Merge branch 'master' into dev

OpenDrift · Jun 27, 2024 · 07b943b · 07b943b
2 parents ea1a81d + 59bbd8f
commit 07b943b
Show file tree

Hide file tree

Showing 29 changed files with 595 additions and 389 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,23 +1,26 @@
 # See https://opendrift.github.io for usage
 
-FROM condaforge/mambaforge
+# Use a minimal base image
+FROM mambaorg/micromamba:1.4.2
 
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
+ENV MAMBA_DOCKERFILE_ACTIVATE=1
 
-RUN mkdir /code
-WORKDIR /code
+RUN mkdir code
+WORKDIR code
 
-# Install opendrift environment into base conda environment
+# Copy environment file
 COPY environment.yml .
-RUN mamba env update -n base -f environment.yml
+
+# Install opendrift environment into base micromamba environment
+RUN micromamba install -n base -f environment.yml
 
 # Cache cartopy maps
 RUN /bin/bash -c "echo -e \"import cartopy\nfor s in ('c', 'l', 'i', 'h', 'f'): cartopy.io.shapereader.gshhs(s)\" | python"
 
 # Install opendrift
-ADD . /code
+ADD . .
 RUN pip install -e .
 
 # Test installation
 RUN /bin/bash -c "echo -e \"import opendrift\" | python"
-
diff --git a/examples/example_leeway_capsizing.py b/examples/example_leeway_capsizing.py
@@ -28,7 +28,7 @@
 #%%
 # Activating capsizing for high winds, with probability per hour given by
 # p(windspeed) = 0.5 + 0.5*tanh((windspeed-wind_threshold)/sigma)
-o.set_config('capsizing', True)
+o.set_config('processes:capsizing', True)
 o.set_config('capsizing:wind_threshold', 30)
 o.set_config('capsizing:wind_threshold_sigma', 5)
 o.set_config('capsizing:leeway_fraction', 0.4)  # Reducing leeway coefficients to 40% of original after capsize
@@ -62,7 +62,7 @@
 o = Leeway()
 o.add_reader(reader_norkyst)
 o.add_reader(reader_arome)
-o.set_config('capsizing', True)
+o.set_config('processes:capsizing', True)
 o.seed_elements(lon=4.4, lat=61.0, radius=100, number=1000,
                 capsized=1,  # now we seed all objects as already capsized
                 time=reader_arome.end_time, object_type=object_type)

diff --git a/examples/example_long_global_thredds.py b/examples/example_long_global_thredds.py
@@ -14,7 +14,7 @@
 # - Ocean forecast from global HYCOM model
 # - Weather forecast from NOAA/NCEP
 o.add_readers_from_list([
-    'https://tds.hycom.org/thredds/dodsC/GLBy0.08/latest',
+    'https://www.ncei.noaa.gov/thredds-coastal/dodsC/hycom/hycom_sfc_agg/HYCOM_Surface_Aggregation_best.ncd',
     'https://pae-paha.pacioos.hawaii.edu/thredds/dodsC/ncep_global/NCEP_Global_Atmospheric_Model_best.ncd'])
 
 o.seed_elements(lat=24, lon=-81, time=datetime.utcnow(),

diff --git a/examples/example_long_vietnam.py b/examples/example_long_vietnam.py
@@ -13,7 +13,7 @@
 # - Ocean forecast from global Hycom
 # - Weather forecast from NOAA/NCEP
 o.add_readers_from_list([
-    'https://tds.hycom.org/thredds/dodsC/GLBy0.08/latest',
+    'https://www.ncei.noaa.gov/thredds-coastal/dodsC/hycom/hycom_sfc_agg/HYCOM_Surface_Aggregation_best.ncd',
     'https://pae-paha.pacioos.hawaii.edu/thredds/dodsC/ncep_global/NCEP_Global_Atmospheric_Model_best.ncd'])
 
 # Seed some particles

diff --git a/examples/example_oilspill_seafloor_biodegradation.py b/examples/example_oilspill_seafloor_biodegradation.py
@@ -15,7 +15,7 @@
 #%%
 # Current from HYCOM and wind from NCEP GFS
 o.add_readers_from_list([
-    'https://tds.hycom.org/thredds/dodsC/GLBy0.08/expt_93.0/uv3z',
+    'https://www.ncei.noaa.gov/thredds-coastal/dodsC/hycom/hycom_sfc_agg/HYCOM_Surface_Aggregation_best.ncd',
     'https://pae-paha.pacioos.hawaii.edu/thredds/dodsC/ncep_global/NCEP_Global_Atmospheric_Model_best.ncd'])
 o.set_config('environment:constant:ocean_mixed_layer_thickness', 20)
 o.set_config('drift', {'current_uncertainty': 0, 'wind_uncertainty': 0, 'horizontal_diffusivity': 20})

diff --git a/examples/example_openoil.py b/examples/example_openoil.py
@@ -31,9 +31,7 @@
 #%%
 # Seeding some particles
 time = reader_arome.start_time
-oil_type = 'GULLFAKS, EXXON'
-oil_type = 'ARABIAN MEDIUM, API'
-oil_type = 'ALGERIAN CONDENSATE, STATOIL'
+oil_type = 'HEIDRUN AARE 2023'
 o.seed_elements(lon=4.9, lat=60.1, radius=3000, number=2000,
                 time=time, z=0, oil_type=oil_type)
 

diff --git a/examples/example_radionuclides.py b/examples/example_radionuclides.py
@@ -22,50 +22,27 @@
 
 # Adjusting some configuration
 o.set_config('drift:vertical_mixing', True)
-#o.set_config('environment:constant:ocean_vertical_diffusivity', 0)
 #o.set_config('vertical_mixing:diffusivitymodel','constant')  # include settling without vertical turbulent mixing
-o.set_config('vertical_mixing:diffusivitymodel','environment')  # include settling without vertical turbulent mixing
+o.set_config('vertical_mixing:diffusivitymodel','environment')  # apply vertical diffusivity from ocean model
 # Vertical mixing requires fast time step
 o.set_config('vertical_mixing:timestep', 600.) # seconds
 o.set_config('drift:horizontal_diffusivity', 10)
 
 #%%
-# Activate the desired species
-#o.set_config('radionuclide:species:LMM', True)
-#o.set_config('radionuclide:species:LMMcation', True)
-#o.set_config('radionuclide:species:LMManion', True)
-#o.set_config('radionuclide:species:Colloid', True)
-#o.set_config('radionuclide:species:Humic_colloid', True)
-#o.set_config('radionuclide:species:Polymer', True)
-#o.set_config('radionuclide:species:Particle_reversible', True)
-#o.set_config('radionuclide:species:Particle_irreversible', True)
-#o.set_config('radionuclide:species:Particle_slowly_reversible', True)
-
-#o.set_config('radionuclide:species:Sediment_reversible', True)
-#o.set_config('radionuclide:species:Sediment_irreversible', True)
-#o.set_config('radionuclide:species:Sediment_slowly_reversible', True)
-
 o.set_config('radionuclide:particle_diameter',5.e-6)  # m
-#o.set_config('radionuclide:particle_diameter_uncertainty',1.e-7) # m
-o.set_config('radionuclide:transformations:Kd',2.e0) # (m3/kg)
-#o.set_config('radionuclide:transformations:slow_coeff',1.e-6)
 
 o.set_config('radionuclide:sediment:resuspension_depth',2.)
 o.set_config('radionuclide:sediment:resuspension_depth_uncert',0.1)
 o.set_config('radionuclide:sediment:resuspension_critvel',0.15)
 
 
 #
-#o.set_config('radionuclide:transfer_setup','custom')
-o.set_config('radionuclide:transfer_setup','Bokna_137Cs')
-#o.set_config('radionuclide:transfer_setup','137Cs_rev')
-#o.set_config('radionuclide:transfer_setup','Sandnesfj_Al')
+o.set_config('radionuclide:isotope', '137Cs')
+o.set_config('radionuclide:specie_setup','LMM + Rev')
 
 # By default, radionuclides do not strand towards coastline
 o.set_config('general:coastline_action', 'previous')
 o.set_config('general:seafloor_action','lift_to_seafloor')
-#o.set_config('general:seafloor_action','previous')
-#o.set_config('general:use_auto_landmask',False)
 
 
 o.set_config('seed:LMM_fraction',.45)
@@ -80,20 +57,13 @@
 td=datetime.today()
 time = datetime(td.year, td.month, td.day, 0)
 
-#latseed= 61.2; lonseed= 4.3    # Sognesjen
-#latseed= 59.0;   lonseed= 10.75 # Hvaler/Koster
-#latseed= 57.5;   lonseed= 9.3 # Kattegat
-latseed= 60.0;   lonseed= 4.5 # Bergen (?)
+latseed= 60.0;   lonseed= 4.5 
 
 ntraj=5000
 iniz=np.random.rand(ntraj) * -10. # seeding the radionuclides in the upper 10m
 
 o.seed_elements(lonseed, latseed, z=iniz, radius=1000,number=ntraj,
                 time=time, 
-#                LMM_fraction=0.25,
-#                particle_fraction=0.75
-#                diameter=99.e-6#diam, 
-                #specie=init_speciation
                 )
 
 
@@ -137,17 +107,7 @@
 
 
 
-# Postprocessing: write to concentration netcdf file
-o.conc_lat  = reader_norkyst.get_variables('latitude',
-                                       x=[reader_norkyst.xmin,reader_norkyst.xmax],
-                                       y=[reader_norkyst.ymin,reader_norkyst.ymax])['latitude'][:]
-o.conc_lon  = reader_norkyst.get_variables('longitude',
-                                       x=[reader_norkyst.xmin,reader_norkyst.xmax],
-                                       y=[reader_norkyst.ymin,reader_norkyst.ymax])['longitude'][:]
-o.conc_topo  = reader_norkyst.get_variables('sea_floor_depth_below_sea_level',
-                                       x=[reader_norkyst.xmin,reader_norkyst.xmax],
-                                       y=[reader_norkyst.ymin,reader_norkyst.ymax])['sea_floor_depth_below_sea_level'][:]
-#o.conc_mask  = reader_norkyst.land_binary_mask
+# # Postprocessing: write to concentration netcdf file
 
 #%%
 #
@@ -160,8 +120,8 @@
                                       smoothing_cells=1,
                                       time_avg_conc=True,
                                       deltat=2., # hours
-                                      llcrnrlon=4.4, llcrnrlat=59.9,
-                                      urcrnrlon=4.8, urcrnrlat=60.2,
+#                                      llcrnrlon=4.4, llcrnrlat=59.9,
+#                                      urcrnrlon=4.8, urcrnrlat=60.2,
                                      )
 
 

diff --git a/examples/example_wind_measurements.py b/examples/example_wind_measurements.py
@@ -123,8 +123,7 @@
 
 o.seed_elements(lon=lon, lat=lat, radius=radius, number=number, time=time_start, wind_drift_factor=wind_drift_factor)
 o.run(end_time=time_end, time_step=time_step, time_step_output=time_step_output)
-o.plot(fast = False, background=['x_sea_water_velocity', 'y_sea_water_velocity'], legend=['Norkyst onlyt', 'Gaussian measurment'], buffer = .023, markersize = 150, linewidth = 3, title = "", xlocs = mpl.ticker.MaxNLocator(5), ylocs = mpl.ticker.MaxNLocator(5), clabel = r"Wind speed $\mathrm{(m.s^{-1})}$", cpad = 0.08, text=text)
-
+o.plot(fast = False, background=['x_sea_water_velocity', 'y_sea_water_velocity'], legend=['Norkyst only', 'Gaussian measurement'], buffer = .023, markersize = 150, linewidth = 3, title = "", xlocs = mpl.ticker.MaxNLocator(5), ylocs = mpl.ticker.MaxNLocator(5), clabel = r"Wind speed $\mathrm{(m.s^{-1})}$", cpad = 0.08, text=text)
 
 #%%
 # Measurement modified model simulation
@@ -139,8 +138,7 @@
 o2.seed_elements(lon=lon, lat=lat, radius=radius, number=number, time=time_start, wind_drift_factor=wind_drift_factor)
 o2.run(end_time=time_end, time_step=time_step, time_step_output=time_step_output)
 
-o.plot(fast = False, compare=o2, background=['x_sea_water_velocity', 'y_sea_water_velocity'], legend=['Norkyst onlyt', 'Gaussian measurment'], buffer = .023, markersize = 150, linewidth = 3, title = "", xlocs = mpl.ticker.MaxNLocator(5), ylocs = mpl.ticker.MaxNLocator(5), clabel = r"Wind speed $\mathrm{(m.s^{-1})}$", cpad = 0.08, text=text)
-
+o.plot(fast = False, compare=o2, background=['x_sea_water_velocity', 'y_sea_water_velocity'], legend=['Norkyst only', 'Gaussian measurement'], buffer = .023, markersize = 150, linewidth = 3, title = "", xlocs = mpl.ticker.MaxNLocator(5), ylocs = mpl.ticker.MaxNLocator(5), clabel = r"Wind speed $\mathrm{(m.s^{-1})}$", cpad = 0.08, text=text)
 
 #%%
 # Here, we generate more particles and look
@@ -161,8 +159,7 @@
 o2.seed_elements(lon=lon, lat=lat, radius=radius, number=number, time=time_start, wind_drift_factor=wind_drift_factor)
 o2.run(end_time=time_end, time_step=time_step, time_step_output=time_step_output)
 
-o.plot(fast = False, compare=o2, background=['x_sea_water_velocity', 'y_sea_water_velocity'], legend=['Norkyst onlyt', 'Gaussian measurment'], buffer = .023, markersize = 70, linewidth = 1, title = "", xlocs = mpl.ticker.MaxNLocator(5), ylocs = mpl.ticker.MaxNLocator(5), clabel = r"Wind speed $\mathrm{(m.s^{-1})}$", cpad = 0.08, text=text)
-
+o.plot(fast = False, compare=o2, background=['x_sea_water_velocity', 'y_sea_water_velocity'], legend=['Norkyst only', 'Gaussian measurement'], buffer = .023, markersize = 70, linewidth = 1, title = "", xlocs = mpl.ticker.MaxNLocator(5), ylocs = mpl.ticker.MaxNLocator(5), clabel = r"Wind speed $\mathrm{(m.s^{-1})}$", cpad = 0.08, text=text)
 
 lon_drifters_1, lat_drifters_1 = o.get_lonlats()
 lon_drifters_2, lat_drifters_2 = o2.get_lonlats()

diff --git a/history.rst b/history.rst
@@ -1,14 +1,67 @@
 History
 =======
 
+2024-06-27 / Release v1.11.9
+----------------------------
+* New feature to blend model field with point measurement (Ugo Martinez)
+* Hack in generic reader to make sure wind from ECMWF files is at 10m height
+
+* Raising now error if all elements are seeded on land
+2024-06-26 / Release v1.11.8
+----------------------------
+* Raising now error if all elements are seeded on land
+
+2024-06-25 / Release v1.11.7
+----------------------------
+* Decreased config_level of general:simulation_name to BASIC, due to wrong interpretation of config_level by Drifty
+
+2024-06-24 / Release v1.11.6
+----------------------------
+* Credentials for copernicusmarine client can now be stored in environment variables COPERNICUSMARINE_USER and COPERNICUSMARINE_PASSWORD, as alternative to .netrc file
+* Removed GRIB reader from list included in add_readers_from_list
+* Replaced two obsolete URLS for HYCOM (tds.hycom.org) with new aggregate from ncei.noaa.gov
+* Removed double quote from docstring, as giving problems for Drifty
+* Updated max water content of new oils
+* OpenDriftGUI now logs to file in addition to GUI window
+* config general:simulation_name is now ESSENTIAL, meaning that it will appear on front page of GUI
+
+2024-06-18 / Release v1.11.5
+----------------------------
+* Leeway config categori capsizing (bool) renamed to processes:capsizing
+* adios<1.2 removed from pyproject.toml, as this it not found on conda
+
+2024-06-14 / Release v1.11.4
+----------------------------
+* Updating requirements in pyproject.toml
+* config setting general:simulation_name is now ESSENTIAL, to be on fron page of GUI
+
+2024-06-14 / Release v1.11.3
+----------------------------
+* reader.plot() now takes time as optional argument for plotting background field at specific time
+* Using now product_id instead of OPeNDAP URL for CMEMS datasets, and using copernicusmarineclient through new reader_copernicusmarine. username/password can be stored in netrc-file with machine name equal to *copernicusmarine* or *nrt.cmems-du.eu*
+* Model property reguired_profiles_z_range is now replaced with config setting drift:profile_depth, and profiles are retrieved from surface to this depth. profiles_depth is now input parameter to get_environment, and not anymore a property of Environment class. prepare_run must now always call prepare_run of parent class, since profile_depth is copied to object in basemodel.prepare_run
+* get_variables_along_trajectory now also takes depth (z) as input parameter
+* updates to wetting/drying in ROMS reader (Kristin Thyng)
+* Fill value in output netCDF files is now set to NaN for floats and -999 for integers
+* Moving basereader.prepare() to variables.prepare(), as the former was overriding structured.prepare() due to multiple inheritance, and thus config *drift:max_speed* was not applied if config setting was made after reader was added. Also increasing *drift:max_speed* of OceanDrift from 1 to 2m/s
+* Leeway model now allows capsizing (and un-capsizing for backwards runs), with given probability and reduction of leeway coefficients when wind exceeds given threshold
+* New internal method simulation_direction() is 1 for forward runs, and -1 for backwards runs
+* First version of gaussian merging of model and point measurements (Ugo Martinez)
+* Added utility method open_mfdataset_overlap to create manual threds aggregates, and example_manual_aggregate to illustrate usage
+* Added new config type 'str' with properties min_length and max_length (default 64). Added generic config 'general:simulation_name' (default empty)
+* Changing >= to > in condition regarding at which timestep to export buffer to file
+* Added new oil, HEIDRUN AARE 2023 
+
 2024-04-02 / Release v1.11.2
 ----------------------------
 * Proper handling of sea_surface_height implemented by Kristin Thyng. All subclasses of OceanDrift now have `sea_surface_height` (default 0) as new parameter. z=0 is always sea surface (including sea_surface_height), and seafloor is now where z = -(sea_floor_depth + sea_surface_height)
 * Improvements of ROMS reader by Kristin Thyng:
+
   * Roppy-method `sdepth` (used by ROMS reader) now accounts for `sea_surface_height` (zeta).
   * Improved handling of rotation of vectors.
   * Interpolator can be saved/cached to file to save time on repeated simulations.
   * Improved handling of landmasks, for wetting-drying-applications.
+
 * Added alternative biodegradation to OpenOil by specifying half_tiome [days], which can be different for slick and submerged droplets.
 * Memory usage is now logged once every timestep, and can be plotted after simulation with new method `o.plot_memory_usage()`
 * Exporting directly to parquet file is now an alternative to netCDF (#1259, Achim Randelhoff)
@@ -17,9 +70,11 @@ History
 * Bugfix for attibute of vertical coordinate in SCISM raeder (Calvin Quigley)
 * Can make faster and smaller animation by selcting frames as range or list (Manuel Aghito)
 * Updates to reader_netCDF_CF_generic:
+
   * Now also rotating ensemble vectors from east/north to x/y
   * Now using dynamic instead of hardcoded order of dimensions
   * Removing unnecessary ensemble dimension for seafloor depth
+
 * Now ending timer[total time] before finalizing output netCDF file, so that complete performance is included.
 
 2024-01-25 / Release v1.11.1

diff --git a/opendrift/__init__.py b/opendrift/__init__.py
@@ -125,6 +125,16 @@ def versions():
     import matplotlib
     import netCDF4
     import xarray
+    try:
+        import adios_db
+        adios_version = adios_db.__version__
+    except:
+        adios_version = ': Not installed'
+    try:
+        import copernicusmarine
+        copernicus_version = copernicusmarine.__version__
+    except:
+        copernicus_version = ': Not installed'
     import sys
     s = '\n------------------------------------------------------\n'
     s += 'Software and hardware:\n'
@@ -143,6 +153,8 @@ def versions():
     s += '  Matplotlib version %s\n' % matplotlib.__version__
     s += '  NetCDF4 version %s\n' % netCDF4.__version__
     s += '  Xarray version %s\n' % xarray.__version__
+    s += '  ADIOS (adios_db) version %s\n' % adios_version
+    s += '  Copernicusmarine version %s\n' % copernicus_version
     s += '  Python version %s\n' % sys.version.replace('\n', '')
     s += '------------------------------------------------------\n'
     return s

diff --git a/opendrift/models/basemodel/__init__.py b/opendrift/models/basemodel/__init__.py
@@ -55,7 +55,7 @@
 from opendrift.timer import Timeable
 from opendrift.errors import WrongMode
 from opendrift.models.physics_methods import PhysicsMethods
-from opendrift.config import Configurable, CONFIG_LEVEL_BASIC, CONFIG_LEVEL_ADVANCED
+from opendrift.config import Configurable, CONFIG_LEVEL_BASIC, CONFIG_LEVEL_ADVANCED, CONFIG_LEVEL_ESSENTIAL
 
 Mode = Enum('Mode', ['Config', 'Ready', 'Run', 'Result'])
 
@@ -915,6 +915,8 @@ def closest_ocean_points(self, lon, lat):
                                          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.')
+            if land.min() == 1:
+                raise ValueError('All elements seeded on land')
             return lon, lat
 
         oceangridlons = longrid[landgrid == 0]

diff --git a/opendrift/models/leeway.py b/opendrift/models/leeway.py
@@ -76,7 +76,7 @@ class LeewayObj(LagrangianArray):
          ('capsized', {
             'dtype': np.uint8,
             'units': '1',
-            'description': '0 is not capsized, changed to 1 after capsizing (irreversible). After capsizing, leeway coeffieiencts are reduced as given by config item "capsized:leeway_fraction"',
+            'description': '0 is not capsized, changed to 1 after capsizing (irreversible). After capsizing, leeway coeffieiencts are reduced as given by config item capsized:leeway_fraction',
             'seed': True,
             'default': 0
         }),
@@ -231,7 +231,7 @@ def __init__(self, d=None, *args, **kwargs):
                 'units': 'probability',
                 'level': CONFIG_LEVEL_BASIC
             },
-              'capsizing': {
+            'processes:capsizing': {
                 'type': 'bool',
                 'default': False,
                 'min': 0,
@@ -424,7 +424,7 @@ def update(self):
         winddir = np.arctan2(self.environment.x_wind, self.environment.y_wind)
 
         # Capsizing
-        if self.get_config('capsizing') is True:
+        if self.get_config('processes:capsizing') is True:
             wind_threshold = self.get_config('capsizing:wind_threshold')
             wind_threshold_sigma = self.get_config('capsizing:wind_threshold_sigma')
             # For forward run, elements can be capsized, but for backwards run, only capsized elements can be un-capsized

diff --git a/opendrift/models/openoil/adios/README.md b/opendrift/models/openoil/adios/README.md
@@ -1,2 +1 @@
-The oils in oils.xz are scared from https://adios.orr.noaa.gov/oils using
-harvest_oils.py. Re-run to update list.
+The oils in oils.xz are downloaded from https://github.com/OpenDrift/noaa-oil-data using harvest_oils.py. Re-run to update list.