Add support for having non-displaced atoms in Phonopy routines

[tomdemeyere]

Summary of Changes

Should be much better

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• I have added relevant, comprehensive unit tests.

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[buildbot-princeton]

Can one of the admins verify this patch?

[Andrew-S-Rosen]

@tomdemeyere: Thank you for taking the time to revisit this. It is certainly a lot cleaner and is very easy to follow now! I have some minor comments below, none of which are anything crazy. Overall, very clever modification to the original approach!

I do just have one question: the additional_atoms is an interesting idea. I'm curious to hear more about how you intend to use this in practice (or see people using it in practice).

In surface catalysis, I am most familiar with the opposite scenario to some degree. To calculate thermochemical corrections, people will invoke weak coupling between adsorbate and the metal surface. They'll then vibrate the adsorbate atoms and, perhaps, a few of the adjacent atoms on the surface while fixing the rest. They'll then use the harmonic approximation (e.g. with ASE utilities) to calculate the corrections. This is implicitly assuming that when you compare the energies of two different states along the reaction coordinate, the vibrational modes of the slab are effectively unchanged.

Here, it looks like it's almost the opposite perspective. I guess that's simply because here you are trying to calculate the phonon spectra of the material? Is that right? If doing so, wouldn't fixing a few adsorbate atoms not really make a big difference compared to the size of the slab?

[Andrew-S-Rosen]

Note to self: we'll want to add this parameter to the other recipes calling the phonon_subflow (tblite and MLP I think?).

[tomdemeyere]

Overall additional atoms can be seen as the same to "fixed_atoms". I renamed it to put an emphasis on the fact that these atoms are merely spectators of the Phonons calculation, only having an implicit influence through the forces. When you think about this has nothing to do with "fixing".

If you want to calculate an adsorbate on a slab that way you would just send the adsorbate part to regular atoms and the slab as "additional_atoms".

This could be renamed as "fixed_atoms" as well, I am trying to explore the semantic here

[Andrew-S-Rosen]

Overall additional atoms can be seen as the same to "fixed_atoms". I renamed it to put an emphasis on the fact that these atoms are merely spectators of the Phonons calculation, only having an implicit influence through the forces. When you think about this has nothing to do with "fixing".

If you want to calculate an adsorbate on a slab that way you would just send the adsorbate part to regular atoms and the slab as "additional_atoms".

This could be renamed as "fixed_atoms" as well, I am trying to explore the semantic here

To clarify, I understand that part. My question was about understanding why and when this is relevant, given that it is the opposite from what is usually invoked in the literature.

Edit: Ah, you are saying the slab would go to additional atoms. Sure, that makes sense. I think that conflicts with what you wrote in one of the docstrings. I think additional_atoms makes sense.

[Andrew-S-Rosen]

Historically, in such scenarios, I have used ASE's Vibrations module (specifying the atoms to vibrate with indices) and then passed that information into ASE's HarmonicThermo class. However, using phonopy for this seems like it might be even better because it would be possible to run the displacement calculations in parallel rather than sequentially.

At some point, I was going to add HarmonicThermo to quacc.runners.thermochemistry to support this, but the phonopy approach is great.

[Andrew-S-Rosen]

What if we rename the first positional argument to unfixed_atoms and then additional_atoms as fixed_atoms? Not sure if that helps or hurts...

[tomdemeyere]

Claude 3 Opus is suggesting (😅):

1. primary_atoms (instead of atoms) and auxiliary_atoms
2. atoms and fixed_atoms
3. displaced_atoms (instead of atoms) and nondisplaced_atoms

In this order of "preference", I might actually lean towards 2, (let's just be pragmatic?)

EDIT: To be fair, 3 looks like your last suggestion but without the double negative of "unfixed", this might be the best option to clearly distinguish between what is being moved and the rest, "nondisplaced_atoms" might just be "fixed_atoms" for simplicity?

[Andrew-S-Rosen]

Ooh I like 3! It's better than my suggestion because it doesn't accidentally imply a FixAtoms constraint. But I'm okay with 2 if you have a strong opinion about it.

[tomdemeyere]

That's a good argument let's go with that, I just added an extra underscore

[tomdemeyere]

This is a little bit problematic, another option is to send both displaced and non_displaced and optimise them and separate them again...

[Andrew-S-Rosen]

I see. I mean, I guess we can ask if we really even need a relaxation step beforehand? Presumably one could just call relax_job() before calling the flow and it would be exactly the same (although without a tight force tolerance).

If there's a desire to keep this though, then yeah I think the only route would be to relax displaced_atoms+non_displaced_atoms as a single combined_atoms and then pass in combined_atoms[:len(displaced_atoms)] etc. to phonon_subflow. It does, admittedly, complicate things a bit because it seems weird to relax something that is called "non-displaced", but... 🤷

[tomdemeyere]

@Andrew-S-Rosen

I did not forget this PR, as you may know I am very busy currently, I will definitely come back to it ASAP!

[Andrew-S-Rosen]

There is no rush at all :) Good luck with wrapping up the PhD!

[tomdemeyere]

I have some more time to do what I like now :)

I added some of your suggestions, namely:

• The type hinting in the internal _thermo_job
• Fixed the unnecessary comments
• Added a test for the get_phonopy_supercell

You will see that I added the non_displaced_atoms object to additional_fields in the phonopy_subflow. I did it because otherwise the result dict does not contain any information about these atoms at all. There might be a better way to do this? I will let you decide.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.42%. Comparing base (97b5923) to head (495c99b).

Additional details and impacted files

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+ Hits         3427     3440   +13     
  Misses         91       91           

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