Error reading 'extended' xyz format files

[venkatkapil24]

Describe the bug
MACE returns error for an ".extxyz" file.

Traceback (most recent call last):
File "/home/ucapvka/source/mace/scripts/run_train.py", line 6, in
main()
File "/lustre/home/ucapvka/mace-venv/lib/python3.9/site-packages/mace/cli/run_train.py", line 157, in main
assert args.train_file.endswith(".xyz"), "Must specify atomic_numbers when using .h5 train_file input"
AssertionError: Must specify atomic_numbers when using .h5 train_file input

Typically XYZ files do not include anything other than positions/velovities. On the other hand, the extended XYZ in ASE/libatoms '.extxyz' is the standard format. I think MACE should include it and not assume .h5. Again, happy to open a quick PR.

[ilyes319]

Hey @venkatkapil24, MACE can read extended xyz, but you need to rename the extension just .xyz.

[bernstei]

That's essentially a bug, I'd argue. If anything, I'd say it should required ".extxyz"

[gabor1]

I agree it should accept both .xyz and .extxyz

[bernstei]

I'm not even convinced it should check anything except, I guess, special-casing .h5. Anything else it could just pass to ase.io.read and let it deal with it automatically.

[venkatkapil24]

I'm not even convinced it should check anything except, I guess, special-casing .h5. Anything else it could just pass to ase.io.read and let it deal with it automatically.

I agree. This will also help read directly from json.

[bernstei]

I agree. This will also help read directly from json.

iff it's json that ase.io.read can parse