Merge pull request #1274 from knutfrode/dev

Model property reguired_profiles_z_range is now replaced with config …

opendrift/models/basemodel/__init__.py

@@ -223,6 +223,8 @@ def __init__(self,
 
         super().__init__()
 
+        self.profiles_depth = None
+
         self.show_continuous_performance = False
 
         self.origin_marker = None  # Dictionary to store named seeding locations
@@ -234,8 +236,7 @@ def __init__(self,
         # List to store GeoJSON dicts of seeding commands
         self.seed_geojson = []
 
-        self.env = Environment(self.required_variables,
-                               self.required_profiles_z_range, self._config)
+        self.env = Environment(self.required_variables, self._config)
 
         # Make copies of dictionaries so that they are private to each instance
         self.status_categories = ['active']  # Particles are active by default
@@ -409,6 +410,9 @@ def __init__(self,
                 'description': 'Add horizontal diffusivity (random walk)',
                 'level': CONFIG_LEVEL_BASIC
             },
+            'drift:profiles_depth': {'type': 'float', 'default': 50, 'min': 0, 'max': None,
+                'level': CONFIG_LEVEL_ADVANCED, 'units': 'meters', 'description':
+                'Environment profiles will be retrieved from surface and down to this depth'},
             'drift:wind_uncertainty': {
                 'type': 'float',
                 'default': 0,
@@ -592,8 +596,10 @@ def add_readers_from_file(self, *args, **kwargs):
         '''Make readers from a file containing list of URLs or paths to netCDF datasets'''
         self.env.add_readers_from_file(*args, **kwargs)
 
+    # To be overloaded by sublasses, but this parent method must be called
     def prepare_run(self):
-        pass  # to be overloaded when needed
+        # Copy profile_depth from config
+        self.profiles_depth = self.get_config('drift:profiles_depth')
 
     def store_present_positions(self, IDs=None, lons=None, lats=None):
         """Store present element positions, in case they shall be moved back"""
@@ -661,8 +667,7 @@ def interact_with_coastline(self, final=False):
                                      self.time,
                                      self.elements.lon,
                                      self.elements.lat,
-                                     self.elements.z,
-                                     None)
+                                     self.elements.z)
             self.environment.land_binary_mask = en.land_binary_mask
 
         if i == 'stranding':  # Deactivate elements on land, but not in air
@@ -749,10 +754,6 @@ def ElementType(self):
     def required_variables(self):
         """Any trajectory model implementation must list needed variables."""
 
-    @abstractproperty
-    def required_profiles_z_range(self):
-        """Any trajectory model implementation must list range or return None."""
-
     def test_data_folder(self):
         import opendrift
         return os.path.abspath(
@@ -914,8 +915,7 @@ def closest_ocean_points(self, lon, lat):
                                      lon=lon,
                                      lat=lat,
                                      z=0 * lon,
-                                     time=land_reader.start_time,
-                                     profiles=None)[0]['land_binary_mask']
+                                     time=land_reader.start_time)[0]['land_binary_mask']
         if land.max() == 0:
             logger.info('All points are in ocean')
             return lon, lat
@@ -936,8 +936,7 @@ def closest_ocean_points(self, lon, lat):
                                          lon=longrid,
                                          lat=latgrid,
                                          z=0 * longrid,
-                                         time=land_reader.start_time,
-                                         profiles=None)[0]['land_binary_mask']
+                                         time=land_reader.start_time)[0]['land_binary_mask']
         if landgrid.min() == 1 or np.isnan(landgrid.min()):
             logger.warning('No ocean pixels nearby, cannot move elements.')
             return lon, lat
@@ -1092,8 +1091,7 @@ def seed_elements(self,
                     self.time = time[0]
                 env, env_profiles, missing = \
                     self.env.get_environment(['sea_floor_depth_below_sea_level'],
-                                         time=time[0], lon=lon, lat=lat,
-                                         z=0*lon, profiles=None)
+                                         time=time[0], lon=lon, lat=lat, z=0*lon)
             elif seafloor_fallback is not None:
                 env = {
                     'sea_floor_depth_below_sea_level':
@@ -2046,7 +2044,8 @@ def run(self,
                                          self.elements.lon,
                                          self.elements.lat,
                                          self.elements.z,
-                                         self.required_profiles)
+                                         self.required_profiles,
+                                         self.profiles_depth)
 
                 self.store_previous_variables()
 

opendrift/models/basemodel/environment.py

@@ -21,23 +21,21 @@ class Environment(Timeable, Configurable):
     readers: OrderedDict
     priority_list: OrderedDict
     required_variables: Dict
-    required_profiles_z_range: List[float]  # [min_depth, max_depth]
 
     discarded_readers: Dict
 
     proj_latlon = pyproj.Proj('+proj=latlong')
 
     __finalized__ = False
 
-    def __init__(self, required_variables, required_profiles_z_range, _config):
+    def __init__(self, required_variables, _config):
         super().__init__()
 
         self.readers = OrderedDict()
         self.priority_list = OrderedDict()
         self.discarded_readers = {}
 
         self.required_variables = required_variables
-        self.required_profiles_z_range = required_profiles_z_range
         self._config = _config # reference to simulation config
 
         # Add constant and fallback environment variables to config
@@ -521,7 +519,7 @@ def missing_variables(self):
             if var not in self.priority_list
         ]
 
-    def get_environment(self, variables, time, lon, lat, z, profiles):
+    def get_environment(self, variables, time, lon, lat, z, profiles=None, profiles_depth=None):
         '''Retrieve environmental variables at requested positions.
 
         Args:
@@ -536,7 +534,9 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
 
             z: depth to get value for
 
-            profiles: ?
+            profiles: list of variables for which profiles are needed
+
+            profiles_depth: depth of profiles in meters, as a positive number
 
         Updates:
             Buffer (raw data blocks) for each reader stored for performance:
@@ -562,6 +562,8 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
         for readername, reader in self.readers.copy().items():
             self.discard_reader_if_not_relevant(reader, time)
 
+        if profiles_depth is None:
+            profiles_depth = np.abs(z).max()
         if 'drift:truncate_ocean_model_below_m' in self._config:
             truncate_depth = self.get_config(
                 'drift:truncate_ocean_model_below_m')
@@ -570,12 +572,7 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
                              truncate_depth)
                 z = z.copy()
                 z[z < -truncate_depth] = -truncate_depth
-                if self.required_profiles_z_range is not None:
-                    self.required_profiles_z_range = np.array(
-                        self.required_profiles_z_range)
-                    self.required_profiles_z_range[
-                        self.required_profiles_z_range <
-                        -truncate_depth] = -truncate_depth
+                profiles_depth = np.minimum(profiles_depth, truncate_depth)
 
         # Initialise more lazy readers if necessary
         missing_variables = ['missingvar']
@@ -631,7 +628,7 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
                                 'Missing variables: calling get_environment recursively'
                             )
                             return self.get_environment(
-                                variables, time, lon, lat, z, profiles)
+                                variables, time, lon, lat, z, profiles, profiles_depth)
                     continue
                 # Fetch given variables at given positions from current reader
                 try:
@@ -648,7 +645,7 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
                     env_tmp, env_profiles_tmp = \
                         reader.get_variables_interpolated(
                             variable_group, profiles_from_reader,
-                            self.required_profiles_z_range, time,
+                            profiles_depth, time,
                             lon[missing_indices], lat[missing_indices],
                             z[missing_indices], self.proj_latlon)
 
@@ -662,7 +659,7 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
                                 'Missing variables: calling get_environment recursively'
                             )
                             return self.get_environment(
-                                variables, time, lon, lat, z, profiles)
+                                variables, time, lon, lat, z, profiles, profiles_depth)
                     continue
 
                 except Exception as e:  # Unknown error
@@ -693,7 +690,7 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
                                 'Missing variables: calling get_environment recursively'
                             )
                             return self.get_environment(
-                                variables, time, lon, lat, z, profiles)
+                                variables, time, lon, lat, z, profiles, profiles_depth)
                     continue
 
                 # Copy retrieved variables to env array, and mask nan-values
@@ -806,9 +803,7 @@ def get_environment(self, variables, time, lon, lat, z, profiles):
                     logger.debug('Creating empty dictionary for profiles not '
                                  'profided by any reader: ' +
                                  str(self.required_profiles))
-                    env_profiles = {}
-                    env_profiles['z'] = \
-                        np.array(self.required_profiles_z_range)[::-1]
+                    env_profiles = {'z': [0, -profiles_depth]}
                 if var not in env_profiles:
                     logger.debug(
                         '      Using fallback value %s for %s for all profiles'

opendrift/models/chemicaldrift.py

@@ -112,9 +112,6 @@ class ChemicalDrift(OceanDrift):
         'pH_sediment':{'fallback': 6.9, 'profiles': False}, # supplied by the user, with pH_sediment as standard name #
         }
 
-    # The depth range (in m) which profiles shall cover
-    required_profiles_z_range = [-20, 0]
-
 
     def specie_num2name(self,num):
         return self.name_species[num]
@@ -374,6 +371,7 @@ def prepare_run(self):
                 if (hasattr(value,'sigma') or hasattr(value,'z') ):
                     self.DOC_vertical_levels_given = True
 
+        super(ChemicalDrift, self).prepare_run()
 
     def init_species(self):
         # Initialize specie types

opendrift/models/larvalfish.py

@@ -82,7 +82,6 @@ class LarvalFish(OceanDrift):
         'sea_surface_wave_stokes_drift_y_velocity': {'fallback': 0},
     }
 
-    required_profiles_z_range = [0, -50]  # The depth range (in m) which profiles should cover
 
     def __init__(self, *args, **kwargs):
 

opendrift/models/model_template.py

@@ -102,11 +102,10 @@ class ModelTemplate(OceanDrift):
     # If the attribute 'profiles' is True for a variable (as for
     # ocean_vertical_diffusivity in the example above), a vertical profile
     # of this variable is obtained over the vertical depth interval as 
-    # defined below. These profiles are used for the vertical turbulence scheme:
+    # defined by config setting drift:profiles_depth. These profiles are used for the vertical turbulence scheme:
     # https://opendrift.github.io/_modules/opendrift/models/oceandrift.html#OceanDrift.vertical_mixing
     # Profiles are typically required for ocean_vertical_diffusivity, and sometimes for 
     # salinity and temperature in order to calculate the stratification.
-    required_profiles_z_range = [-50, 0]
 
     def __init__(self, *args, **kwargs):
 
@@ -236,6 +235,7 @@ def update(self):
 
     def prepare_run(self):
         """Code to be run before a simulation loop (``update()``)"""
+        # This method must also call the corresponding method of parent class
 
     def bottom_interaction(self, seafloor_depth):
         """Sub method of vertical_mixing, determines settling"""

opendrift/models/oceandrift.py

@@ -96,8 +96,6 @@ class OceanDrift(OpenDriftSimulation):
         'land_binary_mask': {'fallback': None},
         }
 
-    # The depth range (in m) which profiles shall cover
-    required_profiles_z_range = [-20, 0]
 
     def __init__(self, *args, **kwargs):
 
@@ -116,6 +114,9 @@ def __init__(self, *args, **kwargs):
         else:
             logger.debug('No machine learning correction available.')
 
+        if hasattr(self, 'required_profiles_z_range'):
+            raise ValueError('self.required_profiles_z_range is obsolete, and replaced by config setting drift:profile_depth. Please update your model.')
+
         # Calling general constructor of parent class
         super(OceanDrift, self).__init__(*args, **kwargs)
 
@@ -138,9 +139,6 @@ def __init__(self, *args, **kwargs):
             'vertical_mixing:TSprofiles': {'type': 'bool', 'default': False, 'level':
                 CONFIG_LEVEL_ADVANCED,
                 'description': 'Update T and S profiles within inner loop of vertical mixing. This takes more time, but may be slightly more accurate.'},
-            'drift:profiles_depth': {'type': 'float', 'default': 50, 'min': 0, 'max': None,
-                'level': CONFIG_LEVEL_ADVANCED, 'units': 'meters', 'description':
-                'Environment profiles will be retrieved from surface and down to this depth'},
             'drift:wind_drift_depth': {'type': 'float', 'default': 0.1,
                 'min': 0, 'max': 10, 'units': 'meters',
                 'description': 'The direct wind drift (windage) is linearly decreasing from the surface value (wind_drift_factor) until 0 at this depth.',
@@ -394,6 +392,9 @@ def update_terminal_velocity(self, Tprofiles=None, Sprofiles=None,
     def prepare_vertical_mixing(self):
         pass  # To be implemented by subclasses as needed
 
+    def prepare_run(self):
+        super(OceanDrift, self).prepare_run()
+
     def vertical_advection(self):
         """Move particles vertically according to vertical ocean current
 
@@ -520,15 +521,15 @@ def vertical_mixing(self, store_depths=False):
                     diffusivity_fallback):
                 Kprofiles = self.environment_profiles[
                     'ocean_vertical_diffusivity']
-                mixing_z = self.environment_profiles['z']
+                mixing_z = self.environment_profiles['z'].copy()
                 logger.debug('Using diffusivity from ocean model')
             else:
                 logger.debug('Using diffusivity from Large1994 since model diffusivities not available')
                 mixing_z = mixing_z_analytical
                 Kprofiles = self.get_diffusivity_profile('windspeed_Large1994', np.abs(mixing_z))
         elif diffusivity_model == 'constant':
             logger.debug('Using constant diffusivity specified by fallback_values[''ocean_vertical_diffusivity''] = %s m2.s-1' % (diffusivity_fallback))
-            mixing_z = self.environment_profiles['z']
+            mixing_z = self.environment_profiles['z'].copy()
             Kprofiles = diffusivity_fallback*np.ones(
                     self.environment_profiles['ocean_vertical_diffusivity'].shape) # keep constant value for ocean_vertical_diffusivity
         else:

opendrift/models/openberg_old.py

@@ -105,8 +105,6 @@ class OpenBergOld(OpenDriftSimulation):
         'land_binary_mask': {'fallback': None},
         }
 
-    required_profiles_z_range = [-120, 0] # [min_depth, max_depth]
-
     # Default colors for plotting
     status_colors = {'initial': 'green', 'active': 'blue',
                      'missing_data': 'gray', 'stranded': 'red'}

opendrift/models/openhns.py

@@ -178,8 +178,6 @@ class OpenHNS(OceanDrift):
         },
     }
 
-    # The depth range (in m) which profiles shall cover
-    required_profiles_z_range = [-20, 0]
 
     max_speed = 1.3  # m/s
 

opendrift/models/openoil/openoil.py

@@ -292,8 +292,6 @@ class OpenOil(OceanDrift):
         },
     }
 
-    # The depth range (in m) which profiles shall cover
-    required_profiles_z_range = [-20, 0]
 
     max_speed = 1.3  # m/s
 
@@ -673,7 +671,6 @@ def oil_weathering(self):
         self.timer_end('main loop:updating elements:oil weathering')
 
     def prepare_run(self):
-
         if self.oil_weathering_model == 'noaa':
             self.noaa_mass_balance = {}
             # Populate with seeded mass spread on oiltype.mass_fraction
@@ -706,6 +703,8 @@ def prepare_run(self):
             logger.warning('Could not load max water content file')
             print(e)
 
+        super(OpenOil, self).prepare_run()
+
     def oil_weathering_noaa(self):
         '''Oil weathering scheme adopted from NOAA PyGNOME model:
         https://github.com/NOAA-ORR-ERD/PyGnome

opendrift/models/pelagicegg.py

@@ -77,8 +77,6 @@ class PelagicEggDrift(OceanDrift):
         'upward_sea_water_velocity': {'fallback': 0},
       }
 
-    # The depth range (in m) which profiles shall cover
-    required_profiles_z_range = [-120, 0]
 
     # Default colors for plotting
     status_colors = {'initial': 'green', 'active': 'blue',

opendrift/models/radionuclides.py

@@ -92,9 +92,6 @@ class RadionuclideDrift(OceanDrift):
         'conc3': {'fallback': 1.e-3},
         }
 
-    # The depth range (in m) which profiles shall cover
-    required_profiles_z_range = [-20, 0]
-
 
     def specie_num2name(self,num):
         return self.name_species[num]
@@ -226,7 +223,7 @@ def prepare_run(self):
         logger.info('nspecies: %s' % self.nspecies)
         logger.info('Transfer rates:\n %s' % self.transfer_rates)
 
-
+        super(RadionuclideDrift, self).prepare_run()
 
 
     def init_species(self):