Merge branch 'main' of https://github.com/materialsproject/atomate2 into atomate2-aims

Author: tpurcell90

.github/workflows/testing.yml

@@ -3,9 +3,9 @@ name: testing
 on:
   push:
     branches: [main]
-    tags: ['v*']
+    tags: ["v*"]
   pull_request:
-    branches: [main]
+  workflow_dispatch:
 
 jobs:
   lint:
@@ -45,7 +45,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-            pip install .[strict,tests]
+          pip install .[strict,tests]
 
       - name: Test
         env:

pyproject.toml

@@ -17,8 +17,8 @@ classifiers = [
     "Intended Audience :: System Administrators",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.9",
     "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
@@ -28,32 +28,33 @@ dependencies = [
     "PyYAML",
     "click",
     "custodian>=2023.3.10",
-    "emmet-core>=0.65.0",
+    "emmet-core>=0.70.0",
     "jobflow>=0.1.11",
-    "monty",
+    "monty>=2023.9.25",
     "numpy",
-    "pydantic",
-    "pymatgen>=2023.1.9",
+    "pydantic-settings>=2.0.3",
+    "pydantic>=2.0.1",
+    "pymatgen>=2023.10.11",
 ]
 
 [project.optional-dependencies]
 amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
-mp = ["mp-api>=0.27.5"]
+mp = ["mp-api>=0.37.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
-lobster = ["lobsterpy>=0.3.1"]
+lobster = ["lobsterpy>=0.3.2"]
 defects = ["dscribe>=1.2.0", "pymatgen-analysis-defects>=2022.11.30"]
-forcefields = ["chgnet==0.2.0", "matgl==0.8.3", "quippy-ase==0.9.14"]
+forcefields = ["chgnet>=0.2.2", "matgl>=0.8.3", "quippy-ase>=0.9.14"]
 docs = [
     "FireWorks==2.0.3",
-    "autodoc_pydantic==1.9.0",
+    "autodoc_pydantic==2.0.1",
     "furo==2023.9.10",
-    "ipython==8.16.0",
+    "ipython==8.16.1",
     "jsonschema[format]",
     "myst_parser==2.0.0",
     "numpydoc==1.6.0",
-    "sphinx==7.2.6",
     "sphinx-copybutton==0.5.2",
+    "sphinx==7.2.6",
     "sphinx_design==0.5.0",
 ]
 dev = ["pre-commit>=2.12.1"]
@@ -62,21 +63,22 @@ aims = ["ase@git+https://gitlab.com/ase/ase.git@793179f4#egg=ase"]
 strict = [
     "PyYAML==6.0.1",
     "cclib==1.8",
-    "chgnet==0.2.0",
+    "chgnet==0.2.2",
     "click==8.1.7",
-    "custodian==2023.7.22",
+    "custodian==2023.10.9",
     "dscribe==2.1.0",
-    "emmet-core==0.68.0",
-    "jobflow==0.1.13",
-    "lobsterpy==0.3.1",
+    "emmet-core==0.70.4",
+    "jobflow==0.1.14",
+    "lobsterpy==0.3.2",
     "matgl==0.8.3",
-    "monty==2023.9.5",
-    "mp-api==0.35.1",
+    "monty==2023.9.25",
+    "mp-api==0.37.5",
     "numpy",
     "phonopy==2.20.0",
-    "pydantic==1.10.9",
+    "pydantic-settings==2.0.3",
+    "pydantic==2.4.2",
     "pymatgen-analysis-defects==2023.8.22",
-    "pymatgen==2023.9.10",
+    "pymatgen==2023.10.11",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",
     "typing-extensions==4.8.0",

src/atomate2/amset/schemas.py

@@ -133,10 +133,8 @@ class AmsetTaskDocument(StructureMetadata):
     )
     soc: bool = Field(None, description="Whether spin-orbit coupling was included")
     structure: Structure = Field(None, description="The structure used in this task")
-    _schema: str = Field(
-        __version__,
-        description="Version of atomate2 used to create the document",
-        alias="schema",
+    schema: str = Field(
+        __version__, description="Version of atomate2 used to create the document"
     )
 
     @classmethod

src/atomate2/common/flows/defect.py

@@ -199,6 +199,13 @@ class FormationEnergyMaker(Maker, ABC):
         sites with selective dynamics set to True. So this setting only works
         with `relax_radius`.
 
+    validate_charge: bool
+        Whether to validate the charge of the defect. If True (default), the charge
+        of the output structure will have to match the charge of the input defect.
+        This helps catch situations where the charge of the output defect is either
+        improperly set or improperly parsed before the data is stored in the
+        database.
+
     collect_defect_entry_data: bool
         Whether to collect the defect entry data at the end of the flow.
         If True, the output of all the charge states for each symmetry distinct
@@ -234,14 +241,14 @@ class FormationEnergyMaker(Maker, ABC):
                 'defect_uuid': 'a1c31095-0494-4eed-9862-95311f80a993'
             }
         ]
-
     """
 
     defect_relax_maker: Maker
     bulk_relax_maker: Maker | None = None
     name: str = "formation energy"
     relax_radius: float | str | None = None
     perturb: float | None = None
+    validate_charge: bool = True
     collect_defect_entry_data: bool = False
 
     def __post_init__(self):
@@ -317,6 +324,7 @@ def make(
             },
             relax_radius=self.relax_radius,
             perturb=self.perturb,
+            validate_charge=self.validate_charge,
         )
         jobs.extend([get_sc_job, spawn_output])
 

src/atomate2/common/jobs/defect.py

@@ -400,18 +400,18 @@ def check_charge_state(charge_state: int, task_structure: Structure) -> Response
     if int(charge_state) != int(task_structure.charge):
         raise ValueError(
             f"The charge of the output structure is {task_structure.charge}, "
-            f"but expect charge state from the Defect object is {charge_state}."
+            f"but expected charge state from the Defect object is {charge_state}."
         )
     return True
 
 
 @job
 def get_defect_entry(charge_state_summary: dict, bulk_summary: dict):
     """Get a defect entry from a defect calculation and a bulk calculation."""
-    bulk_c_entry = bulk_summary["sc_entry"]
+    bulk_sc_entry = bulk_summary["sc_entry"]
     bulk_struct_entry = ComputedStructureEntry(
         structure=bulk_summary["sc_struct"],
-        energy=bulk_c_entry.energy,
+        energy=bulk_sc_entry.energy,
     )
     bulk_dir_name = bulk_summary["dir_name"]
     bulk_locpot = bulk_summary["locpot_plnr"]

src/atomate2/common/jobs/phonons.py

@@ -227,7 +227,6 @@ def generate_frequencies_eigenvectors(
         Born charges
     kwargs: dict
         Additional parameters that are passed to PhononBSDOSDoc.from_forces_born
-
     """
     return PhononBSDOSDoc.from_forces_born(
         structure=structure,

src/atomate2/common/jobs/utils.py

@@ -30,7 +30,6 @@ def structure_to_primitive(
     Returns
     -------
     .Structure
-
     """
     sga = SpacegroupAnalyzer(structure, symprec=symprec)
     return sga.get_primitive_standard_structure()
@@ -53,7 +52,6 @@ def structure_to_conventional(
     Returns
     -------
     .Structure
-
     """
     sga = SpacegroupAnalyzer(structure, symprec=symprec)
     return sga.get_conventional_standard_structure()

src/atomate2/common/schemas/cclib.py

@@ -26,7 +26,7 @@
 _T = TypeVar("_T", bound="TaskDocument")
 
 
-class TaskDocument(MoleculeMetadata):
+class TaskDocument(MoleculeMetadata, extra="allow"):  # type: ignore[call-arg]
     """
     Definition of a cclib-generated task document.
 
@@ -54,10 +54,8 @@ class TaskDocument(MoleculeMetadata):
         default_factory=datetime_str,
         description="Timestamp for this task document was last updated",
     )
-    _schema: str = Field(
-        __version__,
-        description="Version of atomate2 used to create the document",
-        alias="schema",
+    schema: str = Field(
+        __version__, description="Version of atomate2 used to create the document"
     )
 
     @classmethod
@@ -247,7 +245,7 @@ def from_logfile(
             metadata=metadata,
         )
         doc.molecule = final_molecule
-        return doc.copy(update=additional_fields)
+        return doc.model_copy(update=additional_fields)
 
 
 @requires(cclib, "cclib_calculate requires cclib to be installed.")

src/atomate2/common/schemas/defects.py

@@ -150,13 +150,13 @@ class CCDDocument(BaseModel):
         "in charge state (q2).",
     )
 
-    static_uuids1: List[str] = Field(
+    static_uuids1: Optional[List[str]] = Field(
         None,
         description="UUIDs of distorted calculations for the defect (supercell) in "
         "charge state (q1).",
     )
 
-    static_uuids2: List[str] = Field(
+    static_uuids2: Optional[List[str]] = Field(
         None,
         description="UUIDs of distorted calculations for the defect (supercell) in "
         "charge state (q2).",

src/atomate2/common/schemas/elastic.py

@@ -61,7 +61,7 @@ class DerivedProperties(BaseModel):
     snyder_total: float = Field(
         None, description="Synder's total sound velocity (SI units)."
     )
-    clark_thermalcond: float = Field(
+    clark_thermalcond: Optional[float] = Field(
         None, description="Clarke's thermal conductivity (SI units)."
     )
     cahill_thermalcond: float = Field(
@@ -111,7 +111,7 @@ class ElasticDocument(StructureMetadata):
     elastic_tensor: ElasticTensorDocument = Field(
         None, description="Fitted elastic tensor."
     )
-    eq_stress: Matrix3D = Field(
+    eq_stress: Optional[Matrix3D] = Field(
         None, description="The equilibrium stress of the structure."
     )
     derived_properties: DerivedProperties = Field(

src/atomate2/common/schemas/phonons.py

@@ -67,12 +67,14 @@ class ThermalDisplacementData(BaseModel):
 class PhononUUIDs(BaseModel):
     """Collection to save all uuids connected to the phonon run."""
 
-    optimization_run_uuid: str = Field(None, description="optimization run uuid")
-    displacements_uuids: List[str] = Field(
+    optimization_run_uuid: Optional[str] = Field(
+        None, description="optimization run uuid"
+    )
+    displacements_uuids: Optional[List[str]] = Field(
         None, description="The uuids of the displacement jobs."
     )
-    static_run_uuid: str = Field(None, description="static run uuid")
-    born_run_uuid: str = Field(None, description="born run uuid")
+    static_run_uuid: Optional[str] = Field(None, description="static run uuid")
+    born_run_uuid: Optional[str] = Field(None, description="born run uuid")
 
 
 class ForceConstants(MSONable):
@@ -154,17 +156,17 @@ class PhononBSDOSDoc(StructureMetadata):
     )
 
     # needed, e.g. to compute Grueneisen parameter etc
-    force_constants: ForceConstants = Field(
+    force_constants: Optional[ForceConstants] = Field(
         None, description="Force constants between every pair of atoms in the structure"
     )
 
-    born: List[Matrix3D] = Field(
+    born: Optional[List[Matrix3D]] = Field(
         None,
         description="born charges as computed from phonopy. Only for symmetrically "
         "different atoms",
     )
 
-    epsilon_static: Matrix3D = Field(
+    epsilon_static: Optional[Matrix3D] = Field(
         None, description="The high-frequency dielectric constant"
     )
 
@@ -187,7 +189,7 @@ class PhononBSDOSDoc(StructureMetadata):
         "Field including all relevant job directories"
     )
 
-    uuids: PhononUUIDs = Field("Field including all relevant uuids")
+    uuids: Optional[PhononUUIDs] = Field("Field including all relevant uuids")
 
     @classmethod
     def from_forces_born(