Merge branch 'Quantum-Accelerators:main' into skzcam

docs/dev/recipes/jobs.md

@@ -30,6 +30,6 @@ The following are typical guidelines for jobs:
 
 A schema is a dictionary containing tabulated input and output properties from a calculation.
 
-All available schemas are stored in `quacc.schemas`, and type-hints associated with the outputs are stored in `quacc.schemas._aliases`.
+All available schemas are stored in `quacc.schemas`, and type-hints associated with the outputs are stored in `quacc.types`.
 
 All schemas create quacc-compatible dictionaries from a given calculation and also will automatically store results in the user's database, if one is specified in the global settings.

pyproject.toml

@@ -107,9 +107,6 @@ skip_gitignore = true
 
 [tool.coverage.run]
 source = ["src"]
-omit = [
-  "*/_aliases/*"
-]
 
 [tool.coverage.report]
 exclude_also = [

src/quacc/__init__.py

@@ -11,13 +11,15 @@
 from pymatgen.io.ase import MSONAtoms
 
 from quacc.settings import QuaccSettings, change_settings
+from quacc.types import DefaultSetting
 from quacc.utils.dicts import Remove
 from quacc.wflow_tools.customizers import redecorate, strip_decorator
 from quacc.wflow_tools.decorators import Flow, Job, Subflow, flow, job, subflow
 
 if TYPE_CHECKING:
     from typing import Any
 
+
 __all__ = [
     "flow",
     "job",
@@ -30,6 +32,7 @@
     "strip_decorator",
     "Remove",
     "get_settings",
+    "QuaccDefault",
 ]
 
 
@@ -85,6 +88,9 @@ def get_settings() -> QuaccSettings:
 
 _settings = get_settings()
 
+# Dummy value for when a default setting will be applied
+QuaccDefault = DefaultSetting()
+
 # Set logging info
 logging.basicConfig(level=logging.DEBUG if _settings.DEBUG else logging.INFO)
 

src/quacc/atoms/slabs.py

@@ -15,33 +15,11 @@
 from quacc.atoms.core import copy_atoms
 
 if TYPE_CHECKING:
-    from typing import Literal, TypedDict
+    from typing import Literal
 
     from ase.atoms import Atoms
-    from numpy.typing import ArrayLike
 
-    class AdsSiteFinderKwargs(TypedDict, total=False):
-        """
-        Type hint for `ads_site_finder_kwargs` in [quacc.atoms.slabs.make_adsorbate_structures][].
-        """
-
-        selective_dynamics: bool  # default = False
-        height: float  # default = 0.9
-        mi_vec: ArrayLike | None  # default = None
-
-    class FindAdsSitesKwargs(TypedDict, total=False):
-        """
-        Type hint for `find_ads_sites_kwargs` in [quacc.atoms.slabs.make_adsorbate_structures][].
-        """
-
-        distance: float  # default = 2.0
-        put_inside: bool  # default = True
-        symm_reduce: float  # default = 1e-2
-        near_reduce: float  # default = 1e-2
-        positions: list[
-            Literal["ontop", "bridge", "hollow", "subsurface"]
-        ]  # default: ["ontop", "bridge", "hollow"]
-        no_obtuse_hollow: bool  # default = True
+    from quacc.types import AdsSiteFinderKwargs, FindAdsSitesKwargs
 
 
 logger = logging.getLogger(__name__)
@@ -201,7 +179,7 @@ def make_slabs_from_bulk(
         # Add slab to list
         slabs_with_props.append(slab)
 
-    final_slabs = []
+    final_slabs: list[Atoms] = []
     if not slabs_with_props:
         return final_slabs
 
@@ -224,7 +202,7 @@ def make_adsorbate_structures(
     atoms: Atoms,
     adsorbate: Atoms,
     min_distance: float = 2.0,
-    modes: list[str] | None = None,
+    modes: list[Literal["ontop", "bridge", "hollow", "subsurface"]] | None = None,
     allowed_surface_symbols: list[str] | None = None,
     allowed_surface_indices: list[int] | None = None,
     ads_site_finder_kwargs: AdsSiteFinderKwargs | None = None,
@@ -282,7 +260,7 @@ def make_adsorbate_structures(
         msg = "Cannot specify both modes and find_ads_sites_kwargs['positions']"
         raise ValueError(msg)
     find_ads_sites_kwargs["distance"] = min_distance
-    find_ads_sites_kwargs["positions"] = [mode.lower() for mode in modes]
+    find_ads_sites_kwargs["positions"] = modes
 
     # Check the provided surface indices are reasonable
     atom_indices = [atom.index for atom in atoms]

src/quacc/calculators/espresso/espresso.py

@@ -214,7 +214,7 @@ def read_results(self, directory: Path | str) -> dict[str, Any]:
         """
         results = {}
         if self.binary == "pw":
-            atoms = read(directory / self.outputname, format="espresso-out")
+            atoms = read(Path(directory) / self.outputname, format="espresso-out")
             results = dict(atoms.calc.properties())
         elif self.binary in ["ph", "phcg"]:
             with Path(directory, self.outputname).open() as fd:

src/quacc/calculators/espresso/utils.py

@@ -13,7 +13,7 @@
 
     from ase.atoms import Atoms
 
-    from quacc.utils.files import Filenames, SourceDirectory
+    from quacc.types import Filenames, SourceDirectory
 
 LOGGER = logging.getLogger(__name__)
 

src/quacc/calculators/qchem/io.py

@@ -18,7 +18,7 @@
 if TYPE_CHECKING:
     from pymatgen.io.qchem.inputs import QCInput
 
-    from quacc.calculators.qchem.qchem import Results
+    from quacc.types import QchemResults
 
 
 def write_qchem(
@@ -53,7 +53,7 @@ def write_qchem(
     qc_input.write_file(directory / "mol.qin")
 
 
-def read_qchem(directory: Path | str) -> tuple[Results, list[float]]:
+def read_qchem(directory: Path | str) -> tuple[QchemResults, list[float]]:
     """
     Read Q-Chem log files.
 
@@ -74,7 +74,7 @@ def read_qchem(directory: Path | str) -> tuple[Results, list[float]]:
         warnings.simplefilter("ignore", category=UserWarning)
         task_doc = TaskDoc.from_directory(directory, validate_lot=False).model_dump()
 
-    results: Results = {
+    results: QchemResults = {
         "energy": task_doc["output"]["final_energy"] * units.Hartree,
         "taskdoc": task_doc,
     }

src/quacc/calculators/qchem/qchem.py

@@ -11,20 +11,11 @@
 from quacc.calculators.qchem.qchem_custodian import run_custodian
 
 if TYPE_CHECKING:
-    from typing import Any, ClassVar, Literal, TypedDict
+    from typing import Any, ClassVar, Literal
 
     from ase.atoms import Atoms
-    from numpy.typing import NDArray
 
-    class Results(TypedDict, total=False):
-        """
-        Type hint for the `results` attribute in [quacc.calculators.qchem.qchem.QChem][].
-        """
-
-        energy: float  # electronic energy in eV
-        forces: NDArray  # forces in eV/A
-        hessian: NDArray  # Hessian in eV/A^2/amu
-        taskdoc: dict[str, Any]  # Output from `emmet.core.qc_tasks.TaskDoc`
+    from quacc.types import QchemResults
 
 
 class QChem(FileIOCalculator):
@@ -36,7 +27,7 @@ class QChem(FileIOCalculator):
         "hessian",
         "taskdoc",
     ]
-    results: ClassVar[Results] = {}
+    results: ClassVar[QchemResults] = {}
 
     def __init__(
         self,

src/quacc/calculators/qchem/qchem_custodian.py

@@ -7,26 +7,27 @@
 
 from monty.dev import requires
 
-from quacc import get_settings
+from quacc import QuaccDefault, get_settings
 
 if TYPE_CHECKING:
     from pathlib import Path
 
-has_ob = bool(find_spec("openbabel"))
+    from quacc.types import DefaultSetting
+
 
-_DEFAULT_SETTING = ()
+has_ob = bool(find_spec("openbabel"))
 
 
 @requires(
     has_ob, "Openbabel must be installed. Try conda install -c conda-forge openbabel"
 )
 def run_custodian(
-    qchem_cmd: str = _DEFAULT_SETTING,
-    qchem_cores: int = _DEFAULT_SETTING,
-    qchem_local_scratch: str | Path = _DEFAULT_SETTING,
-    qchem_use_error_handlers: bool = _DEFAULT_SETTING,
-    qchem_custodian_max_errors: int = _DEFAULT_SETTING,
-    qchem_nbo_exe: str | Path = _DEFAULT_SETTING,
+    qchem_cmd: str | DefaultSetting = QuaccDefault,
+    qchem_cores: int | DefaultSetting = QuaccDefault,
+    qchem_local_scratch: str | Path | DefaultSetting = QuaccDefault,
+    qchem_use_error_handlers: bool | DefaultSetting = QuaccDefault,
+    qchem_custodian_max_errors: int | DefaultSetting = QuaccDefault,
+    qchem_nbo_exe: str | Path | DefaultSetting = QuaccDefault,
     directory: str | Path | None = None,
 ) -> list[list[dict]]:
     """
@@ -65,26 +66,26 @@ def run_custodian(
 
     # Set defaults
     qchem_cores = (
-        settings.QCHEM_NUM_CORES if qchem_cores == _DEFAULT_SETTING else qchem_cores
+        settings.QCHEM_NUM_CORES if qchem_cores == QuaccDefault else qchem_cores
     )
-    qchem_cmd = settings.QCHEM_CMD if qchem_cmd == _DEFAULT_SETTING else qchem_cmd
+    qchem_cmd = settings.QCHEM_CMD if qchem_cmd == QuaccDefault else qchem_cmd
     qchem_local_scratch = (
         settings.QCHEM_LOCAL_SCRATCH
-        if qchem_local_scratch == _DEFAULT_SETTING
+        if qchem_local_scratch == QuaccDefault
         else qchem_local_scratch
     )
     qchem_use_error_handlers = (
         settings.QCHEM_USE_ERROR_HANDLERS
-        if qchem_use_error_handlers == _DEFAULT_SETTING
+        if qchem_use_error_handlers == QuaccDefault
         else qchem_use_error_handlers
     )
     qchem_custodian_max_errors = (
         settings.QCHEM_CUSTODIAN_MAX_ERRORS
-        if qchem_custodian_max_errors == _DEFAULT_SETTING
+        if qchem_custodian_max_errors == QuaccDefault
         else qchem_custodian_max_errors
     )
     qchem_nbo_exe = (
-        settings.QCHEM_NBO_EXE if qchem_nbo_exe == _DEFAULT_SETTING else qchem_nbo_exe
+        settings.QCHEM_NBO_EXE if qchem_nbo_exe == QuaccDefault else qchem_nbo_exe
     )
 
     # Error handlers for Q-Chem

src/quacc/calculators/vasp/params.py

@@ -23,8 +23,7 @@
     from ase.atoms import Atoms
     from pymatgen.io.vasp.sets import DictSet
 
-    from quacc.utils.files import SourceDirectory
-    from quacc.utils.kpts import PmgKpts
+    from quacc.types import PmgKpts, SourceDirectory
 
     if has_atomate2:
         from atomate2.vasp.jobs.base import BaseVaspMaker

src/quacc/calculators/vasp/vasp.py

@@ -12,7 +12,7 @@
 from ase.calculators.vasp import setups as ase_setups
 from ase.constraints import FixAtoms
 
-from quacc import get_settings
+from quacc import QuaccDefault, get_settings
 from quacc.calculators.vasp.io import load_vasp_yaml_calc
 from quacc.calculators.vasp.params import (
     get_param_swaps,
@@ -30,7 +30,7 @@
 
     from ase.atoms import Atoms
 
-_DEFAULT_SETTING = ()
+    from quacc.types import DefaultSetting
 
 
 class Vasp(Vasp_):
@@ -43,11 +43,12 @@ def __init__(
         self,
         input_atoms: Atoms,
         preset: None | str = None,
-        use_custodian: bool = _DEFAULT_SETTING,
-        incar_copilot: Literal["off", "on", "aggressive"] = _DEFAULT_SETTING,
-        copy_magmoms: bool = _DEFAULT_SETTING,
-        preset_mag_default: float = _DEFAULT_SETTING,
-        mag_cutoff: float = _DEFAULT_SETTING,
+        use_custodian: bool | DefaultSetting = QuaccDefault,
+        incar_copilot: Literal["off", "on", "aggressive"]
+        | DefaultSetting = QuaccDefault,
+        copy_magmoms: bool | DefaultSetting = QuaccDefault,
+        preset_mag_default: float | DefaultSetting = QuaccDefault,
+        mag_cutoff: float | DefaultSetting = QuaccDefault,
         elemental_magmoms: dict[str, float] | None = None,
         pmg_kpts: (
             dict[Literal["line_density", "kppvol", "kppa"], float]
@@ -112,28 +113,26 @@ def __init__(
         # Set defaults
         use_custodian = (
             self._settings.VASP_USE_CUSTODIAN
-            if use_custodian == _DEFAULT_SETTING
+            if use_custodian == QuaccDefault
             else use_custodian
         )
         incar_copilot = (
             self._settings.VASP_INCAR_COPILOT
-            if incar_copilot == _DEFAULT_SETTING
+            if incar_copilot == QuaccDefault
             else incar_copilot
         )
         copy_magmoms = (
             self._settings.VASP_COPY_MAGMOMS
-            if copy_magmoms == _DEFAULT_SETTING
+            if copy_magmoms == QuaccDefault
             else copy_magmoms
         )
         preset_mag_default = (
             self._settings.VASP_PRESET_MAG_DEFAULT
-            if preset_mag_default == _DEFAULT_SETTING
+            if preset_mag_default == QuaccDefault
             else preset_mag_default
         )
         mag_cutoff = (
-            self._settings.VASP_MAG_CUTOFF
-            if mag_cutoff == _DEFAULT_SETTING
-            else mag_cutoff
+            self._settings.VASP_MAG_CUTOFF if mag_cutoff == QuaccDefault else mag_cutoff
         )
 
         # Assign variables to self
@@ -281,7 +280,7 @@ def _cleanup_params(self) -> None:
 
     def _run(
         self,
-        command: list[str] | None = None,
+        command: str | None = None,
         out: Path | str | None = None,
         directory: Path | str | None = None,
     ) -> int: