Add support for having non-displaced atoms in Phonopy routines #2110

tomdemeyere · 2024-05-10T08:14:10Z

Summary of Changes

Should be much better

Checklist

I have read the "Guidelines" section of the contributing guide. Don't lie! 😉
My PR is on a custom branch and is not named main.
I have added relevant, comprehensive unit tests.

Notes

Your PR will likely not be merged without proper and thorough tests.
If you are an external contributor, you will see a comment from @buildbot-princeton. This is solely for the maintainers.
When your code is ready for review, ping one of the active maintainers.

…y_fixed_atoms

buildbot-princeton · 2024-05-10T08:14:13Z

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?

src/quacc/atoms/phonons.py

src/quacc/recipes/common/phonons.py

Andrew-S-Rosen · 2024-05-10T15:32:10Z

src/quacc/recipes/emt/phonons.py

@@ -27,6 +27,7 @@ def phonon_flow(
        tuple[tuple[int, int, int], tuple[int, int, int], tuple[int, int, int]] | None
    ) = None,
    displacement: float = 0.01,
+    additional_atoms: Atoms | None = None,


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

tests/core/atoms/test_phonons.py

src/quacc/atoms/phonons.py

tests/core/recipes/emt_recipes/test_emt_phonons.py

tomdemeyere · 2024-05-10T16:37:53Z

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 · 2024-05-10T16:44:12Z

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.

src/quacc/recipes/common/phonons.py

Andrew-S-Rosen · 2024-05-10T16:53:23Z

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 · 2024-05-10T17:41:45Z

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 · 2024-05-10T17:54:03Z

Claude 3 Opus is suggesting (😅):

primary_atoms (instead of atoms) and auxiliary_atoms
atoms and fixed_atoms
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 · 2024-05-10T17:57:39Z

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 · 2024-05-10T18:00:38Z

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

tomdemeyere · 2024-05-10T18:08:54Z

src/quacc/recipes/emt/phonons.py

@@ -92,15 +98,16 @@ def phonon_flow(
        parameters=job_params,
        decorators=job_decorators,
    )
-    if run_relax:
+    if run_relax and not non_displaced_atoms:


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

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... 🤷

…nopy_fixed_atoms_v2

tomdemeyere · 2024-07-15T20:00:49Z

@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 · 2024-07-15T20:28:39Z

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

tomdemeyere · 2024-10-06T11:43:28Z

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 · 2024-10-06T11:46:33Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.42%. Comparing base (7fef05b) to head (3c9bb51).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2110      +/-   ##
==========================================
+ Coverage   97.41%   97.42%   +0.01%     
==========================================
  Files          85       85              
  Lines        3518     3536      +18     
==========================================
+ Hits         3427     3445      +18     
  Misses         91       91

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Andrew-S-Rosen

@tomdemeyere: What a surprise! Thanks for taking care of this. I think it will be a very nice feature.

I left a few very minor comments but am happy to merge thereafter. I think your changes make a lot of sense.

Andrew-S-Rosen · 2024-10-06T22:11:07Z

src/quacc/recipes/common/phonons.py

@@ -89,17 +117,25 @@ def _get_forces_subflow(supercells: list[Atoms]) -> list[dict]:
    @job
    def _thermo_job(
        atoms: Atoms,
-        phonopy: Phonopy,
+        phonopy,


Looks like we lost a type hint.

Andrew-S-Rosen · 2024-10-06T22:12:30Z

src/quacc/recipes/common/phonons.py

+    displaced_atoms: Atoms,
    force_job: Job,
+    non_displaced_atoms: Atoms | None = None,


Out of curiosity, what is the motivation to have two separate Atoms objects rather than one Atoms objects for the full thing and specific indices to not displace? It seems like it might be a bit awkward if they are separate Atoms objects because wouldn't the user have to split up their Atoms object into two before calling this function? I'm sure there's a reason for your suggestion --- just trying to pick up on what it is. We may have gone over this a long time ago.

In commit "24608c9" I left a comment.

I think we moved out of this approach to the "FixAtoms" approach, but that did not work as well so we ended up here.

@tomdemeyere: Apologies if we're revisiting history here (it's been a while...). I'm not sure the commit shows the comment, but my question is mostly about what if we had an Atoms object as input with a list[int] of indices to not displace. Was there an issue with that approach? If so, we can stick with what you have here.

src/quacc/recipes/common/phonons.py

tomdemeyere · 2024-10-07T12:37:59Z

src/quacc/recipes/common/phonons.py

@@ -31,6 +32,7 @@ def phonon_subflow(
    atoms: Atoms,
    force_job: Job,
    relax_job: Job | None = None,
+    fixed_atoms: list[int] | None = None,


Do we want to come back to this approach?

@tomdemeyere: Ah, we did that before. Sorry for the memory issues..........

Let me read up on what happened before.

tomdemeyere · 2024-10-07T12:38:52Z

src/quacc/recipes/common/phonons.py

+    displaced_atoms: Atoms,
    force_job: Job,
+    non_displaced_atoms: Atoms | None = None,


In commit "24608c9" I left a comment.

I think we moved out of this approach to the "FixAtoms" approach, but that did not work as well so we ended up here.

Andrew-S-Rosen · 2024-10-07T14:44:06Z

@tomdemeyere: Sorry about the back-and-forth. Could you remind me the motivation to switch from specifying a list[int] to two Atoms objects?

Otherwise, once the type hint is fixed, I'll merge pending resolution of the above discussion.

tomdemeyere · 2024-10-08T15:20:23Z

@Andrew-S-Rosen I don't really remember, this might be linked to other problems at the time.

It seems that changing to the index approach is rather straightforward, and might make more sense?

Andrew-S-Rosen · 2024-10-08T15:22:40Z

Let's give it a go and see what happens! It seems a tad easier on the user in my opinion. Since it should also support negative indexing, that should make things pretty trivial for the user since it's usually the last N indices where an adsorbate is.

tomdemeyere · 2024-10-11T15:06:11Z

@Andrew-S-Rosen Tell me what you think.

I also made sure that the Schema returns the same Atoms object as the one being sent. I also included non_displaced_atoms and displaced_atoms when relevant.

Andrew-S-Rosen · 2024-10-11T15:28:07Z

Thanks! This looks great! Happy to merge!

tomdemeyere and others added 9 commits May 5, 2024 00:51

initial

d2aa51a

done

24608c9

fix

d6deffc

fix?

1f31546

suggestions

a7b3a0c

pre-commit auto-fixes

38a4230

tests

7430b8a

Merge remote-tracking branch 'origin/phonopy_fixed_atoms' into phonop…

6939b90

…y_fixed_atoms

initial

54c4e5f

tomdemeyere and others added 2 commits May 10, 2024 09:25

Merge branch 'main' into phonopy_fixed_atoms_v2

b7789d2

pre-commit auto-fixes

5536691

Andrew-S-Rosen reviewed May 10, 2024

View reviewed changes

tests/core/recipes/emt_recipes/test_emt_phonons.py Show resolved Hide resolved

Andrew-S-Rosen reviewed May 10, 2024

View reviewed changes

src/quacc/recipes/common/phonons.py Outdated Show resolved Hide resolved

tomdemeyere and others added 3 commits May 10, 2024 19:04

some changes

93a66a6

some changes

75b8f9f

pre-commit auto-fixes

56fc1ac

tomdemeyere commented May 10, 2024

View reviewed changes

tomdemeyere added 2 commits May 10, 2024 19:09

some changes

b98984e

Merge remote-tracking branch 'origin/phonopy_fixed_atoms_v2' into pho…

15f4469

…nopy_fixed_atoms_v2

Andrew-S-Rosen mentioned this pull request May 10, 2024

Phonopy: fixing atoms #2073

Closed

3 tasks

Andrew-S-Rosen changed the title ~~Demeyere phonopy fixed atoms v2~~ Add support for having non-displaced atoms in Phonopy routines May 10, 2024

Andrew-S-Rosen and others added 9 commits June 11, 2024 19:39

Update phonons.py

2f3e943

pre-commit auto-fixes

1d710db

Update phonons.py

7329f9b

fix

e102d40

fix

98d0274

Update phonons.py

4f1027e

Merge branch 'main' into phonopy_fixed_atoms_v2

0dec274

Merge branch 'main' into phonopy_fixed_atoms_v2

5f99ce4

Merge branch 'main' into phonopy_fixed_atoms_v2

b87a8f7

Andrew-S-Rosen and others added 5 commits July 27, 2024 11:41

Merge branch 'main' into phonopy_fixed_atoms_v2

5ff4044

Merge branch 'main' into phonopy_fixed_atoms_v2

626ab00

Merge branch 'main' into phonopy_fixed_atoms_v2

9bc911c

Merge branch 'main' into phonopy_fixed_atoms_v2

bf17288

suggestions + test + non_displaced_atoms in additional_fields

495c99b

Andrew-S-Rosen reviewed Oct 6, 2024

View reviewed changes

tomdemeyere commented Oct 7, 2024

View reviewed changes

fixed_atom_indices

6c3fc90

pre-commit auto-fixes

5eac754

Andrew-S-Rosen enabled auto-merge (squash) October 11, 2024 15:28

Merge branch 'main' into phonopy_fixed_atoms_v2

3c9bb51

Andrew-S-Rosen merged commit e99d41a into Quantum-Accelerators:main Oct 11, 2024
20 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add support for having non-displaced atoms in Phonopy routines #2110

Add support for having non-displaced atoms in Phonopy routines #2110

tomdemeyere commented May 10, 2024

buildbot-princeton commented May 10, 2024

Andrew-S-Rosen left a comment •

edited

Loading

Andrew-S-Rosen May 10, 2024

tomdemeyere commented May 10, 2024

Andrew-S-Rosen commented May 10, 2024 •

edited

Loading

Andrew-S-Rosen commented May 10, 2024

Andrew-S-Rosen commented May 10, 2024

tomdemeyere commented May 10, 2024 •

edited

Loading

Andrew-S-Rosen commented May 10, 2024

tomdemeyere commented May 10, 2024

tomdemeyere May 10, 2024

Andrew-S-Rosen May 10, 2024 •

edited

Loading

tomdemeyere commented Jul 15, 2024

Andrew-S-Rosen commented Jul 15, 2024

tomdemeyere commented Oct 6, 2024

codecov bot commented Oct 6, 2024 •

edited

Loading

Andrew-S-Rosen left a comment

Andrew-S-Rosen Oct 6, 2024

Andrew-S-Rosen Oct 6, 2024

tomdemeyere Oct 7, 2024 •

edited

Loading

Andrew-S-Rosen Oct 7, 2024 •

edited

Loading

tomdemeyere Oct 7, 2024

Andrew-S-Rosen Oct 7, 2024

tomdemeyere Oct 7, 2024 •

edited

Loading

Andrew-S-Rosen commented Oct 7, 2024 •

edited

Loading

tomdemeyere commented Oct 8, 2024

Andrew-S-Rosen commented Oct 8, 2024

tomdemeyere commented Oct 11, 2024

Andrew-S-Rosen commented Oct 11, 2024

Add support for having non-displaced atoms in Phonopy routines #2110

Add support for having non-displaced atoms in Phonopy routines #2110

Conversation

tomdemeyere commented May 10, 2024

Summary of Changes

Checklist

Notes

buildbot-princeton commented May 10, 2024

Andrew-S-Rosen left a comment • edited Loading

Choose a reason for hiding this comment

Andrew-S-Rosen May 10, 2024

Choose a reason for hiding this comment

tomdemeyere commented May 10, 2024

Andrew-S-Rosen commented May 10, 2024 • edited Loading

Andrew-S-Rosen commented May 10, 2024

Andrew-S-Rosen commented May 10, 2024

tomdemeyere commented May 10, 2024 • edited Loading

Andrew-S-Rosen commented May 10, 2024

tomdemeyere commented May 10, 2024

tomdemeyere May 10, 2024

Choose a reason for hiding this comment

Andrew-S-Rosen May 10, 2024 • edited Loading

Choose a reason for hiding this comment

tomdemeyere commented Jul 15, 2024

Andrew-S-Rosen commented Jul 15, 2024

tomdemeyere commented Oct 6, 2024

codecov bot commented Oct 6, 2024 • edited Loading

Codecov Report

Andrew-S-Rosen left a comment

Choose a reason for hiding this comment

Andrew-S-Rosen Oct 6, 2024

Choose a reason for hiding this comment

Andrew-S-Rosen Oct 6, 2024

Choose a reason for hiding this comment

tomdemeyere Oct 7, 2024 • edited Loading

Choose a reason for hiding this comment

Andrew-S-Rosen Oct 7, 2024 • edited Loading

Choose a reason for hiding this comment

tomdemeyere Oct 7, 2024

Choose a reason for hiding this comment

Andrew-S-Rosen Oct 7, 2024

Choose a reason for hiding this comment

tomdemeyere Oct 7, 2024 • edited Loading

Choose a reason for hiding this comment

Andrew-S-Rosen commented Oct 7, 2024 • edited Loading

tomdemeyere commented Oct 8, 2024

Andrew-S-Rosen commented Oct 8, 2024

tomdemeyere commented Oct 11, 2024

Andrew-S-Rosen commented Oct 11, 2024

Andrew-S-Rosen left a comment •

edited

Loading

Andrew-S-Rosen commented May 10, 2024 •

edited

Loading

tomdemeyere commented May 10, 2024 •

edited

Loading

Andrew-S-Rosen May 10, 2024 •

edited

Loading

codecov bot commented Oct 6, 2024 •

edited

Loading

tomdemeyere Oct 7, 2024 •

edited

Loading

Andrew-S-Rosen Oct 7, 2024 •

edited

Loading

tomdemeyere Oct 7, 2024 •

edited

Loading

Andrew-S-Rosen commented Oct 7, 2024 •

edited

Loading