mat3ra-esse 2025.5.13.post0__py3-none-any.whl → 2025.5.16.post1__py3-none-any.whl

mat3ra/esse/models/materials_category/defects/zero_dimensional/adatom/__init__.py

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+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.28.5

mat3ra/esse/models/materials_category/defects/zero_dimensional/adatom/base_configuration.py

@@ -0,0 +1,418 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category/defects/zero_dimensional/adatom/base_configuration.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Literal, Optional, Union
+
+from pydantic import BaseModel, Field, RootModel, confloat, conint
+
+
+class AtomicElementSchema(BaseModel):
+    value: str
+    """
+    value of this entry
+    """
+    id: int
+    """
+    integer id of this entry
+    """
+
+
+class AtomicCoordinateSchema(BaseModel):
+    value: List[float] = Field(..., max_length=3, min_length=3, title="coordinate 3d schema")
+    """
+    value of this entry
+    """
+    id: int
+    """
+    integer id of this entry
+    """
+
+
+class BasisUnitsEnum(Enum):
+    crystal = "crystal"
+    cartesian = "cartesian"
+
+
+class AtomicLabelSchema(BaseModel):
+    value: Union[Union[int, str, float], conint(ge=1, le=9)]
+    """
+    value of this entry
+    """
+    id: int
+    """
+    integer id of this entry
+    """
+
+
+class BasisSchema(BaseModel):
+    elements: List[AtomicElementSchema] = Field(..., title="atomic elements schema")
+    """
+    atomic elements schema
+    """
+    coordinates: List[AtomicCoordinateSchema] = Field(..., title="atomic coordinates schema")
+    """
+    atomic coordinates schema
+    """
+    units: Optional[BasisUnitsEnum] = Field("crystal", title="basis units enum")
+    labels: Optional[List[AtomicLabelSchema]] = Field(None, title="atomic labels schema")
+    """
+    atomic labels schema
+    """
+
+
+class LatticeVectorsUnitsEnum(Enum):
+    angstrom = "angstrom"
+    bohr = "bohr"
+
+
+class LatticeVectorsSchema(BaseModel):
+    a: List[float] = Field(..., max_length=3, min_length=3, title="vector 3d schema")
+    b: List[float] = Field(..., max_length=3, min_length=3, title="vector 3d schema")
+    c: List[float] = Field(..., max_length=3, min_length=3, title="vector 3d schema")
+    alat: Optional[float] = 1
+    """
+    lattice parameter for fractional coordinates
+    """
+    units: Optional[LatticeVectorsUnitsEnum] = Field("angstrom", title="lattice vectors units enum")
+
+
+class LatticeTypeEnum(Enum):
+    CUB = "CUB"
+    BCC = "BCC"
+    FCC = "FCC"
+    TET = "TET"
+    MCL = "MCL"
+    ORC = "ORC"
+    ORCC = "ORCC"
+    ORCF = "ORCF"
+    ORCI = "ORCI"
+    HEX = "HEX"
+    BCT = "BCT"
+    TRI = "TRI"
+    MCLC = "MCLC"
+    RHL = "RHL"
+
+
+class LatticeUnitsLengthEnum(Enum):
+    angstrom = "angstrom"
+    bohr = "bohr"
+
+
+class LatticeUnitsAngleEnum(Enum):
+    degree = "degree"
+    radian = "radian"
+
+
+class LatticeUnitsSchema(BaseModel):
+    length: Optional[LatticeUnitsLengthEnum] = Field("angstrom", title="lattice units length enum")
+    angle: Optional[LatticeUnitsAngleEnum] = Field("degree", title="lattice units angle enum")
+
+
+class LatticeSchema(BaseModel):
+    a: float
+    """
+    length of the first lattice vector
+    """
+    b: float
+    """
+    length of the second lattice vector
+    """
+    c: float
+    """
+    length of the third lattice vector
+    """
+    alpha: float
+    """
+    angle between first and second lattice vector
+    """
+    beta: float
+    """
+    angle between second and third lattice vector
+    """
+    gamma: float
+    """
+    angle between first and third lattice vector
+    """
+    vectors: Optional[LatticeVectorsSchema] = Field(None, title="lattice vectors schema")
+    type: Optional[LatticeTypeEnum] = Field("TRI", title="lattice type enum")
+    units: Optional[LatticeUnitsSchema] = Field(
+        default_factory=lambda: LatticeUnitsSchema.model_validate({"length": "angstrom", "angle": "degree"}),
+        title="Lattice units schema",
+    )
+
+
+class Name(Enum):
+    volume = "volume"
+
+
+class Units(Enum):
+    angstrom_3 = "angstrom^3"
+
+
+class VolumeSchema(BaseModel):
+    name: Literal["0#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units] = None
+    value: float
+
+
+class Name7(Enum):
+    density = "density"
+
+
+class Units9(Enum):
+    g_cm_3 = "g/cm^3"
+
+
+class DensitySchema(BaseModel):
+    name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units9] = None
+    value: float
+
+
+class Units10(Enum):
+    angstrom = "angstrom"
+
+
+class ScalarSchema(BaseModel):
+    units: Optional[Units10] = None
+    value: float
+
+
+class Name8(Enum):
+    symmetry = "symmetry"
+
+
+class SymmetrySchema(BaseModel):
+    pointGroupSymbol: Optional[str] = None
+    """
+    point group symbol in Schoenflies notation
+    """
+    spaceGroupSymbol: Optional[str] = None
+    """
+    space group symbol in Hermann–Mauguin notation
+    """
+    tolerance: Optional[ScalarSchema] = Field(None, title="scalar schema")
+    """
+    tolerance used for symmetry calculation
+    """
+    name: Literal["2#-datamodel-code-generator-#-object-#-special-#"]
+
+
+class Name9(Enum):
+    elemental_ratio = "elemental_ratio"
+
+
+class ElementalRatio(BaseModel):
+    name: Literal["3#-datamodel-code-generator-#-object-#-special-#"]
+    value: confloat(ge=0.0, le=1.0)
+    element: Optional[str] = None
+    """
+    the element this ratio is for
+    """
+
+
+class Name10(Enum):
+    p_norm = "p-norm"
+
+
+class PNorm(BaseModel):
+    name: Literal["4#-datamodel-code-generator-#-object-#-special-#"]
+    degree: Optional[int] = None
+    """
+    degree of the dimensionality of the norm
+    """
+    value: float
+
+
+class Name11(Enum):
+    inchi = "inchi"
+
+
+class InChIRepresentationSchema(BaseModel):
+    name: Literal["5#-datamodel-code-generator-#-object-#-special-#"]
+    value: str
+
+
+class Name12(Enum):
+    inchi_key = "inchi_key"
+
+
+class InChIKeyRepresentationSchema(BaseModel):
+    name: Literal["6#-datamodel-code-generator-#-object-#-special-#"]
+    value: str
+
+
+class DerivedPropertiesSchema(
+    RootModel[
+        Union[
+            VolumeSchema,
+            DensitySchema,
+            SymmetrySchema,
+            ElementalRatio,
+            PNorm,
+            InChIRepresentationSchema,
+            InChIKeyRepresentationSchema,
+        ]
+    ]
+):
+    root: Union[
+        VolumeSchema,
+        DensitySchema,
+        SymmetrySchema,
+        ElementalRatio,
+        PNorm,
+        InChIRepresentationSchema,
+        InChIKeyRepresentationSchema,
+    ] = Field(..., discriminator="name")
+
+
+class DatabaseSourceSchema(BaseModel):
+    id: Union[str, float]
+    """
+    ID string for the materials uploaded from a third party source inside the third party source. For materialsproject.org an example ID is mp-32
+    """
+    source: str
+    """
+    Third party source name, e.g. materials project, 2dmatpedia, ICSD, etc.
+    """
+    origin: bool
+    """
+    Deprecated. To be removed. A flag that is true when material is initially imported from a third party * (as opposed to being independently designed from scratch).
+    """
+    data: Optional[Dict[str, Any]] = None
+    """
+    Original response from external source.
+    """
+    doi: Optional[str] = None
+    """
+    Digital Object Identifier, e.g. 10.1088/0953-8984/25/10/105506
+    """
+    url: Optional[str] = None
+    """
+    The URL of the original record, e.g. https://next-gen.materialsproject.org/materials/mp-48; ToDo: update to use URI type per https://json-schema.org/understanding-json-schema/reference/string#resource-identifiers
+    """
+
+
+class FileSourceSchema(BaseModel):
+    extension: Optional[str] = None
+    """
+    file extension
+    """
+    filename: str
+    """
+    file name without extension
+    """
+    text: str
+    """
+    file content as raw text
+    """
+    hash: str
+    """
+    MD5 hash based on file content
+    """
+
+
+class Name13(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class MaterialConsistencyCheckSchema(BaseModel):
+    name: Name13
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    key: str
+    """
+    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+    """
+    severity: Severity
+    """
+    Severity level of the problem, which is used in UI to differentiate.
+    """
+    message: str
+    """
+    Message generated by the consistency check describing the problem.
+    """
+
+
+class MaterialSchema(BaseModel):
+    formula: Optional[str] = None
+    """
+    reduced chemical formula
+    """
+    unitCellFormula: Optional[str] = None
+    """
+    chemical formula based on the number of atoms of each element in the supercell
+    """
+    basis: BasisSchema = Field(..., title="basis schema")
+    lattice: LatticeSchema = Field(..., title="lattice schema")
+    derivedProperties: Optional[List[DerivedPropertiesSchema]] = Field(None, title="derived properties schema")
+    external: Optional[DatabaseSourceSchema] = Field(None, title="database source schema")
+    """
+    information about a database source
+    """
+    src: Optional[FileSourceSchema] = Field(None, title="file source schema")
+    """
+    file source with the information inside
+    """
+    scaledHash: Optional[str] = None
+    """
+    Hash string for a scaled structure with lattice vector a set to 1 (eg. for materials under pressure).
+    """
+    icsdId: Optional[int] = None
+    """
+    Corresponding ICSD id of the material
+    """
+    isNonPeriodic: Optional[bool] = None
+    """
+    Whether to work in the finite molecular picture (usually with atomic orbital basis)
+    """
+    consistencyChecks: Optional[List[MaterialConsistencyCheckSchema]] = None
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    schemaVersion: Optional[str] = "2022.8.16"
+    """
+    entity's schema version. Used to distinct between different schemas.
+    """
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    isDefault: Optional[bool] = False
+    """
+    Identifies that entity is defaultable
+    """
+    metadata: Optional[Dict[str, Any]] = None
+
+
+class AdatomConfigurationWithoutCrystalSchema(BaseModel):
+    crystal: Optional[MaterialSchema] = Field(None, title="material schema")
+    defect_type: Literal["adatom"] = "adatom"
+    position_on_surface: List[float] = Field(..., max_length=2, min_length=2, title="coordinate 2d schema")
+    distance_z: confloat(ge=0.0)
+    """
+    Distance from the surface in Angstroms
+    """
+    chemical_element: str
+    """
+    Chemical element of the adatom
+    """