Remove redundant call to get_phonopy and fix bug in common phonon s…

…ubflow (#2105)

This PR removes the redundant call to `get_phonopy()` in
`quacc.recipes.common.phonons`. It also fixes a bug (?) where the
`Phonopy` object was constructed based on the _unrelaxed_ structure
rather than the relaxed structure.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/quacc/recipes/common/phonons.py

@@ -22,6 +22,9 @@
     from quacc import Job
     from quacc.schemas._aliases.phonons import PhononSchema
 
+    if has_deps:
+        from phonopy import Phonopy
+
 
 @subflow
 @requires(
@@ -30,7 +33,6 @@
 def phonon_subflow(
     atoms: Atoms,
     force_job: Job,
-    relax_job: Job | None = None,
     symprec: float = 1e-4,
     min_lengths: float | tuple[float, float, float] | None = 20.0,
     supercell_matrix: (
@@ -52,8 +54,6 @@ def phonon_subflow(
         Atoms object with calculator attached.
     force_job
         The static job to calculate the forces.
-    relax_job
-        The job used to relax the structure before calculating the forces.
     symprec
         Precision for symmetry detection.
     min_lengths
@@ -72,58 +72,56 @@ def phonon_subflow(
     phonopy_kwargs
         Additional kwargs to pass to the Phonopy class.
     additional_fields
-        Additional fields to store in the database.
+        Additional fields to add to the output schema.
 
     Returns
     -------
     PhononSchema
         Dictionary of results from [quacc.schemas.phonons.summarize_phonopy][]
     """
 
-    phonon = get_phonopy(
-        atoms,
-        min_lengths=min_lengths,
-        supercell_matrix=supercell_matrix,
-        symprec=symprec,
-        displacement=displacement,
-        phonopy_kwargs=phonopy_kwargs,
-    )
-    supercells = [
-        phonopy_atoms_to_ase_atoms(s) for s in phonon.supercells_with_displacements
-    ]
-
     @subflow
     def _get_forces_subflow(supercells: list[Atoms]) -> list[dict]:
         return [
             force_job(supercell) for supercell in supercells if supercell is not None
         ]
 
     @job
-    def _thermo_job(atoms: Atoms, force_job_results: list[dict]) -> PhononSchema:
-        phonon = get_phonopy(
-            atoms,
-            min_lengths=min_lengths,
-            supercell_matrix=supercell_matrix,
-            symprec=symprec,
-            displacement=displacement,
-            phonopy_kwargs=phonopy_kwargs,
-        )
+    def _thermo_job(
+        atoms: Atoms,
+        phonopy: Phonopy,
+        force_job_results: list[dict],
+        t_step: float,
+        t_min: float,
+        t_max: float,
+        additional_fields: dict[str, Any] | None,
+    ) -> PhononSchema:
         parameters = force_job_results[-1].get("parameters")
         forces = [output["results"]["forces"] for output in force_job_results]
-        phonon_results = run_phonopy(
-            phonon, forces, t_step=t_step, t_min=t_min, t_max=t_max
+        phonopy_results = run_phonopy(
+            phonopy, forces, t_step=t_step, t_min=t_min, t_max=t_max
         )
 
         return summarize_phonopy(
-            phonon,
+            phonopy,
             atoms,
-            phonon_results.directory,
+            phonopy_results.directory,
             parameters=parameters,
             additional_fields=additional_fields,
         )
 
-    if relax_job is not None:
-        atoms = relax_job(atoms)["atoms"]
-
+    phonopy = get_phonopy(
+        atoms,
+        min_lengths=min_lengths,
+        supercell_matrix=supercell_matrix,
+        symprec=symprec,
+        displacement=displacement,
+        phonopy_kwargs=phonopy_kwargs,
+    )
+    supercells = [
+        phonopy_atoms_to_ase_atoms(s) for s in phonopy.supercells_with_displacements
+    ]
     force_job_results = _get_forces_subflow(supercells)
-    return _thermo_job(atoms, force_job_results)
+    return _thermo_job(
+        atoms, phonopy, force_job_results, t_step, t_min, t_max, additional_fields
+    )

src/quacc/recipes/emt/phonons.py

@@ -92,11 +92,12 @@ def phonon_flow(
         parameters=job_params,
         decorators=job_decorators,
     )
+    if run_relax:
+        atoms = relax_job_(atoms)["atoms"]
 
     return phonon_subflow(
         atoms,
         static_job_,
-        relax_job=relax_job_ if run_relax else None,
         symprec=symprec,
         min_lengths=min_lengths,
         supercell_matrix=supercell_matrix,

src/quacc/recipes/mlp/phonons.py

@@ -105,11 +105,12 @@ def phonon_flow(
         parameters=job_params,
         decorators=job_decorators,
     )
+    if run_relax:
+        atoms = relax_job_(atoms)["atoms"]
 
     return phonon_subflow(
         atoms,
         static_job_,
-        relax_job=relax_job_ if run_relax else None,
         symprec=symprec,
         min_lengths=min_lengths,
         supercell_matrix=supercell_matrix,

src/quacc/recipes/tblite/phonons.py

@@ -105,11 +105,12 @@ def phonon_flow(
         parameters=job_params,
         decorators=job_decorators,
     )
+    if run_relax:
+        atoms = relax_job_(atoms)["atoms"]
 
     return phonon_subflow(
         atoms,
         static_job_,
-        relax_job=relax_job_ if run_relax else None,
         symprec=symprec,
         min_lengths=min_lengths,
         supercell_matrix=supercell_matrix,