lint

Author: esoteric-ephemera

README.md

@@ -57,7 +57,7 @@ Rationale
 | IMAGES | IMAGES must be set to 0 to match MP calculations. |
 | INIWAV | INIWAV must be set as the VASP default of 1 to be consistent with MP calculations. |
 | ISPIN | All values of ISPIN are allowed, though it should be noted that virtuall all MP calculations permit spin symmetry breaking, and have ferromagnetic, antiferrogmanetic, or nonmagnetic ordering. |
-| ISMEAR | The appropriate ISMEAR depends on the bandgap of the material (which cannot be known a priori). As per the VASP manual: for metals (bandgap = 0), any ISMEAR value in [0, 1, 2] is acceptable. For nonmetals (bandgap > 0), any ISMEAR value in [-5, 0] is acceptable. Hence, for those who are performing normal relaxations/static calculations and want to ensure their calculations are MP-compatible, we recommend setting ISMEAR to 0. | 
+| ISMEAR | The appropriate ISMEAR depends on the bandgap of the material (which cannot be known a priori). As per the VASP manual: for metals (bandgap = 0), any ISMEAR value in [0, 1, 2] is acceptable. For nonmetals (bandgap > 0), any ISMEAR value in [-5, 0] is acceptable. Hence, for those who are performing normal relaxations/static calculations and want to ensure their calculations are MP-compatible, we recommend setting ISMEAR to 0. |
 | ISIF | MP allows any ISIF $\geq 2$. This value is restricted as such simply because all ISIF values $\geq 2$ output the complete stress tensor. |
 | ISYM | ISYM must be one of -1, 0, 1, 2, except for when the relevant MP input set uses a hybrid functional, in which case ISYM=3 is also allowed. |
 | ISTART | ISTART must be one of: 0, 1, 2. |
@@ -110,4 +110,4 @@ Rationale
 | SYMPREC | SYMPREC must be less than or equal to 1e-3 (as this is the maximum value that the Custodian package will set SYMPREC as of March 2024). |
 | SIGMA | There are several rules for setting SIGMA:  <ol> <li> SIGMA  must be $\leq 0.05$ for non-metals (bandgap $>  0$). </li> <li> SIGMA must be $\leq 0.2$ for a metal (bandgap = 0). </li> <li> For metals, the SIGMA value must be small enough that the entropy term in the energy is $\leq$ 1 meV/atom (as suggested by the VASP manual). </li> </ol> |
 | VCA | MP data does not include Virtual Crystal Approximation (VCA) calculations from VASP. As such, this parameter should not be set. |
-| VASP version | The following versions of VASP are allowed: 5.4.4 or $>$6.0.0. Versions $<=$ 5.4.3 are not allowed. Version 6.3.1, for example, is allowed. |
+| VASP version | The following versions of VASP are allowed: 5.4.4 or $>$6.0.0. Versions $<=$ 5.4.3 are not allowed. Version 6.3.1, for example, is allowed. |

examples/MP_compliant_job.py

@@ -1,4 +1,3 @@
-
 from __future__ import annotations
 
 from emmet.core.utils import jsanitize
@@ -9,117 +8,110 @@
 from pymatgen.core import Structure, Lattice
 
 
-def get_GaAs_structure(
-    a0 : float = 5.6
-) -> Structure:
+def get_GaAs_structure(a0: float = 5.6) -> Structure:
 
-    lattice_vectors = a0*np.array([
-        [0.0 if i == j else 0.5 for j in range(3)]
-        for i in range(3)
-    ])
+    lattice_vectors = a0 * np.array([[0.0 if i == j else 0.5 for j in range(3)] for i in range(3)])
     return Structure(
-        lattice = Lattice(lattice_vectors),
-        species = ["Ga","As"],
-        coords = [[0.125, 0.125, 0.125], [0.875, 0.875, 0.875]],
+        lattice=Lattice(lattice_vectors),
+        species=["Ga", "As"],
+        coords=[[0.125, 0.125, 0.125], [0.875, 0.875, 0.875]],
         coords_are_cartesian=False,
     )
 
-def assign_meta(flow, metadata : dict, name : str | None = None):
-    if hasattr(flow,"jobs"):
+
+def assign_meta(flow, metadata: dict, name: str | None = None):
+    if hasattr(flow, "jobs"):
         for ijob in range(len(flow.jobs)):
-            assign_meta(flow.jobs[ijob],metadata,name=name)
+            assign_meta(flow.jobs[ijob], metadata, name=name)
         if name:
             flow.name = name
     else:
         flow.metadata = metadata.copy()
         if name:
             flow.name = name
 
+
 def get_MP_compliant_r2SCAN_flow(
-    structure : Structure,
-    user_incar_settings : dict | None = None,
-    metadata : dict | None = None,
-    name : str | None = None
+    structure: Structure, user_incar_settings: dict | None = None, metadata: dict | None = None, name: str | None = None
 ) -> Flow:
-    
+
     from atomate2.vasp.jobs.mp import MPMetaGGAStaticMaker
     from atomate2.vasp.powerups import update_user_incar_settings
 
     maker = MPMetaGGAStaticMaker()
 
     user_incar_settings = user_incar_settings or {}
     if len(user_incar_settings) > 0:
-        maker = update_user_incar_settings(
-            maker, incar_updates = user_incar_settings
-        )
+        maker = update_user_incar_settings(maker, incar_updates=user_incar_settings)
 
     flow = maker.make(structure)
 
     metadata = metadata or {}
-    assign_meta(flow,metadata,name=name)
+    assign_meta(flow, metadata, name=name)
 
     return flow
 
-def run_job_fully_locally(flow, job_store = None):
+
+def run_job_fully_locally(flow, job_store=None):
 
     from jobflow import run_locally, JobStore
     from maggma.stores import MemoryStore
 
     if job_store is None:
         job_store = JobStore(MemoryStore(), additional_stores={"data": MemoryStore()})
-    
-    response = run_locally(flow, store = job_store, create_folders = True)
+
+    response = run_locally(flow, store=job_store, create_folders=True)
     uuid = list(response)[0]
     return response[uuid][1].output
 
+
 def MP_compliant_calc():
 
     structure = get_GaAs_structure()
     flow = get_MP_compliant_r2SCAN_flow(
-        structure = structure,
-        user_incar_settings = { # some forward-looking settings
+        structure=structure,
+        user_incar_settings={  # some forward-looking settings
             "LREAL": False,
             "LMAXMIX": 6,
-            "LCHARG": False, # following tags just set for convenience
+            "LCHARG": False,  # following tags just set for convenience
             "LWAVE": False,
             "LAECHG": False,
             "NCORE": 16,
-            "KPAR": 2
-        }
+            "KPAR": 2,
+        },
     )
     return run_job_fully_locally(flow)
 
+
 def MP_non_compliant_calc():
 
     structure = get_GaAs_structure()
     flow = get_MP_compliant_r2SCAN_flow(
-        structure = structure,
-        user_incar_settings = { # some backward-looking settings
-            "ENCUT": 450.,
-            "ENAUG": 900.,
+        structure=structure,
+        user_incar_settings={  # some backward-looking settings
+            "ENCUT": 450.0,
+            "ENAUG": 900.0,
             "KSPACING": 0.5,
-            "LCHARG": False, # following tags just set for convenience
+            "LCHARG": False,  # following tags just set for convenience
             "LWAVE": False,
             "LAECHG": False,
             "NCORE": 16,
-            "KPAR": 2
-        }
+            "KPAR": 2,
+        },
     )
     return run_job_fully_locally(flow)
 
+
 def MP_flows() -> None:
-    
+
     compliant_task_doc = MP_compliant_calc()
-    dumpfn(jsanitize(compliant_task_doc),"./MP_compatible_GaAs_r2SCAN_static.json.gz")
+    dumpfn(jsanitize(compliant_task_doc), "./MP_compatible_GaAs_r2SCAN_static.json.gz")
 
     non_compliant_task_doc = MP_non_compliant_calc()
-    dumpfn(jsanitize(non_compliant_task_doc),"./MP_incompatible_GaAs_r2SCAN_static.json.gz")
+    dumpfn(jsanitize(non_compliant_task_doc), "./MP_incompatible_GaAs_r2SCAN_static.json.gz")
 
-def generate_task_documents(
-    cdir,
-    task_id : str | None = None,
-    filename : str | None = None
-) -> TaskDocument:
+
+def generate_task_documents(cdir, task_id: str | None = None, filename: str | None = None) -> TaskDocument:
 
     from atomate.vasp.drones import VaspDrone
     from emmet.core.mpid import MPID
@@ -132,10 +124,11 @@ def generate_task_documents(
     task_doc = TaskDocument(**task_doc_dict)
 
     if filename:
-        dumpfn(jsanitize(task_doc),filename)
-    
+        dumpfn(jsanitize(task_doc), filename)
+
     return task_doc
 
+
 if __name__ == "__main__":
 
-    MP_flows()
+    MP_flows()

pymatgen/io/validation/check_potcar.py

@@ -110,12 +110,23 @@ def check(self, reasons: list[str], valid_input_set: VaspInputSet, structure: St
                 "other errors have been seen. Hence, it is marked as invalid."
             )
 
-    def compare_potcar_stats(self, potcar_stats_1: dict, potcar_stats_2 : dict) -> bool:
-        """ Utility function to compare PotcarSingle._summary_stats. """
-
-        if (
-            not all(potcar_stats_1.get(key) for key in ("keywords","stats",))
-            or (not all(potcar_stats_2.get(key) for key in ("keywords","stats",)))
+    def compare_potcar_stats(self, potcar_stats_1: dict, potcar_stats_2: dict) -> bool:
+        """Utility function to compare PotcarSingle._summary_stats."""
+
+        if not all(
+            potcar_stats_1.get(key)
+            for key in (
+                "keywords",
+                "stats",
+            )
+        ) or (
+            not all(
+                potcar_stats_2.get(key)
+                for key in (
+                    "keywords",
+                    "stats",
+                )
+            )
         ):
             return False
 
@@ -127,10 +138,10 @@ def compare_potcar_stats(self, potcar_stats_1: dict, potcar_stats_2 : dict) -> b
         data_match = False
         if key_match:
             data_diff = [
-                abs(potcar_stats_1["stats"].get(key,{}).get(stat) - potcar_stats_2["stats"].get(key,{}).get(stat))  # type: ignore
+                abs(potcar_stats_1["stats"].get(key, {}).get(stat) - potcar_stats_2["stats"].get(key, {}).get(stat))  # type: ignore
                 for stat in ["MEAN", "ABSMEAN", "VAR", "MIN", "MAX"]
                 for key in ["header", "data"]
             ]
             data_match = all(np.array(data_diff) < self.data_match_tol)
-        
-        return key_match and data_match
+
+        return key_match and data_match

pymatgen/io/validation/validation.py

@@ -37,7 +37,7 @@
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from typing import Any, Union
+    from typing import Any
 
 SETTINGS = IOValidationSettings()
 _vasp_defaults = loadfn(SETTINGS.VASP_DEFAULTS_FILENAME)
@@ -97,7 +97,7 @@ class Config:  # noqa
     @classmethod
     def from_task_doc(
         cls,
-        task_doc: Union[TaskDoc | TaskDocument],
+        task_doc: TaskDoc | TaskDocument,
         input_sets: dict[str, ImportString] = SETTINGS.VASP_DEFAULT_INPUT_SETS,
         check_potcar: bool = True,
         kpts_tolerance: float = SETTINGS.VASP_KPTS_TOLERANCE,
@@ -123,7 +123,7 @@ def from_task_doc(
                 initial equillibriation period. Note this is in eV per atom.
         """
 
-        if isinstance(task_doc,TaskDocument):
+        if isinstance(task_doc, TaskDocument):
             task_doc = TaskDoc(**task_doc.model_dump())
 
         bandgap = task_doc.output.bandgap

tests/test_validation.py

@@ -552,6 +552,7 @@ def test_vasp_version_check(test_dir, object_name):
     temp_task_doc.input.parameters["ISPIN"] = 2
     run_check(temp_task_doc, "POTENTIAL BUG --> We believe", False)
 
+
 def test_task_document(test_dir):
 
     from emmet.core.vasp.task_valid import TaskDocument
@@ -561,21 +562,16 @@ def test_task_document(test_dir):
         str(test_dir / "vasp" / "TaskDocuments" / "MP_compatible_GaAs_r2SCAN_static_TaskDocument.json.gz")
     )
     calcs["non-compliant"] = loadfn(
-         str(test_dir / "vasp" / "TaskDocuments" / "MP_incompatible_GaAs_r2SCAN_static_TaskDocument.json.gz")       
+        str(test_dir / "vasp" / "TaskDocuments" / "MP_incompatible_GaAs_r2SCAN_static_TaskDocument.json.gz")
     )
 
     valid_docs = {}
     for calc in calcs:
-        valid_docs[calc] = ValidationDoc.from_task_doc(
-            TaskDocument(**calcs[calc])
-        )
+        valid_docs[calc] = ValidationDoc.from_task_doc(TaskDocument(**calcs[calc]))
 
     assert valid_docs["compliant"].valid
     assert not valid_docs["non-compliant"].valid
 
-    expected_reasons = ["KPOINTS","ENCUT","ENAUG"]
+    expected_reasons = ["KPOINTS", "ENCUT", "ENAUG"]
     for expected_reason in expected_reasons:
-        assert any(
-            expected_reason in reason 
-            for reason in valid_docs["non-compliant"].reasons
-        )
+        assert any(expected_reason in reason for reason in valid_docs["non-compliant"].reasons)