Hello Team, First of all, Congratulations and thanks so much for developing easy to use open source trajectory modelling software. I'm new to python and hope i can use this software for my PhD research here at University of Stavanger in Norway. I've installed Opendrift and trying to run tutorials and examples. However, when running tutorials, I'm getting error when trying to add reader from a local file and also when trying to import landmask. Can someone please guide me about this issue. I'm pasting errors below. Thanks in advance!

-------------Error while trying to add reader from a local file--------------

reader_norkyst = reader_netCDF_CF_generic.Reader('norkyst800_16Nov2015.nc') 13:40:31 INFO: Opening dataset: norkyst800_16Nov2015.nc 13:40:31 INFO: Opening file with Dataset Traceback (most recent call last): File "C:\Users\mevo.conda\envs\opendrift\lib\site-packages\opendrift\readers\reader_netCDF_CF_generic.py", line 142, in init self.Dataset = Dataset(filename, 'r') File "netCDF4_netCDF4.pyx", line 2321, in netCDF4._netCDF4.Dataset.init File "netCDF4_netCDF4.pyx", line 1885, in netCDF4._netCDF4._ensure_nc_success FileNotFoundError: [Errno 2] No such file or directory: b'norkyst800_16Nov2015.nc'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "C:\Users\mevo.conda\envs\opendrift\lib\site-packages\opendrift\readers\reader_netCDF_CF_generic.py", line 144, in init raise ValueError(e) ValueError: [Errno 2] No such file or directory: b'norkyst800_16Nov2015.nc'

-------------------- Error when importing landmask--------------------

reader_landmask = reader_global_landmask.Reader( ... extent=[2, 8, 59, 63]) 13:43:39 DEBUG: Adding new variable mappings ERROR:root:could not verify read permissions for group and others on landmask. Traceback (most recent call last): File "C:\Users\mevo.conda\envs\opendrift\lib\site-packages\opendrift_landmask_data-0.6-py3.8.egg\opendrift_landmask_data\mask.py", line 77, in check_permissions if not os.stat(self.lockf).st_mode & 0o777 == 0o777: FileNotFoundError: [WinError 2] The system cannot find the file specified: 'C:\Users\mevo\AppData\Local\Temp\landmask\.mask.dat.lock'

I'm new here, just going through the tutorial, and have a couple of very basic questions.

1. I have never fully understood the reason for the wind_drift_factor in offline particle tracking. Is it used mainly in cases where there is windage? Or is it more because the particles are assumed to be in the upper millimetres of a top layer that is perhaps a half metre or more thick? Are there any observational studies to support its use?
2. If I change 'u': 'x_sea_water_velocity' to 'u_eastward': 'x_sea_water_velocity' in my reader (and similarly for v), will the code know not to rotate by angle?

-new method based on saving and grab_frame method in matplotlib.animation writers

the new method works significantly faster when MPLBACKEND=agg is used as for
example for generation of sphinx gallery images in circleCI headless server

the previous method ( baed on FuncAnimation ) is still used in interactive
mode locally when no filename is given

-taking out the code that build filenames in sphinx gallery in separate method

-fix for comparing animations of different length (example_rungekutta_norkyst.py)

hey OpenDrift! I've finished a Docker container, along with instructions for export to Singularity (likely the more needed one for use on a shared resource) and would like to propose adding the Dockerfile and markdown document (instructions for usage, see files section in this PR for both) to the repository. I've built the container and provided it on Docker Hub, and would be happy to update when new versions are available, or help you to build it automatically on Docker Hub from the repository. Our user at Stanford reports that the Singularity container is running smoothly for her, so I am hopeful this might be useful to others.

Issues Addressed

• this will close #79

I am changing viscosity and density in the model, but there are no changes taking place (Evaporation remains same) how to change those values .... please help!!

Thanks in Advance!!!

Improvements to animation generation and saving, and on plot_vertical_distribution()

With the default parameter fastwriter=False everything is still as before sho it should be safe to merge, but I think we can use fastwriter=True in all animation(), animation_profile() and animate_vertical_distribution(), or put it True directly in _save_animation(). I tested many examples and couldn't find problems

But nice if you also check first. logger.info call in _save_animation() shows elapsed time. Check enclosed example

Hi all,

When running most of the examples (except those for OilSpil) I get the following warning:

UserWarning: No labelled objects found. Use label='...' kwarg on individual plots. warnings.warn("No labelled objects found. "

I'm relatively new to python, so maybe there is a simple solution to this but I haven't found it so far.

Thanks for any help!

I have tested the Telemac Selafin Reader and I noticed a consequent drop in performances when there are more than 30 000 particles. In comparison with the other particle tracker I know it seems very little (have done up to 10⁶ particles without much trouble). The quantity of RAM used, even with an output file, is very large (40Gb for 30000 particles). I am wondering what is the interest to always convert the projection system when you already have a metric projection with metric velocities? I would think that reprojection is one of the main culprit. Is that for Coriolis? I would think that you could avoid millions of operation of reprojection by using an approximation. The fact that each time-step of the ocean model calls the reader is also an issue as it is over-sampled most of the time. I understood that you were working on this. Finally the reader is parallelised but it is not clear if the model is. I have used OceanDrift as a model with coastline action previous

I used multiple single gfs and hycom files to run the leeway model. I have added the "standard_name" attributes to the files. The names of gfs and hycom files are as follows: gfs_1p00_sfc_wind_uv_Global_2020070600_t000.nc, gfs_1p00_sfc_wind_uv_Global_2020070600_t003.nc, ..., gfs_1p00_sfc_wind_uv_Global_2020070600_t072.nc and hycom_glb_sfc_water_uv_Global_2020070600_t000.nc, hycom_glb_sfc_water_uv_Global_2020070600_t003.nc, hycom_glb_sfc_water_uv_Global_2020070600_t072.nc. I used the wildcards simply like gfs_1p00_sfc_wind_uv_Global_2020070600_t0*.nc and hycom_glb_sfc_water_uv_Global_2020070600_t0*.nc to read these files. But there is an error: nc file does not have a aggregation dimension. How to solve the error, thanks a lot.

2021-06-21 5d629b2b julien introduced vertical mixing 2021-06-18 0160dcbf julien Debugging reader selafin the lice are now able to sense and move vertically There is a memory leak 2021-06-18 84afb9a7 julien Functional superindividuals actively swimming towards light and sinking at night 2021-06-17 f4f2a82e julien first successful loading no run yet 2021-06-16 260911ce julien Modification of variables in sea lice model minor other fiel editions 2021-06-16 4b1b1a66 julien New method for parametrisation Not working 2021-06-16 199dc25b julien use of add_config to setup the parameters Use the biomass in elements and compute the population based on proportions of the reference population (linear relation) 2021-06-16 266abf90 julien first try

This pull request will update the CircleCI recipe to build containers for all of:

• opendrift/opendrift (python 3 without oil)
• opendrift/opendrift:py2 (python 2 without oil)
• opendrift/opendrift-oil (python 2 with oil)

Specifically, containers will be built (for preview and that the build is successful) on any PRs, and then merge to master will build and deploy the same.

There's an entire namespace that includes python 2 / python 3, along with version, and these are printed in the CI and listed in the docker/README.md. I didn't get a chance to build these all locally because it would take a looong time (conda!) but thankfully we can use the parallel Circle workflow setup to run builds at the same time. This might need some tweaking, so I'm labeling as a WIP.

I renamed the Dockerfile.oil to Dockerfile.oil.py2 in anticipation that some day we will have a Python 3 too :)

Signed-off-by: Vanessa Sochat [email protected]

Hi all,

It should be quite obvious but I'm a beginner with OpenDrift, apologies! ... May someone tell me some URLs where I could download subsets for the zone and time I'm analyzing? Something similar to that: https://psl.noaa.gov/mddb2/makePlot.html?variableID=155703... but for U/V together in a nc file and for ocean currents

Thanks a lot! Best regards,

Sergio

think we should move the data in

def emission_factors(self, scrubber_type, chemical_compound):

def init_chemical_compound(self, chemical_compound = None):

out in a separate file, do you agree? what is the recommended format / way

Hi Opendrift dev team @knutfrode @gauteh , I think we came across a bug that affects the initial (i.e. at t0) and following particle positions in backward simulations.

We realized that by looking at the first timestep of our backward simulations (that use a one-off release) and noting that it wasn't the same as specified in seed_elements() (it looked like a step after the initial position specified). The problem doesn't seem to happen for forward simulations.

I prepared a set of simple simulations with constant currents so the issue can be reproduced. test_initial_position_backwards_runs.zip

Content is summarized below

• test_FORWARD.py : run a few steps in forward time
• test_BACKWARD.py : run a few steps in backward time
• test_BACKWARD_output_step_equals_simulation_step.py : run a few steps in backward time using the output step equal to simulation step They each produce a netcdf file, and these were used to make the plots below. In these, I plot the first and following particle clouds at t0, t1, t2 etc... and overlay the release location. See how the first cloud of particle is does not fit with the release location in the second plot. Using an output step equal to simulation steps seems to fix the issue (third plot down).

I'll have a go at stepping through the code to see where the issue might come from but I think you'll likely be much faster than me to pinpoint where it might come from !

Hi All

I am playing around with using ROMS input files which are stored monthly. As my OpenDrift simulations can span multiple months, I am adding the required ROMS input files as separate readers i.e. one reader per calendar month. I encounter a problem when transitioning from one month to the next, when the time in the OpenDrift simulation is not actually covered by either file i.e. the last date of one file might be 2005-01-31 00:00:00 and the first time-step of the next file would be 2005-02-01 00:00:00, so neither reader covers the time between these two files, and so OpenDrift terminates at 2005-01-31 00:00:00.

I am presently getting around this by using netcdf operators to add the first time-step of the each file to the end of the file for the previous month. This solves my problem, but I was wondering if there is another way around the problem without having to edit the input files? There are probably others out there who have tried to run simulations using multiple monthly ROMS input files?

Thanks in advance! Giles

• Data integrity: reduce chance of aliasing
  • Less chance of confusion
  • Can reuse init object, since it is not mutated by simulation
  • Since it can be reused it can be used for parallelization
• Methods can only be run on a simulation that is in a valid state:
  • Plot is only meaningful on result (at least as it is)
• Easier to separate data from functionality:
  • Result should (hopefully) have a single data member (xarray dataset?), with some convenience methods
• Generic Analysis package can work on this data member, and thus be non-opendrift specific.
• Less coupled code: maintenance should be easier and more fun!