, y)
+            return shapely.contains_xy(self.land, x, y)
         else:  # Inverse if polygons are lakes and not land areas
-            return 1 - shapely.vectorized.contains(self.land, x, y)
+            return 1 - shapely.contains_xy(self.land, x, y)
 
     def get_variables(self, requestedVariables, time = None,
                       x = None, y = None, z = None):
diff --git a/tests/models/openoil/test_openoil.py b/tests/models/openoil/test_openoil.py
@@ -133,7 +133,7 @@ def test_seed_oil_type():
     lonstart = 16.040701
     latend = 69.991446
     lonend = 17.760061
-    time = [datetime.utcnow(), datetime.utcnow() + timedelta(hours=12)]
+    time = [datetime.now(), datetime.now() + timedelta(hours=12)]
 
     # changing oil type on first seed is ok
     o.seed_cone(lon=[lonstart, lonend], lat=[latstart, latend],
diff --git a/tests/models/test_environment.py b/tests/models/test_environment.py
@@ -1,3 +1,5 @@
+from datetime import datetime, timedelta
+import pytest
 from opendrift.models.basemodel.environment import Environment
 from opendrift.models.oceandrift import OceanDrift
 from opendrift.config import Configurable
@@ -22,3 +24,40 @@ def test_add_readers(test_data_roms):
         test_data_roms.start_time, [10], [50], [0], [])
     assert e[0][0] == 0
     assert e[0][1] == 10
+
+def test_previous():
+    o = OceanDrift()  # With coastline_action = none
+    o.set_config('general:coastline_action', 'none')
+    o.set_config('environment:constant:land_binary_mask', 0)
+    o.set_config('environment:constant:x_sea_water_velocity', 1)
+    o.seed_elements(lon=3, lat=60, time=datetime.now())
+    o.run(steps=1)
+    assert o.elements.lon == pytest.approx(3.0645, .001)
+    assert o.elements_previous is None
+    assert o.environment_previous is None
+
+    o = OceanDrift()  # With coastline_action = previous
+    o.set_config('general:coastline_action', 'previous')
+    o.set_config('environment:constant:land_binary_mask', 0)
+    o.set_config('environment:constant:x_sea_water_velocity', 1)
+    o.seed_elements(lon=3, lat=60, time=datetime.now())
+    o.run(steps=1)
+    assert o.elements.lon == pytest.approx(3.0645, .001)
+    assert o.elements_previous.lon == pytest.approx(3.0, .001)
+    assert o.elements_previous is not None
+    assert o.environment_previous is None
+ 
+def test_skip_env_variable():
+    o = OceanDrift()
+    o.set_config('drift:vertical_mixing', True)  # Diffusivity shall be included
+    o.set_config('environment:constant:land_binary_mask', 0)
+    o.seed_elements(lon=3, lat=60, time=datetime.now())
+    o.run(steps=1)
+    assert 'ocean_vertical_diffusivity' in o.required_variables
+
+    o = OceanDrift()
+    o.set_config('drift:vertical_mixing', False)  # Diffusivity shall be skipped
+    o.set_config('environment:constant:land_binary_mask', 0)
+    o.seed_elements(lon=3, lat=60, time=datetime.now())
+    o.run(steps=1)
+    assert 'ocean_vertical_diffusivity' not in o.required_variables
