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bjmorgan / kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.
https://kinisi.readthedocs.io
MIT License
49 stars 11 forks source link

Support for ASE trajectory objects #31

Closed alexsquires closed 1 year ago

alexsquires commented 1 year ago

Any plans to support ASE trajectory objects in the parsing functionality? https://wiki.fysik.dtu.dk/ase/ase/io/trajectory.html#trajectory

In principle, you can get at it from pymatgen.io.ase.AseAtomsAdaptor and then work with the pymatgen parser, but that can be quite a large computational overhead.

If it's not something you've considered, is it something you'd be interested in a contribution for?

alexsquires commented 1 year ago

I've just seen this was mentioned in #22 - at least I'm not the only one.

arm61 commented 1 year ago

I was just about to link that previous issue.

It is definitely something I want to support (ideally “natively” instead of introducing computational overhead). But I just haven’t found the time to add it. Given your more experienced with ase, I would be happy to get a contribution (I can obviously help with your understanding of what kinisi expects) and it would save me time!

alexsquires commented 1 year ago

I'm on it. I'll come back with a draft when it's ready

alexsquires commented 1 year ago

draft in #32

alexsquires commented 1 year ago

Great, this is now addressed from my end, and I assume the wider questions about file reading can be tackled separately