Refactor atoms handling

CHANGELOG.md

@@ -9,6 +9,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Changed
 
 - Pydantic field type validation has been improved.
+- Moved `quacc.utils.atoms`/`.slabs`/`.defects` into `quacc.atoms.core`/`.slabs`/`.defects`
 - Moved `quacc.custodian` to `quacc.calculators.custodian`
 - Moved `quacc.utils.thermo.ideal_gas` to `quacc.builders.thermo.build_ideal_gas`
 - Renamed `quacc.schemas.ase.summarize_thermo` to `quacc.schemas.ase.summarize_igt_thermo`

src/quacc/atoms/__init__.py

@@ -0,0 +1 @@
+"""Tools for handling and manipulating Atoms objects"""

src/quacc/utils/slabs.py → src/quacc/atoms/slabs.py

@@ -12,7 +12,7 @@
 from pymatgen.core.surface import Slab, center_slab, generate_all_slabs
 from pymatgen.io.ase import AseAtomsAdaptor
 
-from quacc.utils.atoms import copy_atoms
+from quacc.atoms.core import copy_atoms
 
 if TYPE_CHECKING:
     from pymatgen.core import Structure

src/quacc/calculators/vasp.py

@@ -20,9 +20,9 @@
 from pymatgen.symmetry.bandstructure import HighSymmKpath
 
 from quacc import SETTINGS
+from quacc.atoms.core import check_is_metal
 from quacc.calculators.custodian import vasp as custodian_vasp
 from quacc.runners.prep import set_magmoms
-from quacc.utils.atoms import check_is_metal
 from quacc.utils.files import load_yaml_calc
 
 if TYPE_CHECKING:

src/quacc/recipes/emt/defects.py

@@ -6,8 +6,8 @@
 from pymatgen.analysis.defects.generators import VacancyGenerator
 
 from quacc import fetch_atoms, flow, job, subflow
+from quacc.atoms.defects import make_defects_from_bulk
 from quacc.recipes.emt.core import relax_job, static_job
-from quacc.utils.defects import make_defects_from_bulk
 
 if TYPE_CHECKING:
     from ase import Atoms
@@ -57,7 +57,7 @@ def bulk_to_defects_flow(
     defect_charge
         Charge state of the defect
     make_defects_kwargs
-        Keyword arguments to pass to [quacc.utils.defects.make_defects_from_bulk][]
+        Keyword arguments to pass to [quacc.atoms.defects.make_defects_from_bulk][]
     run_static
         Whether to run the static calculation.
     defect_relax_kwargs

src/quacc/recipes/emt/slabs.py

@@ -4,8 +4,8 @@
 from typing import TYPE_CHECKING
 
 from quacc import fetch_atoms, flow, job, subflow
+from quacc.atoms.slabs import make_slabs_from_bulk
 from quacc.recipes.emt.core import relax_job, static_job
-from quacc.utils.slabs import make_slabs_from_bulk
 
 if TYPE_CHECKING:
     from ase import Atoms
@@ -37,7 +37,7 @@ def bulk_to_slabs_flow(
         the value
     make_slabs_kwargs
         Additional keyword arguments to pass to
-        [quacc.utils.slabs.make_slabs_from_bulk][]
+        [quacc.atoms.slabs.make_slabs_from_bulk][]
     run_static
         Whether to run the static calculation.
     slab_relax_kwargs

src/quacc/recipes/vasp/slabs.py

@@ -4,8 +4,8 @@
 from typing import TYPE_CHECKING
 
 from quacc import fetch_atoms, flow, job, subflow
+from quacc.atoms.slabs import make_adsorbate_structures, make_slabs_from_bulk
 from quacc.recipes.vasp.core import _base_job
-from quacc.utils.slabs import make_adsorbate_structures, make_slabs_from_bulk
 
 if TYPE_CHECKING:
     from ase import Atoms
@@ -168,7 +168,7 @@ def bulk_to_slabs_flow(
         Atoms object or a dictionary with the key "atoms" and an Atoms object as
         the value
     make_slabs_kwargs
-        Additional keyword arguments to pass to [quacc.utils.slabs.make_slabs_from_bulk][]
+        Additional keyword arguments to pass to [quacc.atoms.slabs.make_slabs_from_bulk][]
     run_static
         Whether to run the static calculation.
     slab_relax_kwargs
@@ -233,7 +233,7 @@ def slab_to_ads_flow(
     adsorbate
         Atoms object for the adsorbate.
     make_ads_kwargs
-        Additional keyword arguments to pass to [quacc.utils.slabs.make_adsorbate_structures][]
+        Additional keyword arguments to pass to [quacc.atoms.slabs.make_adsorbate_structures][]
     run_static
         Whether to run the static calculation.
     slab_relax_kwargs

src/quacc/runners/calc.py

@@ -17,7 +17,7 @@
 from monty.shutil import copy_r, gzip_dir
 
 from quacc import SETTINGS
-from quacc.utils.atoms import copy_atoms
+from quacc.atoms.core import copy_atoms
 from quacc.utils.files import copy_decompress, make_unique_dir
 
 try:

src/quacc/runners/prep.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from quacc.utils.atoms import copy_atoms, get_atoms_id
+from quacc.atoms.core import copy_atoms, get_atoms_id
 
 if TYPE_CHECKING:
     from ase import Atoms

src/quacc/schemas/atoms.py

@@ -9,7 +9,7 @@
 from monty.json import jsanitize
 from pymatgen.io.ase import AseAtomsAdaptor
 
-from quacc.utils.atoms import copy_atoms
+from quacc.atoms.core import copy_atoms
 from quacc.utils.dicts import clean_dict
 
 if TYPE_CHECKING:

src/quacc/utils/__init__.py

@@ -1,5 +1,5 @@
 """Miscellaneous utility functions"""
 
-from quacc.utils.atoms import check_charge_and_spin
+from quacc.atoms.core import check_charge_and_spin
 
 __all__ = ["check_charge_and_spin"]

tests/recipes/qchem_recipes/test_qchem_recipes.py

@@ -12,8 +12,8 @@
 from pymatgen.io.qchem.inputs import QCInput
 
 from quacc import SETTINGS
+from quacc.atoms.core import check_charge_and_spin
 from quacc.calculators.qchem import QChem
-from quacc.utils import check_charge_and_spin
 
 pytest.importorskip("sella")
 pytestmark = pytest.mark.skipif(

tests/runners/test_prep.py

@@ -6,9 +6,9 @@
 from ase.build import bulk, molecule
 from ase.io import read
 
+from quacc.atoms.core import get_atoms_id
 from quacc.calculators.vasp import Vasp
 from quacc.runners.prep import prep_next_run
-from quacc.utils.atoms import get_atoms_id
 
 FILE_DIR = Path(__file__).resolve().parent
 ATOMS_MAG = read(os.path.join(FILE_DIR, "..", "calculators", "vasp", "OUTCAR_mag.gz"))

tests/utils/test_slabs.py

@@ -7,7 +7,7 @@
 from ase.build import bulk, fcc100, molecule
 from ase.io import read
 
-from quacc.utils.slabs import (
+from quacc.atoms.slabs import (
     flip_atoms,
     get_surface_energy,
     make_adsorbate_structures,

tests/utils/test_utils_atoms.py

@@ -8,9 +8,9 @@
 from ase.build import bulk, molecule
 from ase.io import read
 
+from quacc.atoms.core import check_charge_and_spin, check_is_metal, get_atoms_id
 from quacc.calculators.vasp import Vasp
 from quacc.runners.prep import prep_next_run
-from quacc.utils.atoms import check_charge_and_spin, check_is_metal, get_atoms_id
 
 FILE_DIR = Path(__file__).resolve().parent
 ATOMS_MAG = read(os.path.join(FILE_DIR, "..", "calculators", "vasp", "OUTCAR_mag.gz"))