mat3ra-esse 2024.4.8.post1__py3-none-any.whl → 2024.4.8.post3__py3-none-any.whl

mat3ra/esse/models/material/__init__.py

@@ -0,0 +1,420 @@
+# generated by datamodel-codegen:
+#   filename:  material.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, Field, RootModel, confloat
+from typing_extensions import Literal
+
+
+class AtomicElements(BaseModel):
+    id: float
+    value: str
+    occurrence: Optional[float] = None
+    """
+    Occurrence is for fractional occupations
+    """
+    oxidationState: Optional[float] = None
+
+
+class Label(BaseModel):
+    id: Optional[float] = None
+    value: Optional[float] = None
+
+
+class AtomicCoordinate(BaseModel):
+    id: Optional[float] = None
+    value: Optional[Union[List[float], List[bool]]] = Field(None, title="vector schema")
+
+
+class AtomicId(BaseModel):
+    id: Optional[int] = None
+    """
+    integer id of this entry
+    """
+
+
+class BondType(Enum):
+    single = "single"
+    double = "double"
+    triple = "triple"
+    quadruple = "quadruple"
+    aromatic = "aromatic"
+    tautomeric = "tautomeric"
+    dative = "dative"
+    other = "other"
+
+
+class BondsSchemaItem(BaseModel):
+    atomPair: Optional[List[AtomicId]] = Field(None, max_length=2, min_length=2, title="atomic ids")
+    """
+    indices of the two connected atoms
+    """
+    bondType: Optional[BondType] = None
+
+
+class BasisSchema(BaseModel):
+    elements: List[AtomicElements]
+    labels: Optional[List[Label]] = None
+    """
+    Optional numeric label (e.g., 1, 2, as in Fe1, Fe2) to distinguish same atomic species to attach different spin magnetic moment.
+    """
+    coordinates: List[AtomicCoordinate]
+    name: Optional[str] = None
+    units: Optional[str] = None
+    bonds: Optional[List[BondsSchemaItem]] = Field(None, title="bonds schema")
+
+
+class Name(Enum):
+    lattice = "lattice"
+
+
+class Units(Enum):
+    km = "km"
+    m = "m"
+    pm = "pm"
+    nm = "nm"
+    angstrom = "angstrom"
+    a_u_ = "a.u."
+    bohr = "bohr"
+    fractional = "fractional"
+    crystal = "crystal"
+    cartesian = "cartesian"
+    alat = "alat"
+
+
+class LatticeExplicitUnit(BaseModel):
+    alat: Optional[float] = 1
+    """
+    lattice parameter for fractional coordinates
+    """
+    units: Optional[Units] = None
+    a: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")
+    b: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")
+    c: List[float] = Field(..., max_length=3, min_length=3, title="array of 3 number elements schema")
+
+
+class LatticeTypeSchema(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 Length(Enum):
+    angstrom = "angstrom"
+    bohr = "bohr"
+
+
+class Angle(Enum):
+    degree = "degree"
+    radian = "radian"
+
+
+class Units41(BaseModel):
+    length: Optional[Length] = None
+    angle: Optional[Angle] = None
+
+
+class LatticeSchema(BaseModel):
+    name: Optional[Name] = None
+    vectors: Optional[LatticeExplicitUnit] = Field(None, title="lattice explicit unit")
+    type: LatticeTypeSchema = Field(..., title="lattice type schema")
+    units: Optional[Units41] = None
+    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
+    """
+
+
+class Name128(Enum):
+    volume = "volume"
+
+
+class Units42(Enum):
+    angstrom_3 = "angstrom^3"
+
+
+class VolumeSchema(BaseModel):
+    name: Literal["0#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units42] = None
+    value: float
+
+
+class Name129(Enum):
+    density = "density"
+
+
+class Units43(Enum):
+    g_cm_3 = "g/cm^3"
+
+
+class DensitySchema(BaseModel):
+    name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units43] = None
+    value: float
+
+
+class Units44(Enum):
+    angstrom = "angstrom"
+
+
+class ScalarSchema(BaseModel):
+    units: Optional[Units44] = None
+    value: float
+
+
+class Name130(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 Name131(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 Name132(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 Name133(Enum):
+    inchi = "inchi"
+
+
+class InChIRepresentationSchema(BaseModel):
+    name: Literal["5#-datamodel-code-generator-#-object-#-special-#"]
+    value: str
+
+
+class Name134(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 Name135(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class ConsistencyCheck(BaseModel):
+    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'
+    """
+    name: Name135
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    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)
+    """
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    consistencyChecks: Optional[List[ConsistencyCheck]] = 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

mat3ra/esse/models/material/conventional.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  material/conventional.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Any, Dict, Optional
+
+from pydantic import BaseModel
+
+
+class MaterialConventionalSchema(BaseModel):
+    conventional: Optional[Dict[str, Any]] = None

mat3ra/esse/models/method/__init__.py

@@ -0,0 +1,28 @@
+# generated by datamodel-codegen:
+#   filename:  method.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Any, Dict, Optional
+
+from pydantic import BaseModel
+
+
+class BaseMethod(BaseModel):
+    type: str
+    """
+    general type of this method, eg. `pseudopotential`
+    """
+    subtype: str
+    """
+    general subtype of this method, eg. `ultra-soft`
+    """
+    precision: Optional[Dict[str, Any]] = None
+    """
+    Object showing the actual possible precision based on theory and implementation
+    """
+    data: Optional[Dict[str, Any]] = None
+    """
+    additional data specific to method, eg. array of pseudopotentials
+    """

mat3ra/esse/models/method/categorized_method.py

@@ -0,0 +1,86 @@
+# generated by datamodel-codegen:
+#   filename:  method/categorized_method.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, Field
+
+
+class SlugifiedEntry(BaseModel):
+    name: str
+    """
+    descriptive human-readable name of entry
+    """
+    slug: str
+    """
+    machine-readable identifier
+    """
+
+
+class ReusableCategoriesSchema(BaseModel):
+    tier1: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier2: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier3: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    type: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    subtype: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+
+
+class CategorizedUnitMethod(BaseModel):
+    categories: Optional[ReusableCategoriesSchema] = Field(None, title="Reusable categories schema")
+    """
+    Used to categorize entities such as models and methods
+    """
+    parameters: Optional[Dict[str, Any]] = None
+    """
+    Instructive parameters defining the method
+    """
+    precision: Optional[Dict[str, Any]] = None
+    """
+    Object showing the actual possible precision based on theory and implementation
+    """
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    path: Optional[str] = Field(None, title="category path schema")
+    """
+    TODO: Use regex once schema draft version has been updated
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """
+
+
+class CategorizedMethod(BaseModel):
+    units: List[CategorizedUnitMethod]
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    path: Optional[str] = Field(None, title="category path schema")
+    """
+    TODO: Use regex once schema draft version has been updated
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """

mat3ra/esse/models/method/method_parameters.py

@@ -0,0 +1,48 @@
+# generated by datamodel-codegen:
+#   filename:  method/method_parameters.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Optional, Union
+
+from pydantic import BaseModel, Field, RootModel
+
+
+class BasisSlug(Enum):
+    cc_pvdz = "cc-pvdz"
+    cc_pvtz = "cc-pvtz"
+    cc_pvqz = "cc-pvqz"
+
+
+class MethodParameters(BaseModel):
+    basisSlug: Optional[BasisSlug] = None
+
+
+class BasisSlug3(Enum):
+    field_3_21G = "3-21G"
+    field_6_31G = "6-31G"
+    field_6_311G = "6-311G"
+
+
+class MethodParameters1(BaseModel):
+    basisSlug: Optional[BasisSlug3] = None
+
+
+class BasisSlug4(Enum):
+    sto_3g = "sto-3g"
+    sto_4g = "sto-4g"
+    sto_6g = "sto-6g"
+    def2_svp = "def2-svp"
+    def2_tzvp = "def2-tzvp"
+    def2_qzvp = "def2-qzvp"
+    cbs_qb3 = "cbs-qb3"
+
+
+class MethodParameters2(BaseModel):
+    basisSlug: Optional[BasisSlug4] = None
+
+
+class ESSE(RootModel[Union[MethodParameters, MethodParameters1, MethodParameters2]]):
+    root: Union[MethodParameters, MethodParameters1, MethodParameters2] = Field(..., title="MethodParameters")

mat3ra/esse/models/method/unit_method.py

@@ -0,0 +1,70 @@
+# generated by datamodel-codegen:
+#   filename:  method/unit_method.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, Field
+
+
+class SlugifiedEntry(BaseModel):
+    name: str
+    """
+    descriptive human-readable name of entry
+    """
+    slug: str
+    """
+    machine-readable identifier
+    """
+
+
+class ReusableCategoriesSchema(BaseModel):
+    tier1: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier2: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    tier3: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    type: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+    subtype: Optional[Union[SlugifiedEntry, str]] = Field(None, title="slugified entry or slug")
+    """
+    contains either object with slugified entry or slug only as a string
+    """
+
+
+class CategorizedUnitMethod(BaseModel):
+    categories: Optional[ReusableCategoriesSchema] = Field(None, title="Reusable categories schema")
+    """
+    Used to categorize entities such as models and methods
+    """
+    parameters: Optional[Dict[str, Any]] = None
+    """
+    Instructive parameters defining the method
+    """
+    precision: Optional[Dict[str, Any]] = None
+    """
+    Object showing the actual possible precision based on theory and implementation
+    """
+    name: Optional[str] = None
+    """
+    entity name
+    """
+    path: Optional[str] = Field(None, title="category path schema")
+    """
+    TODO: Use regex once schema draft version has been updated
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """

mat3ra/esse/models/methods_category/mathematical/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5