search

MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
https://mdanalysis.org
Other
1.3k stars 648 forks source link

Interoperability with PyIron #3880

Open hmacdope opened 1 year ago

hmacdope commented 1 year ago

Is your feature request related to a problem?

PyIron is a growing package ecosystem focused on streamlining materials science workflows and running calculations at scale.

Similar to discussions surrounding ASE in #3827 PyIron has a great series of tools for running simulations and capacity for simulation analysis. It would likely be beneficial to both parties be able to seamlessly move between PyIron objects and MDA universes.

It may be possible to build this bridge via ASE (#3827) as IIRC PyIron has ASE interoperability.

Tagging @jan-janssen (hopefully you get this) to let you know that this is on our radar. :)

Anyone feel free to let me know anything I may have missed.

jan-janssen commented 1 year ago

Hi @hmacdope, we are definitely interested to grow the ecosystem and as you already mentioned as the pyiron atoms class is directly derived from the ASE atoms class it should be easy to interface with pyiron once an ASE interface is in place. In terms of trajectories, the ASE and pyiron formats are currently slightly different, but we are working on improving the compatibility there as well.

IAlibay commented 1 year ago

Once I get the mdakits repo to a working state (docs finally build 🎉 ), I'm going to start putting together that converter mdakit for all things GPL-like (including that long fabled ASE converter I had to put on halt again). We can target that there if there's an ASE dependency?

hmacdope commented 1 year ago

Yeah I think that is likely the best way forward for now. :)