- 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)
- The size and color of particles of animation and animation_profile methods can now be scaled with any element or environment property by specifying marker=<property>. Sizes can eventually be scaled by spcifying markersize_scaling. Transparency (alpha) can also be provided. Some examples are updated.
- Bugfix for cases with no active particles at the same timestep as exporting to file (#1251, Lenny Hucher)
- 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.
- ROMS reader can take xarray datasets (Rich Signell)
- Norwegian oils: maximum water fractions are overriden with Sintef values.
- set_config can take dictionary as input for faster setting of multiple options.
- New example to illustrate new Copernicus Marine Client.
- Norwegian oil data (json files) are moved from OpenDrift repository to https://github.com/OpenDrift/noaa-oil-data, from where they are harvested to oils.xz.
- adios_db is new dependency, and old oil methods are removed from openoil.py and companion scripts.
- lazy_reader can now pass zarr auth info
- Renamed OpenBerg to OpenBergOld, to give place for a new full-fledged ice berg drift model which includes thermodynamics
- Order of initializing a simulation is now strict: configuration and adding readers must be done before seeding elements and starting simulation. Internally this is regulated by modes: ['Config', 'Ready', 'Run', 'Result'] and use of decorators for when methods are applicable.
- Related restructuring, including new Config and Environment classes, and renaming basemodel.py to basemodel/__init__.py. reset method is removed, and a clone method is intruduced instead.
- drift:max_speed is now a config value. fallback_values it not anymore a cached dict, but must be retrieved from config. Updated all examples and tests to seed elements after config and readers
- Several updates to ChemicalDrift module
- Fixed bug related to rotation of east/north-oriented vectors from reader_netCDF_generic with projection of different orientation
- Fixed bug for buffer size for negative time steps and readers with no time dimension
- dbyte type landmask now allowed in ROMS reader
- Removing u_eastward and v_northward from ROMS variable mappings, as these are wrongly rotated. Rotation should be fixed if these are re-inserted
- Readers are now quarantined/discarded if they fail more than the number of times given by config readers:max_number_of_fails (default 1)
- Added method plot_stokes_profile to plot vertical profiles of Stokes drift
- Added standard_name aliases for baroclinic_x_sea_water_velocity, baroclinic_eastward_sea_water_velocity, and y/north counterparts
- Added normal and lognormal droplet size distributions for subsea blowout (author Giles Fearon)
- Fixed bug for solar_coeff in sealice model (author Julien Moreau)
- vector_pairs_xy now also contains name of magnitude and direction_to components, i.e. 4 elements array (xname, yname, magnitude, direction_to). For future automatic conversion between x_comp,ycomp and speed,magnitude
- More generic environment mapping methods, from vectors to magnitude/direction and vice versa. Need improvement formapping based on other mapped variables. Readerinfo now use get_variables_interpolated_xy instead of get_variables to report data at point
- Fixed wrong distribution of angles when seeding with uniform distribution. Thanks to Oyvind Breivik for spotting.
- oil_type can be decided at first seeding, but not changed at second seeding. I.e. as before, only a single oil type can be used for a simulation.
- CF projection info is now parsed with pyproj.CF.from_cf()
- Fixed bug in rotate_variable_dict for rotated pole projection
- netCDF generic reader now accepts Xarray Datasets in addition to filenames or URLs
- ROMS reader now accepts also time variable named 'bulk_time' and unit of days. Added uwnd,uwind,vwnd,wvind,tair,wspd to mapping variables
- Added five new oils to OpenOil/ADIOS. Mapped NJORD 1997 to NJORD 2002.
- Temporary hack to let reader_netCDF_CF_generic read Zarr datasets
- Particles in air (z>0) are not stranded/deactivated when land_binary_mask==1
- Updated Thredds URL to CMEMS wave model
- Not dropping Vtransform in reader_ROMS_native when using MFDataset (wildcards). Thanks to Tianning Wu for spotting bug
- GUI: Timezone CET can be chosen, and added button to copy netCDF outfile to selected folder
- Multiple improvements to the chemicaldrift model.
- Fix issue where oil type alias for 'EKOFISK BLEND 2002' did not work.
- Leeway: number of elements now equal to length of lon,lat input array (if number not given).
- Leeway: ASCII output gives small numerical difference on different platforms, presumably because of numerical errors.
- Fixing bug in get_environment, where unmasked arrays of nan did not lead to call for more readers.
- Add trajan as dependency.
- Workaround in reader_netCDF_CF_generic to prevent wrong wind field from ECMWF model to be selected
- Fix paths in opendrift_gui.
- Optimizations to reading results files.
- ROMS reader improvements.
- ChemD: many improvements.
- Bugfixes.
- Using cartopy shapes for full resolution again because of performance issues.
- Unit of oil viscosity (which is kinematic viscosity) is now consistent.
- When importing a subset in time, the number of actual active elements is now detected and used for initialization.
- OpenDrift and roaring-landmask is now available as conda packages in conda-forge.
- Roaring landmask is now the only standard landmask provider. The extent and corners arguments have been removed from the global_landmask reader. They have not been in use when roaring-landmask was installed.
- The land shapes included with roaring-landmask is used if full resolution is used during plotting. Otherwise the cartopy provider is used.
- Two bugs in OpenOil fixed by Giles Fearon: in vertical mixing procedure, Temperature has wrong unit when calculating water density, and diameter was used instead of radius to calculate terminal velocity. This lead to moderate errors in vertical distribution of oil droplets: https://github.com/OpenDrift/opendrift/commit/457ed0ff263fb2cd51125cbc3df8c972e0b16fe7
- Fixed offset error in plotting of background fields on animations, which arose due to recent updates of matplotlib.
- Added fix (suggested by user lyingTree) for problem when seeding small number of elements within polygons.
- figsize is new optional argument to plot and animation methods (default is 11 inches).
- Possible to specify custom title for animation method.
- Oil type is now retrieved from stored netCDF files from OpenOil simulations.
- Fixed bug for readers with property always_valid=True
- Added boolean option show_trajectories to plot method.
- reader_netCDF_CF_generic does now only detect 1D-variables as x- and y-coordinates.
- For animated drifters, trajectory is now shown only up to current time step.
- Variables may now also be specified for add_readers_from_list.
- Allowing more than one drifter-dictionary to be animated, if keyword drifter (previously named trajectory_dict) is a list instead of dict.
- New convenience method for structured readers to calculate ocean depth, area and volume within given coordinates.
- Generic netCDF reader now raises an error of file/URL is (apparently) raw ROMS output.
- ROMS native reader is now not rotating vectors with east/north in either variable or standard-name.
- Updates to ROMS native reader: standard_name_mapping may be provided by user, and mask, coordinates and angle may all be read from eventual gridfile.
- Added option to chose ensemble member in reader_netCDF_CF_generic (by user mateuszmatu).
- An experimental drift model based on the Eulerian modeling scheme has been added.
- It is now possible to combine readers using operators, e.g. to take the mean of two readers, or tune the intensity of a variable. See the example_reader_operators.py for an example.
- Now using Cartopy >= 0.20. Cartopy < 0.20 is longer supported.
- Updated thredds URL to Barents2.5 ocean model
- ROMS native reader now detects variables having standard_name attribute
- Using more explicit exceptions internally, e.g. OutsideSpatialCoverageError, CouldNotInitializeReaderError etc.
- Added 7 Norwegian oils
- roaring_landmask (written in Rust) is now installed as default (faster landmask checking)
- Fixed discarding of irrelevant readers, which was not working properly. Readers are now discarded if they do not cover simuation temporal or spatial coverage, or do not contain relevant variables
- Updating/renaming global CMEMS MERCATOR thredds URL. Removing obsoleted CMEMS reader
- Config setting drift:horizontal_diffusivity is changed from ADVANCED to BASIC, so that it is configurable from e.g. Drifty
- Fixed bug preventing export of final time step if the final time_step output is not completed
- Fixed bug in ShipDrift model: beta2 was not updated in loop, giving minor directional error
- Fixed bug in ShipDrift model: left and right directions were swapped
- Removing duplicate oils in OpenOil
- Re-inserted missing oil UTGARD CONDENSATE 2021, and added mapping from EKOFISK BLEND 2002 to 2000
- Fixed bug in ShipDrift: erroneous direction used for wave forcing when Stokes drift was provided as forcing.
- New methods to calculate Liu-Weissberg and DARPA skillscores
- Blit is now an input parameter to animation, defaulting to False, as blitting destroys zorder (background field is always overlaid landmask)
- The oil-library has been replaced with the new ADIOS database. Oils are retrieved from adios.orr.noaa.gov, but shipped with OpenDrift. They will be updated occasionally. Additional oils not yet included in ADIOS are also supplied with OpenDrift.
- A custom oil can be specified to OpenOil as a JSON string in the format of ADIOS. This means that if you want to use a new or updated oil from the ADIOS database, you can download it as JSON and specify it manually.
- The dependency on the oillibrary is now removed, and we should no longer have any conda-specific package dependencies.
- Faster writing of animations to file (mp4 and gif) using grab_frame and saving methods in matplotlib.animation writers
- New element property current_drift_factor (default 1) to OceanDrift and submodels - allowing to move particles with a fraction of ocean current.
- OpenOil and PlastDrift now inherits ElementType class from OceanDrift, instead of from Elements.PassiveTracer
- Fixed bug for vertical mixing with depths below 255m
- A new model :mod:`sealice <opendrift.models.sealice>` has been added, written by Julien Moreau.
- Machine learning correction in OceanDrift model. Used for DARPA FFT Challenge, with machine learning data generated by Jean Rabault. Will be made avaiable for general use in future release.
- reader_from_url is now using requests instead of urllib, fixing problem with add_readers_from_list and .netrc authentication.
- Hidden feature for
reader_netCDF_CF_generic: if attributesshift_xandshift_yare defined, the returned fields are shifted this many meters in the x/y (or east/north) directions - parameter
show_particlesto plot() is now renamed toshow_elements, as for animation() - Map bounds are now extended to cover also comparison simulations and any trajectory_dicts.
skipandscaleas input to plot() and animation() are now None, so that density and length and arrows are determined by matplotlib/quiver, unless overridden by user.- New method (
distance_between_trajectories) to calculate distances between two trajectories, position by position. - Updates to
ChemicalDriftmodel
- Fix bugs in selafin reader.
- Several improvements to the SCHISM reader.
- Add method for tuning windrift factor from observed drift.
- Add method to retrieve environment variables (from given readers) along a given trajectory (e.g. a drifter).
- Improved dateline handling in readers.
- Fix dateline bug in landmask.
reader_netCDF_CF_generic: if x, and y-coordinates are integer sequences, these are not anymore interpreted as projection coordinates.reader_netCDF_CF_generic: taking calendar name into acount when decoding time.- Leeway model: max_speed is increased to 5 m/s, avoiding obtaining too small data-blocks readers.
- Leeway model ASCII export: if all elements are deactivated, write previous mean position, instead of NaN.
- Improved Xarray-postprocessing (based on opendrift.open_xarray), as demonstrated in
example_river_runoff.py. Aotomaticanalysis_fileis omitted. - Fixed problem related to mutating dictionary of readers when discarding.
- Added
mixed_layer_depth(default 50m) as environment variable of OceanDrift (and subclasses). This is used ifSundbyorLargeparameterizations of vertical turbulence is activated. A new config setting defines background diffusivity (default:1.2e-5 m2-s) origin_marker_namecan now be specified when seeding, and is stored as attributesflag_meaningsto output variableorigin_marker.- Quiver plots are now centered on pixels/grid, instead of at corner.
- Using OilLibrary v4+noaa1.1.3
- New method
reader.shift_start_time(start_time)to shift time coverage of reader - Density arrays calculated with method "get_density" for files opened with open_xarray can now be weighted with any property, or a user provided array. origin_marker is now a dimension of the arrays stored in analysis netCDF file. Made new method `get_density_timeseries
- ROMS native reader now accepts datasets where lon and lat are 1-dimensional
- Fixed bug related to extrapolating 3D data to seafloor
- Fixed bug with interpolation where latitude/y-coordinate is decreasing and not increasing (flipped upside down). Also fixed small inaccuracy of structured interpolation.
- Fixed horizontal diffusion for backwards simulations
- Enable the use of roaring-landmask as landmask reader, if installed.
- Add Telemac / Selafin reader (requires telemac python scripts).
- Reader environment mappings (deriving variables from others) can be activated with >>> o.activate_environment_mapping(<mapping_name>). Method to derive wind components from
wind_speedandwind_from_direction / wind_to_directionis activated by default. - New unstructured reader for SHYFEM model output
animationandanimation_profilemethods may now use legend instead of colorbar for element properties- Arguments
colortoanimation()andlinecolortoplot()can now be arrays of length equal to the number of elements. - Improved mechanism for drifter/trajectory overlay on animations, as illustraded by :doc:`example_current_from_drifter <gallery/example_current_from_drifter>`
- Several improvements to module ChemicalDrift
- For PlastDrift model, config
drift:vertical_mixing=Falsestill gave vertical entrainment formixingmodel=analytical, but this is now changed. Sundby83 is now default model for vertical diffusivity in PlastDrift (was Large1994) - Increased valid range of current velocity components from 10 m/s to 15 m/s
- Rotated pole projection (ob_tran) is now parsed from CF attributes by reader_netCDF_CF_generic.
- Leeway jibing probability is calculated with exponential, giving more precise results for larger time steps. Generic arguments are removed from Leeway seeding method.
- lon, lat are now positional arguments also in Leeway.seed_elements method. Leeway.seed_from_shapefile did nor work before this fix.
- Config option
drift:lift_to_seaflooris replaced bygeneral:seafloor_action, analoguos togeneral:coastline_action. Available options arenone,deactivate,lift_to_seaflooras well as new optionprevious- moving elements back to previous position. - New method
get_trajectory_lengthsto calculate length and speeds along trajectories - Basemodel class does not anymore have a projection, internal coordinates are now always lon, lat
- Color of ocean and landmask may now be overridden in plot- and animation methods with new input variables
land_colorandocean_color. A new input dictionarytextallows map annotations. - opendrift-landmask-data only loads mask once for each python process, reducing memory usage and improves performance where you run opendrift multiple times in the same script and process.
- New parallelisation of lonlat2xy for unprojected readers. The flag
<reader>.multiprocessing_failis replaced with<reader>.__parallel_fail__ - plot_property() can now save figure to file if filename is provided
- netCDF attribute seed_geojson is now a GeoJSON FeatureCollection.
- reader_netCDF_CF_generic does not anymore read 2D lon/lat variables if 1D x/y variables are detected, giving much faster initialisation.
- General replacement of
np.floatandnp.intwith eitherfloat,intornp.float32/64andnp.int32/64. np.float and np.int are deprecated in numpy 1.20. - Fixed bug occuring when interpolating environment_profiles in time, and the number of vertical layers in the ocean-model-block is larger at time1 than at time2
- New module LarvalFish, for fish eggs hatching into larvae with swimming behaviour
- Sundby83 parameterisation of vertical diffusivity is now set to 0 below mixed layer depth (default 50m)
- Deprecating seed argument oiltype in favor of oil_type in OpenOil. Warning is issued, but later this will become an error
- Fixed problem with convolution of reader fields
- Fixed newly introduced bug with Leeway ascii output file
- Cleaned up some metadata output, and seeding arguments are written as list of GeoJSON strings to attribute seed_geojson
- seed_cone also accepts time as list with single element
- Min/max values are checked/masked also for ensemble data
- reader_netCDF_CF_generic now detects lon/lat arrays also if their variable name equals lon/lat or longitude/latitude
- Fixed bug related to derived_variables (e.g. calculating x_wind, y_wind from windspeed, winddirection)
- Fixed problem with double or missing logging output
- ShipDrift model now gives warning and not error if input parameter are outside bounds, and parameters are clipped to boundary values
- Fixed problem with multiprocessing/parallelization of lonlat2xy for unprojected readers
- OilLibrary updated to version 1.1.3. Slightly different weathering results, and * is removed from oil names starting with GENERIC
- Major restructuring of Basereader class. Readers now are sublasses of Structured, Unstructured or Continuous.
- Built in GUI is improved with posibillity to adjust all config settings.
- Some Leeway parameters are renamed from camelCase to camel_case, including:
jibeProbability->jibe_probabilityandobjectType->object_type - Renamed config setting
drift:scheme->drift:advection_scheme
- Fixed bug in v1.4.1 that OpenOil and SedimentDrift had fallback_value of 0 for land_binary_mask, this shall be None.
- Built in GUI is improved with docstrings and less hardcoding, based on new config mechanism, including a new bool setting
seed:seafloor. model.required_variablesis now a dictionary, which also includes the earlierfallback_values,desired_variablesandrequired_profiles. Instead of providing fallback values directly in a dictionary, these shall now be provided through the config mechanism:o.set_config('environment:fallback:<variable>', <value>). Correspondingly, config settingenvironment:constant:<variable>may be used to specify constant values for the same variables (overriding any other readers).- seed_elements is simplified, by factoring out a new method seed_cone
- New internal config mechanism, and configobj package is no longer needed. The user API (
get_config(),set_config()) is unchanged, but model developers must use the new mechanism to add configuration settings. - Added new reader for static 2D fields (
reader_constant_2d.py) - Xarray, Dask and Xhistogram are new requirements. New method
opendrift.open_xarrayto open an output netCDF file lazily, with possibility to e.g. calculate density arrays/plots from datasets to large to fit in memory. - New model chemicaldrift
- New seed method
seed_repeated_segment() - New method
animate_vertical_distribution() - Vertical mixing scheme is greatly simplified, and should be faster for large number of elements.
- Vertical mixing is now disabled by default in OceanDrift, but enabled in all submodules (PelagicEggDrift, SedimentDrift, RadionuclideDrift, OpenOil)
- Vertical diffusivity option zero is replaced with
constant, which means using the fallback value. - New config setting
drift:horizontal_diffusivity, providing time-step independent diffusion, in contrast todrift:current_uncertaintyanddrift:wind_uncertainty - Readers may be initialised from a JSON string, where reader is name of reader module, and other parameters are forwarded to reader constructor, e.g.: {"reader": "reader_cmems", "dataset": "global-analysis-forecast-phy-001-024-hourly-t-u-v-ssh"}
- CMEMS reader now obtains username/password from .netrc instead of environment variables. CMEMS-motuclient is added to environment.yml
- CMEMS reader now takes dataset name and not product name as input, and it is possible to provide variable mapping.
- NOAA ADIOS is now default (and only) option for oil weathering, as the "built in" oil weathering module ("basic") is removed.
- GUI is generalised, to be usable for any modules. This includes taking default seed options from config:seed: (e.g. m3_per_hour for OpenOil)
- Fixed
vmaxvalue for animations with density array - Fixed animation marker color for deactivated elements
- Introduced mechanism to store environment variables from previous time step
- New element property
moving, giving possibility to temporarily freeze elements, e.g. used for sedimentation and resuspension in SedimentDrift module - Improved robustness using Xarray in netCDF-readers. Xarray is still optional dependency, but is now tested on Travis
- nc-time-axis is new dependency, providing support for cftime axis in matplotlib
- NOAA oil weathering model is now default choice in OpenOil
- Bugfix in reader_netCDF_CF_generic for particles with negative longitudes combined with global datasets with longitudes from 0-360
- Added module
SedimentDrift - Removed two options from OpenOil, with corresponding config parameters:
- Tkalich(2002) entrainment rate
- Exponential droplet size distribution
- Renamed two config settings:
processes:turbulentmixing->drift:vertical_mixingprocesses:verticaladvection->drift:vertical_advection
- OceanDrift3D and OpenDrift3D have been merged into OceanDrift, and OpenOil3D has been merged into OpenOil. Thus OpenOil and OceanDrift are now 3D modules, but can still be configured for 2D drift.
- Seed from shapefile: GDAL (ogr / osr) changed coordinate order, updates dependencies and call.
- Victor de Aguiar: :mod:`Oil drift in sea ice <opendrift.models.openoil>` following Nordam et al., 2019, doi:10.1016/j.marpolbul.2019.01.019 (Sponsored by the Fram Centre in Tromsø, through the MIKON/OSMICO project).
- OpenBerg module available from the GUI.
- A generic shape reader for landmasks (use polygons directly or convenience method using shp files).
- Drop rasterio dependency and include some significant thread-safety fixes for landmask-data.
- Specifying a positive time step with a negative duration is now an error. Duration should always be specified positive.
- Basemap reader and basemap plotting removed
- Minor improvements and bug fixes
- Example scripts are now available in online :doc:`gallery <gallery/index>`
- Only a single conda environment (named "opendrift"). Fresh :doc:`installation <install>` is recommended.
- Cartopy is used for plotting (with fast option only using raster, see :meth:`opendrift.models.basemap.plot`)
- GSHHS full is used for a dedicated landmask reader (using full resolution always, possibly to :mod:`only use mask <opendrift.readers.reader_global_landmask>` for faster simulations)
- New documentation at https://opendrift.github.io
- Conda packages at https://anaconda.org/OpenDrift/repo
- Pypi packages
- OilLibrary also ported to Python 3
- Python 2 support dropped (but may still work for a while)