fix minor code formatting issues + typos (#1070)

Author: janosh

docs/user/codes/vasp.md

@@ -1,4 +1,5 @@
 (codes.vasp)=
+
 # VASP
 
 At present, most workflows in atomate2 use the Vienna *ab initio* simulation package
@@ -260,21 +261,19 @@ With the help of phonopy, these forces are then converted into a dynamical matri
 The dynamical matrices of three structures are then used as an input to the phonopy Grueneisen api
 to compute mode-dependent Grueneisen parameters.
 
-
 ### Quasi-harmonic Workflow
+
 Uses the quasi-harmonic approximation with the help of Phonopy to compute thermodynamic properties.
 First, a tight relaxation is performed. Subsequently, several optimizations at different constant
 volumes are performed. At each of the volumes, an additional phonon run is performed as well.
 Afterwards, equation of state fits are performed with phonopy.
 
-
-
 ### Equation of State Workflow
+
 An equation of state workflow is implemented. First, a tight relaxation is performed. Subsequently, several optimizations at different constant
 volumes are performed. Additional static calculations might be performed afterwards to arrive at more
 accurate energies. Then, an equation of state fit is performed with pymatgen.
 
-
 ### LOBSTER
 
 Perform bonding analysis with [LOBSTER](http://cohp.de/) and [LobsterPy](https://github.com/jageo/lobsterpy)

src/atomate2/common/flows/anharmonicity.py

@@ -81,7 +81,7 @@ def make(
             A previous calculation directory to use for copying outputs.
             Default is None.
         born: Optional[list[Matrix3D]]
-            Instead of recomputing born charges and epsilon, these values can also be
+            Instead of recomputing Born charges and epsilon, these values can also be
             provided manually. If born and epsilon_static are provided, the born run
             will be skipped it can be provided in the VASP convention with information
             for every atom in unit cell. Please be careful when converting structures

src/atomate2/common/flows/gruneisen.py

@@ -40,7 +40,7 @@ class BaseGruneisenMaker(Maker, ABC):
     generated for all the three structures (ground state, expanded and shrunk volume)
     and accurate forces are computed for these structures. With the help of phonopy,
     these forces are then converted into a dynamical matrix. This dynamical matrix of
-    three structures is then used as an input for the phonopy Grueneisen api
+    three structures is then used as an input for the phonopy Grueneisen API
     to compute Grueneisen parameters.
 
 

src/atomate2/common/flows/phonons.py

@@ -187,7 +187,7 @@ def make(
         prev_dir : str or Path or None
             A previous calculation directory to use for copying outputs.
         born: Matrix3D
-            Instead of recomputing born charges and epsilon, these values can also be
+            Instead of recomputing Born charges and epsilon, these values can also be
             provided manually. If born and epsilon_static are provided, the born run
             will be skipped it can be provided in the VASP convention with information
             for every atom in unit cell. Please be careful when converting structures

src/atomate2/common/flows/qha.py

@@ -25,28 +25,24 @@
     from atomate2.common.flows.phonons import BasePhononMaker
     from atomate2.forcefields.jobs import ForceFieldRelaxMaker
     from atomate2.vasp.jobs.core import BaseVaspMaker
+
 supported_eos = frozenset(("vinet", "birch_murnaghan", "murnaghan"))
 
 
 @dataclass
 class CommonQhaMaker(Maker, ABC):
-    """
-    Use the quasi-harmonic approximation.
+    """Use the quasi-harmonic approximation.
 
-    First relax a structure.
-    Then we scale the relaxed structure, and
-    then compute harmonic phonons for each scaled
-    structure with Phonopy.
-    Finally, we compute the Gibbs free energy and
-    other thermodynamic properties available from
-    the quasi-harmonic approximation.
+    First relax a structure. Then we scale the relaxed structure, and then compute
+    harmonic phonons for each scaled structure with Phonopy. Finally, we compute the
+    Gibbs free energy and other thermodynamic properties available from the
+    quasi-harmonic approximation.
 
     Note: We do not consider electronic free energies so far.
     This might be problematic for metals (see e.g.,
     Wolverton and Zunger, Phys. Rev. B, 52, 8813 (1994).)
 
-    Note: Magnetic Materials have never been computed with
-    this workflow.
+    Note: Magnetic Materials have never been computed with this workflow.
 
     Parameters
     ----------
@@ -84,7 +80,6 @@ class CommonQhaMaker(Maker, ABC):
         with 3 90 degree angles
     get_supercell_size_kwargs: dict
         kwargs that will be passed to get_supercell_size to determine supercell size
-
     """
 
     name: str = "QHA Maker"
@@ -128,10 +123,7 @@ def make(
         .Flow, a QHA flow
         """
         if self.eos_type not in supported_eos:
-            raise ValueError(
-                "EOS not supported.",
-                "Please choose 'vinet', 'birch_murnaghan', 'murnaghan'",
-            )
+            raise ValueError(f"EOS not supported. Choose one of {set(supported_eos)}")
 
         qha_jobs = []
 
@@ -148,7 +140,7 @@ def make(
         eos_job = self.eos.make(structure)
         qha_jobs.append(eos_job)
 
-        # implement a supercell job to get matrix for just the equillibrium structure
+        # implement a supercell job to get matrix for just the equilibrium structure
         if supercell_matrix is None:
             supercell = get_supercell_size(
                 eos_output=eos_job.output,
@@ -162,7 +154,6 @@ def make(
             supercell_matrix = supercell.output
 
         # pass the matrix to the phonon_jobs, allow to set a consistent matrix instead
-
         phonon_jobs = get_phonon_jobs(
             phonon_maker=self.phonon_maker,
             eos_output=eos_job.output,

src/atomate2/common/jobs/anharmonicity.py

@@ -44,15 +44,16 @@ class ImaginaryModeError(Exception):
 
     def __init__(self, largest_mode: float) -> None:
         self.largest_mode = largest_mode
-        self.message = f"""Structure has imaginary modes: the largest optical
-                        eigenmode {largest_mode} < 0.0001"""
+        self.message = (
+            f"Structure has imaginary modes: the largest optical eigenmode "
+            f"{largest_mode} < 0.0001"
+        )
         super().__init__(self.message)
 
 
 @job
 def get_phonon_supercell(
-    structure: Structure,
-    supercell_matrix: np.ndarray,
+    structure: Structure, supercell_matrix: np.ndarray
 ) -> Structure:
     """Get the phonon supercell of a structure.
 
@@ -68,12 +69,9 @@ def get_phonon_supercell(
     Structure
         The phonopy structure
     """
-    cell = get_phonopy_structure(structure)
-    phonon = Phonopy(
-        cell,
-        supercell_matrix,
-    )
-    return get_pmg_structure(phonon.supercell)
+    unit_cell = get_phonopy_structure(structure)
+    phonopy = Phonopy(unit_cell, supercell_matrix)
+    return get_pmg_structure(phonopy.supercell)
 
 
 def get_sigma_per_site(

src/atomate2/common/jobs/gruneisen.py

@@ -17,6 +17,8 @@
 from atomate2.common.schemas.phonons import PhononBSDOSDoc
 
 if TYPE_CHECKING:
+    from pathlib import Path
+
     from pymatgen.core.structure import Structure
 
     from atomate2.common.flows.phonons import BasePhononMaker
@@ -128,11 +130,11 @@ def run_phonon_jobs(
 )
 def compute_gruneisen_param(
     code: str,
-    phonopy_yaml_paths_dict: dict,
-    phonon_imaginary_modes_info: dict,
+    phonopy_yaml_paths_dict: dict[str, Path],
+    phonon_imaginary_modes_info: dict[str, bool],
     kpath_scheme: str,
     symprec: float,
-    mesh: tuple | float = (20, 20, 20),
+    mesh: tuple[int, int, int] | float = (20, 20, 20),
     structure: Structure = None,
     **compute_gruneisen_param_kwargs,
 ) -> GruneisenParameterDocument:

src/atomate2/common/jobs/qha.py

@@ -56,9 +56,7 @@ def get_supercell_size(
     )
 
 
-@job(
-    data=[PhononBSDOSDoc],
-)
+@job(data=[PhononBSDOSDoc])
 def get_phonon_jobs(
     phonon_maker: BasePhononMaker, eos_output: dict, supercell_matrix: list[list[float]]
 ) -> Flow:

src/atomate2/common/schemas/phonons.py

@@ -201,7 +201,7 @@ class PhononBSDOSDoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg
 
     born: Optional[list[Matrix3D]] = Field(
         None,
-        description="born charges as computed from phonopy. Only for symmetrically "
+        description="Born charges as computed from phonopy. Only for symmetrically "
         "different atoms",
     )
 
@@ -280,7 +280,7 @@ def from_forces_born(
         epsilon_static: Matrix3D
             The high-frequency dielectric constant
         born: Matrix3D
-            born charges
+            Born charges
         **kwargs:
             additional arguments
         """
@@ -329,7 +329,7 @@ def from_forces_born(
                 )
             else:
                 raise ValueError(
-                    "Number of born charges does not agree with number of atoms"
+                    "Number of Born charges does not agree with number of atoms"
                 )
             if code == "vasp" and not np.all(np.isclose(borns, 0.0)):
                 phonon.nac_params = {
@@ -595,7 +595,8 @@ def get_kpath(
         **kpath_kwargs:
             additional parameters that can be passed to this method as a dict
         """
-        if kpath_scheme in ("setyawan_curtarolo", "latimer_munro", "hinuma"):
+        valid_schemes = {"setyawan_curtarolo", "latimer_munro", "hinuma", "seekpath"}
+        if kpath_scheme in (valid_schemes - {"seekpath"}):
             high_symm_kpath = HighSymmKpath(
                 structure, path_type=kpath_scheme, symprec=symprec, **kpath_kwargs
             )
@@ -604,7 +605,9 @@ def get_kpath(
             high_symm_kpath = KPathSeek(structure, symprec=symprec, **kpath_kwargs)
             kpath = high_symm_kpath._kpath  # noqa: SLF001
         else:
-            raise ValueError(f"Unexpected {kpath_scheme=}")
+            raise ValueError(
+                f"Unexpected {kpath_scheme=}, must be one of {valid_schemes}"
+            )
 
         path = copy.deepcopy(kpath["path"])
 

tests/vasp/flows/test_phonons.py

@@ -265,66 +265,41 @@ def test_phonon_wf_vasp_only_displacements_kpath(
     responses = run_locally(job, create_folders=True, ensure_success=True)
 
     # validate the outputs
-    # print(type(responses))
-    assert isinstance(responses[job.jobs[-1].uuid][1].output, PhononBSDOSDoc)
+    ph_doc = responses[job.jobs[-1].uuid][1].output
+    assert isinstance(ph_doc, PhononBSDOSDoc)
 
     assert_allclose(
-        responses[job.jobs[-1].uuid][1].output.free_energies,
+        ph_doc.free_energies,
         [5776.14995034, 5617.74737777, 4725.50269363, 3043.81827626, 694.49078355],
         atol=1e-3,
     )
 
+    assert isinstance(ph_doc.phonon_bandstructure, PhononBandStructureSymmLine)
+    assert isinstance(ph_doc.phonon_dos, PhononDos)
+    assert isinstance(ph_doc.thermal_displacement_data, ThermalDisplacementData)
+    assert isinstance(ph_doc.structure, Structure)
+    assert_allclose(ph_doc.temperatures, [0, 100, 200, 300, 400])
+    assert ph_doc.has_imaginary_modes is False
+    force_const = ph_doc.force_constants.force_constants[0][0][0][0]
+    assert force_const == pytest.approx(13.032324)
+    assert isinstance(ph_doc.jobdirs, PhononJobDirs)
+    assert isinstance(ph_doc.uuids, PhononUUIDs)
+    assert ph_doc.total_dft_energy is None
+    assert ph_doc.born is None
+    assert ph_doc.epsilon_static is None
+    assert ph_doc.supercell_matrix == ((-1, 1, 1), (1, -1, 1), (1, 1, -1))
+    assert ph_doc.primitive_matrix == ((1, 0, 0), (0, 1, 0), (0, 0, 1))
+    assert ph_doc.code == "vasp"
     assert isinstance(
-        responses[job.jobs[-1].uuid][1].output.phonon_bandstructure,
-        PhononBandStructureSymmLine,
-    )
-    assert isinstance(responses[job.jobs[-1].uuid][1].output.phonon_dos, PhononDos)
-    assert isinstance(
-        responses[job.jobs[-1].uuid][1].output.thermal_displacement_data,
-        ThermalDisplacementData,
-    )
-    assert isinstance(responses[job.jobs[-1].uuid][1].output.structure, Structure)
-    assert_allclose(
-        responses[job.jobs[-1].uuid][1].output.temperatures, [0, 100, 200, 300, 400]
-    )
-    assert responses[job.jobs[-1].uuid][1].output.has_imaginary_modes is False
-    assert_allclose(
-        responses[job.jobs[-1].uuid][1].output.force_constants.force_constants[0][0][0][
-            0
-        ],
-        13.032324,
-    )
-    assert isinstance(responses[job.jobs[-1].uuid][1].output.jobdirs, PhononJobDirs)
-    assert isinstance(responses[job.jobs[-1].uuid][1].output.uuids, PhononUUIDs)
-    assert responses[job.jobs[-1].uuid][1].output.total_dft_energy is None
-    assert responses[job.jobs[-1].uuid][1].output.born is None
-    assert responses[job.jobs[-1].uuid][1].output.epsilon_static is None
-    assert_allclose(
-        responses[job.jobs[-1].uuid][1].output.supercell_matrix,
-        [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]],
-    )
-    assert_allclose(
-        responses[job.jobs[-1].uuid][1].output.primitive_matrix,
-        [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
-        atol=1e-8,
-    )
-    assert responses[job.jobs[-1].uuid][1].output.code == "vasp"
-    assert isinstance(
-        responses[job.jobs[-1].uuid][1].output.phonopy_settings,
+        ph_doc.phonopy_settings,
         PhononComputationalSettings,
     )
-    assert responses[job.jobs[-1].uuid][1].output.phonopy_settings.npoints_band == 101
-    assert (
-        responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpath_scheme
-        == kpath_scheme
-    )
-    assert (
-        responses[job.jobs[-1].uuid][1].output.phonopy_settings.kpoint_density_dos
-        == 7_000
-    )
+    assert ph_doc.phonopy_settings.npoints_band == 101
+    assert ph_doc.phonopy_settings.kpath_scheme == kpath_scheme
+    assert ph_doc.phonopy_settings.kpoint_density_dos == 7_000
 
 
-# test supply of born charges, epsilon, DFT energy, supercell
+# test supply of Born charges, epsilon, DFT energy, supercell
 def test_phonon_wf_vasp_only_displacements_add_inputs_raises(
     mock_vasp, clean_dir, si_structure: Structure
 ):
@@ -337,16 +312,9 @@ def test_phonon_wf_vasp_only_displacements_add_inputs_raises(
     # automatically use fake VASP and write POTCAR.spec during the test
     mock_vasp(ref_paths, fake_run_vasp_kwargs)
 
-    born = [
-        [[0, 0, 0], [0, 0, 0], [0, 0, 0]],
-        [[0, 0, 0], [0, 0, 0], [0, 0, 0]],
-        [[0, 0, 0], [0, 0, 0], [0, 0, 0.1]],
-    ]
-    epsilon_static = [
-        [5.25, 0, 0],
-        [0, 5.25, 0],
-        [0, 0, 5.25],
-    ]
+    born = np.zeros((3, 3))
+    born[-1, -1] = 0.1
+    epsilon_static = 5.25 * np.eye(3)
     total_dft_energy_per_formula_unit = -5
 
     job = PhononMaker(
@@ -368,7 +336,7 @@ def test_phonon_wf_vasp_only_displacements_add_inputs_raises(
         run_locally(job, create_folders=True, ensure_success=True)
 
 
-# test supply of born charges, epsilon, DFT energy, supercell
+# test supply of Born charges, epsilon, DFT energy, supercell
 def test_phonon_wf_vasp_only_displacements_add_inputs(
     mock_vasp, clean_dir, si_structure: Structure
 ):