Are FESOM2 mesh files (ASCII or NetCDF) supported ?

[fluidnumerics-joe]

I noticed a couple issues that mention FESOM (#425 and #282) but the documentation does not indicate that FESOM2 is supported. In a separate project, I am working with a few folks to add unstructured grid support to Ocean Parcels, and we're keen on trying to use UXArray to support file IO and the unstructured mesh descriptions.

I've documented a simple example here that shows we can't read FESOM2 NetCDF files at the moment, so I may have answered my question.

Nonetheless, if FESOM2 support is not in the works already, how can I help get this going ?

[philipc2]

Hi @fluidnumerics-joe

We haven't done much testing or exploration of FESOM grids, though we would love to support them directly. I'm taking a look at some of the grids listed in ELPHE-WW/unstructured-mesh-parcels-sandbox#2 and will follow up shortly.

Nonetheless, if FESOM2 support is not in the works already, how can I help get this going ?

Here are references for all of our supported grid readers. https://github.com/UXARRAY/uxarray/tree/main/uxarray/io

All we need is to implement a FESOM to UGRID conversion module, supporting at least the following minimal grid representation to follow to the UGRID conventions

• Corner Node Coordinates (typically lat/lon, but Cartesian are acceptable)
• Face Node Connectivity (Indices of the corner nodes that make up each face)

[philipc2]

Would you mind sharing the FESOM grid you used in the simple example notebook?

[fluidnumerics-joe]

Of course. The one example I'm working with to start is here : https://github.com/FESOM/fesom2/tree/main/test/meshes/soufflet

[erogluorhan]

Hi @fluidnumerics-joe , thanks a lot for reaching out! We can work together to investigate getting FESOM grids supported by UXarray.

As #282 and your example suggested, there might be some UGRID conformance issues with FESOM grids, but we can dig into them all together to figure.

[fluidnumerics-joe]

Loading just the vertices and face connectivity can be done with

def load_ascii_mesh(mesh_path):
    """
    Loads the mesh data from the specified path and returns the node coordinates and element connectivity.
    FESOM specific function.

    Args:
        mesh_path (str): The path to the directory containing the model output.

    Returns:
        xr.Dataset: Dataset containing the x-coordinates, y-coordinates, and element connectivity array.

    """
   import pandas as pd
  import numpy as np
  import xarray as xr
    nodes = pd.read_csv(
        mesh_path + "/nod2d.out",
        delim_whitespace=True,
        skiprows=1,
        names=["node_number", "x", "y", "flag"],
    )

    x2 = nodes.x.values
    y2 = nodes.y.values

    file_content = pd.read_csv(
        mesh_path + "/elem2d.out",
        delim_whitespace=True,
        skiprows=1,
        names=["first_elem", "second_elem", "third_elem"],
    )

    x2 = np.where(x2 > 180, x2 - 360, x2)

    elem = file_content.values - 1

    ds = xr.Dataset(
        {
            "x": (("nod2"), x2),
            "y": (("nod2"), y2),
            "elements": (("elem", "n3"), elem),
        }
    )

    return ds
    
    

This would set the face dimensions (called elements here) correctly

[philipc2]

@fluidnumerics-joe

Thanks for the example! I've opened up a pull request (#1013) for this. Will work on it this week.