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

tomdemeyere · 2024-05-10T08:14:10Z

Summary of Changes

Should be much better

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I have added relevant, comprehensive unit tests.

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…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

Andrew-S-Rosen · 2024-05-10T15:19:42Z

src/quacc/atoms/phonons.py

+    supercell_matrix
+        The supercell matrix to use. If specified, it will override any
+        value specified by `min_lengths`.
+    Returns


Missing a line break before Returns.

Andrew-S-Rosen · 2024-05-10T15:20:25Z

src/quacc/atoms/phonons.py

+        The supercell matrix to use. If specified, it will override any
+        value specified by `min_lengths`.


There is no min_lengths in this function. I think we can just ignore that part. Also, it must be specified since it is a positional argument.

Andrew-S-Rosen · 2024-05-10T15:21:31Z

src/quacc/recipes/common/phonons.py

+    In Quacc the ASE constraints can be used to fix atoms. These atoms will
+    not be displaced during the phonon calculation. This will greatly reduce
+    the computational cost of the calculation. However, this is an important
+    approximation and should be used with caution.


I don't think this is relevant anymore.

Andrew-S-Rosen · 2024-05-10T15:21:49Z

src/quacc/recipes/common/phonons.py

    if has_deps:
-        from phonopy import Phonopy
+        pass


Seems to be unnecessary.

src/quacc/recipes/common/phonons.py

Andrew-S-Rosen · 2024-05-10T15:31:07Z

src/quacc/recipes/common/phonons.py

+        phonopy,
        force_job_results: list[dict],
-        t_step: float,
-        t_min: float,
-        t_max: float,
-        additional_fields: dict[str, Any] | None,
+        t_step,
+        t_min,
+        t_max,
+        additional_fields,


I assume you just removed the type hints for brevity's sake since they are basically implied elsewhere? I was also thinking about this since it is an internal function. Although, if we at some point enabled static type checking, having the type hints would ensure there isn't an error. I doubt we will be able to get to the point where we enable static type checking though... certainly not anytime soon.

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?).

Andrew-S-Rosen · 2024-05-10T15:33:02Z

tests/core/atoms/test_phonons.py

I think this test still needs updating. get_phonopy() doesn't return a tuple anymore, and we aren't dealing with FixAtoms. That's the reason for the failure in the CI.

Andrew-S-Rosen · 2024-05-10T15:34:35Z

src/quacc/atoms/phonons.py

+def get_atoms_supercell_by_phonopy(
+    atoms: Atoms,
+    supercell_matrix: tuple[
+        tuple[int, int, int], tuple[int, int, int], tuple[int, int, int]
+    ],
+) -> Atoms:


It would be ideal to have a simple unit test for this specific function.

Andrew-S-Rosen · 2024-05-10T15:39:12Z

tests/core/recipes/emt_recipes/test_emt_phonons.py

@@ -70,4 +70,22 @@ def test_phonon_flow_v4(tmp_path, monkeypatch):
    assert output["results"]["thermal_properties"]["temperatures"][-1] == 1000
    assert output["results"]["force_constants"].shape == (8, 8, 3, 3)
    assert "mesh_properties" in output["results"]
-    assert output["atoms"] != atoms
+    assert output["atoms"] == atoms


Based on the test failure in CI, it looks like the original atoms object is getting mutated somewhere (since it has an EMT calculator attached)? That doesn't seem ideal... 😅

I think this was related to #2230.

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.

Andrew-S-Rosen · 2024-05-10T16:46:34Z

src/quacc/recipes/common/phonons.py

+    additional_atoms
+        Additional atoms to add to the supercells i.e. fixed atoms.
+        These atoms will not be displaced during the phonon calculation.
+        Useful for adsorbates on surfaces with weak coupling etc.


This was my point of confusion. I had thought you were implying that additional atoms would be for the adsorbates (I now see that's not the case). In reality, it would be for the surface of course.

I completely see where this confusion can get from, this is why I am not entirely sure about the current name.

Although this forces the users to stop and think before using this important approximation

EDIT: yes, the doc does not help as well

One downside of fixed_atoms is that it potentially implies that they are sites within atoms (the first positional argument) that are fixed, whereas in reality this is a separate Atoms object. That's one reason why I like additional_atoms since it makes it clear that this is a separate Atoms object, although one would understand that if they read the type hint. Of course, additional_atoms doesn't inherently specify anything about them being fixed until you read the docstring.

I think either could be okay, personally.

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

Incorporate some of the changes from #2110. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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Merge branch 'main' into phonopy_fixed_atoms_v2

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

Phonopy: fixing atoms #2073

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

Merge branch 'main' into phonopy_fixed_atoms_v2

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Merge branch 'main' into phonopy_fixed_atoms_v2

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Update phonons.py #2237

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Update phonons.py (#2237)

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Incorporate some of the changes from #2110. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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

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

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		The supercell matrix to use. If specified, it will override any
		value specified by `min_lengths`.

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

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

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tomdemeyere commented May 10, 2024

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