Issue with MED to XDMF Conversion in FESTIM Workshop 8

User Support
1

Hello,

I’m learing how to use FESTIM and currently working on Workshop 8. I downloaded the mesh.med file from GitHub, but when I run the script, it doesn’t work.
Here’s the code I’m using:

Import meshio

def convert_med_to_xdmf(
    med_file,
    cell_file="mesh_domains.xdmf",
    facet_file="mesh_boundaries.xdmf",
    cell_type="tetra",
    facet_type="triangle",
):
    """Converts a MED mesh to XDMF
    Args:
        med_file (str): the name of the MED file
        cell_file (str, optional): the name of the file containing the
            volume markers. Defaults to "mesh_domains.xdmf".
        facet_file (str, optional): the name of the file containing the
            surface markers.. Defaults to "mesh_boundaries.xdmf".
        cell_type (str, optional): The topology of the cells. Defaults to "tetra".
        facet_type (str, optional): The topology of the facets. Defaults to "triangle".
    Returns:
        dict, dict: the correspondance dict, the cell types
    """
    msh = meshio.read(med_file)

    correspondance_dict = msh.cell_tags

    cell_data_types = msh.cell_data_dict["cell_tags"].keys()

    for mesh_block in msh.cells:
        if mesh_block.type == cell_type:

            meshio.write_points_cells(
                cell_file,
                msh.points,
                [mesh_block],
                cell_data={"f": [-1 * msh.cell_data_dict["cell_tags"][cell_type]]},
            )
        elif mesh_block.type == facet_type:
            meshio.write_points_cells(
                facet_file,
                msh.points,
                [mesh_block],
                cell_data={"f": [-1 * msh.cell_data_dict["cell_tags"][facet_type]]},
            )

    return correspondance_dict, cell_data_types
correspondance_dict, cell_data_types = convert_med_to_xdmf("mesh.med", cell_file="mesh_domains.xdmf", facet_file="mesh_boundaries.xdmf")

print(correspondance_dict)

However, I get the following error:

File "/home/ndrea_i_aio/festim/CAD integration.py", line 47, in <module>
  correspondance_dict, cell_data_types = convert_med_to_xdmf("mesh.med", cell_file="mesh_domains.xdmf", facet_file="mesh_boundaries.xdmf")

File "/home/ndrea_i_aio/festim/CAD integration.py", line 27, in convert_med_to_xdmf
  cell_data_types = msh.cell_data_dict["cell_tags"].keys()
KeyError: 'cell_tags'

How can I solve this issue?

Thank you in advance!

2

Hi @Andrea!

I could not reproduce your issue neither via pulling the Jupyter book from git, nor via making a standalone script.

Would you mind checking the downloaded med-file (or sharing it here) and the installed dependencies (e.g. environment the installation procedure of which is described on the Workshop main page)? The task also works fine in Binder

3

Thank you for your prompt reply!

I’m linking the downloaded .med file below.
I installed meshio using Conda, following the instruction provided on https://github.com/nschloe/meshio, and I verified that all dependencies are installed correctly.

I hope this answers all your questions—please let me know if you need anything else.
mesh.zip (1.8 MB)

4

@Andrea what cells do you have in your mesh? tetrahedra? triangles?

By default, cell_type defaults to "tetra" and facet_type defaults to "triangle".

For exampe, if you have a 2D mesh with triangles for cells then you need

convert_med_to_xdmf(
    med_file,
    cell_file="mesh_domains.xdmf",
    facet_file="mesh_boundaries.xdmf",
    cell_type="triangle",
    facet_type="line",
)
5

Also, what version of meshio are you using?

6

Thank you very much for your help.

I’m using version 5.3.5 of meshio. I replaced the mesh.med file from GitHub with the one used in the Binder environment, and now everything works correctly.

Thanks again for the support!

1 Like
7

@Andrea glad that things are now working!

The files in Github and Binder are the exact same files (because Binder is nothing more than a copy of the github repository with the installed dependencies).

The issue was somewhere else probably.

:smiley:

1 Like