mat3ra-esse 2025.6.14.post0__py3-none-any.whl → 2025.7.1.post0__py3-none-any.whl

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

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

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

@@ -1,567 +0,0 @@
-# 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 Value(Enum):
-    H = "H"
-    He = "He"
-    Li = "Li"
-    Be = "Be"
-    B = "B"
-    C = "C"
-    N = "N"
-    O = "O"
-    F = "F"
-    Ne = "Ne"
-    Na = "Na"
-    Mg = "Mg"
-    Al = "Al"
-    Si = "Si"
-    P = "P"
-    S = "S"
-    Cl = "Cl"
-    Ar = "Ar"
-    K = "K"
-    Ca = "Ca"
-    Sc = "Sc"
-    Ti = "Ti"
-    V = "V"
-    Cr = "Cr"
-    Mn = "Mn"
-    Fe = "Fe"
-    Co = "Co"
-    Ni = "Ni"
-    Cu = "Cu"
-    Zn = "Zn"
-    Ga = "Ga"
-    Ge = "Ge"
-    As = "As"
-    Se = "Se"
-    Br = "Br"
-    Kr = "Kr"
-    Rb = "Rb"
-    Sr = "Sr"
-    Y = "Y"
-    Zr = "Zr"
-    Nb = "Nb"
-    Mo = "Mo"
-    Tc = "Tc"
-    Ru = "Ru"
-    Rh = "Rh"
-    Pd = "Pd"
-    Ag = "Ag"
-    Cd = "Cd"
-    In = "In"
-    Sn = "Sn"
-    Sb = "Sb"
-    Te = "Te"
-    I = "I"
-    Xe = "Xe"
-    Cs = "Cs"
-    Ba = "Ba"
-    La = "La"
-    Ce = "Ce"
-    Pr = "Pr"
-    Nd = "Nd"
-    Pm = "Pm"
-    Sm = "Sm"
-    Eu = "Eu"
-    Gd = "Gd"
-    Tb = "Tb"
-    Dy = "Dy"
-    Ho = "Ho"
-    Er = "Er"
-    Tm = "Tm"
-    Yb = "Yb"
-    Lu = "Lu"
-    Hf = "Hf"
-    Ta = "Ta"
-    W = "W"
-    Re = "Re"
-    Os = "Os"
-    Ir = "Ir"
-    Pt = "Pt"
-    Au = "Au"
-    Hg = "Hg"
-    Tl = "Tl"
-    Pb = "Pb"
-    Bi = "Bi"
-    Po = "Po"
-    At = "At"
-    Rn = "Rn"
-    Fr = "Fr"
-    Ra = "Ra"
-    Ac = "Ac"
-    Th = "Th"
-    Pa = "Pa"
-    U = "U"
-    Np = "Np"
-    Pu = "Pu"
-    Am = "Am"
-    Cm = "Cm"
-    Bk = "Bk"
-    Cf = "Cf"
-    Es = "Es"
-    Fm = "Fm"
-    Md = "Md"
-    No = "No"
-    Lr = "Lr"
-    Rf = "Rf"
-    Db = "Db"
-    Sg = "Sg"
-    Bh = "Bh"
-    Hs = "Hs"
-    Mt = "Mt"
-    Ds = "Ds"
-    Rg = "Rg"
-    Cn = "Cn"
-    Nh = "Nh"
-    Fl = "Fl"
-    Mc = "Mc"
-    Lv = "Lv"
-    Ts = "Ts"
-    Og = "Og"
-
-
-class Value41(Enum):
-    X = "X"
-    Vac = "Vac"
-
-
-class AtomicElementSchema(BaseModel):
-    value: Union[Value, Value41]
-    """
-    All elements, including extra elements
-    """
-    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 Name136(Enum):
-    density = "density"
-
-
-class Units58(Enum):
-    g_cm_3 = "g/cm^3"
-
-
-class DensitySchema(BaseModel):
-    name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
-    units: Optional[Units58] = None
-    value: float
-
-
-class Units59(Enum):
-    angstrom = "angstrom"
-
-
-class ScalarSchema(BaseModel):
-    units: Optional[Units59] = None
-    value: float
-
-
-class Name137(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 Name138(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 Name139(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 Name140(Enum):
-    inchi = "inchi"
-
-
-class InChIRepresentationSchema(BaseModel):
-    name: Literal["5#-datamodel-code-generator-#-object-#-special-#"]
-    value: str
-
-
-class Name141(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 Name142(Enum):
-    default = "default"
-    atomsTooClose = "atomsTooClose"
-    atomsOverlap = "atomsOverlap"
-
-
-class Severity(Enum):
-    info = "info"
-    warning = "warning"
-    error = "error"
-
-
-class MaterialConsistencyCheckSchema(BaseModel):
-    name: Name142
-    """
-    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 Thickness 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 when generating the slab.
-    """
-    use_orthogonal_z: Optional[bool] = Field(True, title="Use Orthogonal Z")
-    """
-    Whether to make vector c orthogonal to ab plane for the slab cell.
-    """

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

@@ -1,129 +0,0 @@
-# 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
-    """