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

[stargolike]

today i upgrade my mace, and i meet this problem. it's not good idea, yesterday i can use extxyz and now i can't.

[ilyes319]

just change your extension to .xyz for now.

[gabor1]

ASE changes its behaviour randomly... we are aware of it.

[bernstei]

yesterday i can use extxyz and now i can't.

I'm actually very surprised that using extxyz isn't working. If anything, I'd expect ASE to have decided that plain xyz is not for extxyz.

@stargolike can you say precisely what versions of mace and ase you're trying to use? I just confirmed that the latest ase (3.23.0) reads .xyz and .extxyz suffix files with no problem.

[bernstei]

just change your extension to .xyz for now.

@ilyes319 Did you actually change something in MACE to cause this change?

[stargolike]

ASE changes its behaviour randomly... we are aware of it.

thanks, it's good method.

[stargolike]

ASE changes its behaviour randomly... we are aware of it.

it sounds so sad :(

[stargolike]

just change your extension to .xyz for now.

i solve the problem, thank you.

[stargolike]

just change your extension to .xyz for now.

@ilyes319 Did you actually change something in MACE to cause this change?

I newly reinstalled MACE, so I met this problem

[bernstei]

@ilyes319 Did you actually change something in MACE to cause this change?

I newly reinstalled MACE, so I met this problem

I was asking @ilyes319 if he intentionally changed anything in MACE to cause this. Because there's really no reason it should start happening, unless he hard-wired something, which isn't a great idea.

[bernstei]

@ilyes319 Did you actually change something in MACE to cause this change?

I newly reinstalled MACE, so I met this problem

I was asking @ilyes319 if he intentionally changed anything in MACE to cause this. Because there's really no reason it should start happening, unless he hard-wired something, which isn't a great idea.

Never mind - I see in the original post that started this thread that .xyz is hardwired. I stand by my statement that it should just defer to what ASE can read. A PR would be essentially trivial, but I don't know what branch to base it on. @ilyes319 ?

[stargolike]

@ilyes319 Did you actually change something in MACE to cause this change?

I newly reinstalled MACE, so I met this problem

I was asking @ilyes319 if he intentionally changed anything in MACE to cause this. Because there's really no reason it should start happening, unless he hard-wired something, which isn't a great idea.

i use

pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu116
git clone https://github.com/ACEsuit/mace.git
pip install ./mace

today i reinstall MACE in a new machine, and i think when i'm running this command, the lastest version ASE was installed.

[gabor1]

We could temporarily pin ASE 3.22 like everyone else...

[bernstei]

OMFG. No. This has _nothing_ to do with ASE's version. ".xyz" is hard-coded into MACE, for no good reason.

[bernstei]

OMFG. No. This has nothing to do with ASE's version. ".xyz" is hard-coded into MACE, for no good reason.

It needs to distinguish .h5 from things that are read with ase.io.read, but that's the only issue. It's easy to clean up, as soon as I know what branch to do it relative to.

[venkatkapil24]

Yes, this is a mace issue. I can only read .xyz or .h5.

[bernstei]

PR coming soon.