Comments (5)
After discussion with the CSIRO regarding the grid, it was discovered that the data was re-grid from C-grid to A-grid already as raw output. There are working with the dimensions, I was able to get the code running. Code is here:
https://github.com/Dinga1990/Drifter_eReefs/blob/main/Parcels%20with%20eReef%20simple.ipynb
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Hello, greetings from WA
A few things:
- Would you mind uploading a NetCDF file to WeTransfer? I'm not familiar with subsetting data from OPeNDAP, and the UI wasn't intuitive to me.
- Would you mind providing a reproducible code sample, and your full error log? See here for how you can include code in GitHub with or without syntax highlighting.
Having the data + code + full error log will allow us to replicate the issue, and better help.
Just a heads up, I don't really have time to give this a proper look this weekend. I'll see if I can take a closer look Mon/Tues.
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Here is a PDF of the code that I'm working through Ereef_parcels-daily - GITHUB.pdf
The error that I'm getting is
ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 2, the array at index 0 has size 2389 and the array at index 1 has size 1021
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@VeckoTheGecko Thanks! I didn't expect answers on the weekend so any help is better than me going in spirals.
The native file is 7GB, so WeTransfer will not work. Here is the direct data link:
https://dapds00.nci.org.au/thredds/fileServer/fx3/gbr1_2.0/gbr1_simple_2022-05-01.nc
I will work on the second part tonight.
Edit: I wasn't sure how to do this another way, but I have uploaded my code here and created a simple example based on the NEMO tutorial. https://github.com/Dinga1990/Drifter_eReefs/blob/main/Parcels%20with%20eReef%20simple.ipynb
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One word of warning -- using C-grid model data that has been re-gridded to A-grid will lead to problems near all solid boundaries, as the flow field boundary condition of no-flow through the bottom is not generally captured by the A-grid data. At a minimum, this will cause problems with particles moving through land or bottom boundaries. It is MUCH, MUCH better to use the original C-grid data. Happy to chat more about this.
You will see this as a problem if you see particles going into the bottom or onto land...
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Related Issues (20)
- Integration tests being skipped HOT 1
- Problem with the simulations outputs in .zarr format HOT 2
- Particles interaction with land-mask HOT 2
- CalledProcessError with RuntimeError on a PC HOT 6
- Breaking integration test CI on example_dask_chunk_OCMs.py
- Create kernels from list of Python functions HOT 4
- LaTeX equations in documentation HOT 4
- Geospatial tutorial HOT 3
- Resuming an interrupted run
- Getting a "Correct cell not found" and no results for a simulation HOT 4
- Reading EFDC NetCDF output into Parcels HOT 16
- issues running regridded ROMS HOT 9
- OutOfBoundsError when particle reaches the North Pole (~ 89.5 deg N)
- Kernel Died Automatically (Ocean Parcels) HOT 2
- OutOfBoundError: I have this code from parcel but it looks like if the particle trajects at shallow depths, it produces an OutOfBounds Error message. I would like to either delete the particles that falls out of the domain or have it bounced back to its original position. I included the 'deleteparticle' function and also produces a different error message. Any help will be much appreciated. Thanks HOT 1
- Broken readthedocs for geospatial tutorial
- `parcels_get_examples` deprecation notice HOT 2
- Cleaning python install process and setup.py
- Typo in documentation of `time_periodic` argument of Fieldset constructors HOT 1
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