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Parcels within eReefs GBR about parcels HOT 5 CLOSED

Dinga1990 avatar Dinga1990 commented on August 10, 2024 1
Parcels within eReefs GBR

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Comments (5)

Dinga1990 avatar Dinga1990 commented on August 10, 2024 2

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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VeckoTheGecko avatar VeckoTheGecko commented on August 10, 2024 1

Hello, greetings from WA 😄 . I think building in compatability for parcels to act natively with model output is a great idea.

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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Dinga1990 avatar Dinga1990 commented on August 10, 2024

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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Dinga1990 avatar Dinga1990 commented on August 10, 2024

@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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JamiePringle avatar JamiePringle commented on August 10, 2024

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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