mat3ra-esse 2025.4.17.post0__py3-none-any.whl → 2025.5.13.post0__py3-none-any.whl

mat3ra/esse/models/material/reusable/slab/thickness.py

@@ -0,0 +1,16 @@
+# generated by datamodel-codegen:
+#   filename:  material/reusable/slab/number_of_layers.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import Optional
+
+from pydantic import Field, RootModel, conint
+
+
+class number_of_layersSchema(RootModel[Optional[conint(ge=1)]]):
+    root: Optional[conint(ge=1)] = Field(1, title="number_of_layers Schema")
+    """
+    Number of atomic layers in a structural component
+    """

mat3ra/esse/models/material/reusable/slab/vacuum.py

@@ -0,0 +1,16 @@
+# generated by datamodel-codegen:
+#   filename:  material/reusable/slab/vacuum.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import Optional
+
+from pydantic import Field, RootModel, confloat
+
+
+class VacuumSchema(RootModel[Optional[confloat(ge=0.0)]]):
+    root: Optional[confloat(ge=0.0)] = Field(5, title="Vacuum Schema")
+    """
+    Vacuum thickness in Angstroms
+    """

mat3ra/esse/models/material/reusable/supercell_matrix_2d.py

@@ -0,0 +1,25 @@
+# generated by datamodel-codegen:
+#   filename:  material/reusable/supercell_matrix_2d.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import List, Optional
+
+from pydantic import Field, RootModel
+
+
+class SupercellMatrix2DSchemaItem(RootModel[List[int]]):
+    root: List[int]
+
+
+class SupercellMatrix2DSchema(RootModel[Optional[List[SupercellMatrix2DSchemaItem]]]):
+    root: Optional[List[SupercellMatrix2DSchemaItem]] = Field(
+        default_factory=lambda: [SupercellMatrix2DSchemaItem.model_validate(v) for v in [[1, 0], [0, 1]]],
+        max_length=2,
+        min_length=2,
+        title="Supercell Matrix 2D Schema",
+    )
+    """
+    Supercell matrix for xy plane transformations
+    """

mat3ra/esse/models/material/reusable/supercell_matrix_3d.py

@@ -0,0 +1,27 @@
+# generated by datamodel-codegen:
+#   filename:  material/reusable/supercell_matrix_3d.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import List, Optional
+
+from pydantic import Field, RootModel
+
+
+class SupercellMatrix3DSchemaItem(RootModel[List[int]]):
+    root: List[int]
+
+
+class SupercellMatrix3DSchema(RootModel[Optional[List[SupercellMatrix3DSchemaItem]]]):
+    root: Optional[List[SupercellMatrix3DSchemaItem]] = Field(
+        default_factory=lambda: [
+            SupercellMatrix3DSchemaItem.model_validate(v) for v in [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+        ],
+        max_length=3,
+        min_length=3,
+        title="Supercell Matrix 3D Schema",
+    )
+    """
+    3x3 matrix of integers for transforming a unit cell into a supercell
+    """

mat3ra/esse/models/materials_category/single_material/two_dimensional/slab/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.28.5

mat3ra/esse/models/materials_category/single_material/two_dimensional/slab/configuration.py

@@ -0,0 +1,445 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category/single_material/two_dimensional/slab/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 Name8(Enum):
+    density = "density"
+
+
+class Units10(Enum):
+    g_cm_3 = "g/cm^3"
+
+
+class DensitySchema(BaseModel):
+    name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
+    units: Optional[Units10] = None
+    value: float
+
+
+class Units11(Enum):
+    angstrom = "angstrom"
+
+
+class ScalarSchema(BaseModel):
+    units: Optional[Units11] = None
+    value: float
+
+
+class Name9(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 Name10(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 Name11(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 Name12(Enum):
+    inchi = "inchi"
+
+
+class InChIRepresentationSchema(BaseModel):
+    name: Literal["5#-datamodel-code-generator-#-object-#-special-#"]
+    value: str
+
+
+class Name13(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 Name14(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class MaterialConsistencyCheckSchema(BaseModel):
+    name: Name14
+    """
+    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 SupercellMatrix2DSchemaItem(RootModel[List[int]]):
+    root: List[int]
+
+
+class SlabConfigurationSchema(BaseModel):
+    bulk: Optional[MaterialSchema] = Field(None, title="material schema")
+    miller_indices: Optional[List[int]] = Field([0, 0, 1], max_length=3, min_length=3, title="Miller Indices Schema")
+    """
+    Miller indices for crystallographic plane designation
+    """
+    number_of_layers: Optional[conint(ge=1)] = Field(1, title="number_of_layers Schema")
+    """
+    Number of atomic layers in a structural component
+    """
+    vacuum: Optional[confloat(ge=0.0)] = Field(5, title="Vacuum Schema")
+    """
+    Vacuum thickness in Angstroms
+    """
+    xy_supercell_matrix: Optional[List[SupercellMatrix2DSchemaItem]] = Field(
+        default_factory=lambda: [SupercellMatrix2DSchemaItem.model_validate(v) for v in [[1, 0], [0, 1]]],
+        max_length=2,
+        min_length=2,
+        title="Supercell Matrix 2D Schema",
+    )
+    """
+    Supercell matrix for xy plane transformations
+    """
+    use_conventional_cell: Optional[bool] = Field(True, title="Use Conventional Cell")
+    """
+    Whether to use conventional cell
+    """
+    use_orthogonal_z: Optional[bool] = Field(False, title="Use Orthogonal Z")
+    """
+    Whether to make z-axis orthogonal
+    """
+    make_primitive: Optional[bool] = Field(False, title="Make Primitive")
+    """
+    Whether to make the slab primitive
+    """

mat3ra/esse/models/methods_directory/physical/psp/file/__init__.py

@@ -0,0 +1,129 @@
+# generated by datamodel-codegen:
+#   filename:  methods_directory/physical/psp/file.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional
+
+from pydantic import BaseModel, ConfigDict, Field, confloat, conint, constr
+
+from ..Reusable_schema_for_energy_value_with_unit_corresponding_to_a_specific_accuracy_level__e import (
+    g,
+)
+
+
+class Slug(Enum):
+    pseudopotential = "pseudopotential"
+
+
+class Type(Enum):
+    us = "us"
+    nc = "nc"
+    nc_fr = "nc-fr"
+    paw = "paw"
+    coulomb = "coulomb"
+
+
+class ExchangeCorrelation(BaseModel):
+    approximation: Optional[str] = None
+    """
+    DFT approximation
+    """
+    functional: Optional[str] = None
+    """
+    Exchange correlation functional
+    """
+    path: Optional[str] = Field(None, title="category path schema")
+    """
+    TODO: Use regex once schema draft version has been updated
+    """
+
+
+class AtomicOrbitalSchema(BaseModel):
+    orbitalName: Optional[constr(pattern=r"^[1-7][sSpPdDfF]$")] = None
+    orbitalIndex: Optional[conint(ge=1)] = None
+    principalNumber: Optional[conint(ge=1, le=7)] = None
+    angularMomentum: Optional[conint(ge=0, le=3)] = None
+    occupation: Optional[confloat(ge=0.0, le=14.0)] = None
+    """
+    Shell occupation
+    """
+
+
+class Name(Enum):
+    pseudopotential = "pseudopotential"
+
+
+class Cutoffs(BaseModel):
+    model_config = ConfigDict(
+        extra="forbid",
+    )
+    wavefunction: Optional[List[g.FieldUsedForSuggestedWavefunctionAndChargeDensityCutoffs]] = None
+    """
+    Energy cutoff values for wavefunction plane wave expansion.
+    """
+    density: Optional[List[g.FieldUsedForSuggestedWavefunctionAndChargeDensityCutoffs]] = None
+    """
+    Energy cutoff values for charge density plane wave expansion.
+    """
+
+
+class FileDataItem(BaseModel):
+    element: str
+    """
+    chemical element
+    """
+    hash: Optional[str] = None
+    """
+    MD5 hash of the pseudopotential file
+    """
+    type: Type
+    source: str
+    """
+    explains where this came from
+    """
+    version: Optional[str] = None
+    """
+    explains the version of where this came from
+    """
+    exchangeCorrelation: ExchangeCorrelation
+    valenceConfiguration: Optional[List[AtomicOrbitalSchema]] = None
+    """
+    contains pseudo orbital information, including orbital names and occupations
+    """
+    path: str
+    """
+    location of the pseudopotential file on filesystem
+    """
+    apps: List[str]
+    """
+    The names of the simulation engines that can use this pseudopotential, e.g. espresso
+    """
+    filename: Optional[str] = None
+    """
+    filename of pseudopotential file on filesystem
+    """
+    name: Optional[Name] = None
+    """
+    name of the data category
+    """
+    cutoffs: Optional[Cutoffs] = None
+    """
+    Suggested cutoff values for wave function and charge density.
+    """
+
+
+class Source(BaseModel):
+    info: Optional[Dict[str, Any]] = None
+    type: Optional[str] = None
+
+
+class PseudopotentialFile(BaseModel):
+    slug: Optional[Slug] = None
+    data: Optional[FileDataItem] = Field(None, title="File data item")
+    source: Optional[Source] = None
+    """
+    TODO: remove in the future
+    """