mat3ra-esse 2025.5.17.post1__py3-none-any.whl → 2025.6.5.post0__py3-none-any.whl

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

@@ -131,13 +131,13 @@ class Value(Enum):
     Og = "Og"
 
 
-class Value33(Enum):
+class Value41(Enum):
     X = "X"
     Vac = "Vac"
 
 
 class AtomicElementSchema(BaseModel):
-    value: Union[Value, Value33]
+    value: Union[Value, Value41]
     """
     All elements, including extra elements
     """
@@ -285,30 +285,30 @@ class VolumeSchema(BaseModel):
     value: float
 
 
-class Name104(Enum):
+class Name136(Enum):
     density = "density"
 
 
-class Units46(Enum):
+class Units58(Enum):
     g_cm_3 = "g/cm^3"
 
 
 class DensitySchema(BaseModel):
     name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
-    units: Optional[Units46] = None
+    units: Optional[Units58] = None
     value: float
 
 
-class Units47(Enum):
+class Units59(Enum):
     angstrom = "angstrom"
 
 
 class ScalarSchema(BaseModel):
-    units: Optional[Units47] = None
+    units: Optional[Units59] = None
     value: float
 
 
-class Name105(Enum):
+class Name137(Enum):
     symmetry = "symmetry"
 
 
@@ -328,7 +328,7 @@ class SymmetrySchema(BaseModel):
     name: Literal["2#-datamodel-code-generator-#-object-#-special-#"]
 
 
-class Name106(Enum):
+class Name138(Enum):
     elemental_ratio = "elemental_ratio"
 
 
@@ -341,7 +341,7 @@ class ElementalRatio(BaseModel):
     """
 
 
-class Name107(Enum):
+class Name139(Enum):
     p_norm = "p-norm"
 
 
@@ -354,7 +354,7 @@ class PNorm(BaseModel):
     value: float
 
 
-class Name108(Enum):
+class Name140(Enum):
     inchi = "inchi"
 
 
@@ -363,7 +363,7 @@ class InChIRepresentationSchema(BaseModel):
     value: str
 
 
-class Name109(Enum):
+class Name141(Enum):
     inchi_key = "inchi_key"
 
 
@@ -442,7 +442,7 @@ class FileSourceSchema(BaseModel):
     """
 
 
-class Name110(Enum):
+class Name142(Enum):
     default = "default"
     atomsTooClose = "atomsTooClose"
     atomsOverlap = "atomsOverlap"
@@ -455,7 +455,7 @@ class Severity(Enum):
 
 
 class MaterialConsistencyCheckSchema(BaseModel):
-    name: Name110
+    name: Name142
     """
     Name of the consistency check that is performed, which is listed in an enum.
     """
@@ -559,13 +559,9 @@ class SlabConfigurationSchema(BaseModel):
     """
     use_conventional_cell: Optional[bool] = Field(True, title="Use Conventional Cell")
     """
-    Whether to use conventional cell
+    Whether to use conventional cell when generating the slab.
     """
-    use_orthogonal_z: Optional[bool] = Field(False, title="Use Orthogonal Z")
+    use_orthogonal_z: Optional[bool] = Field(True, 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
+    Whether to make vector c orthogonal to ab plane for the slab cell.
     """

mat3ra/esse/models/materials_category_components/entities/auxiliary/three_dimensional/__init__.py

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

mat3ra/esse/models/materials_category_components/entities/auxiliary/three_dimensional/supercell_matrix_3d.py

@@ -0,0 +1,27 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category_components/entities/auxiliary/three_dimensional/supercell_matrix_3d.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import List, Optional
+
+from pydantic import Field, RootModel
+
+
+class ArrayOf3IntegerElementsSchema(RootModel[List[int]]):
+    root: List[int] = Field(..., title="array of 3 integer elements schema")
+
+
+class SupercellMatrix3DSchema(RootModel[Optional[List[ArrayOf3IntegerElementsSchema]]]):
+    root: Optional[List[ArrayOf3IntegerElementsSchema]] = Field(
+        default_factory=lambda: [
+            ArrayOf3IntegerElementsSchema.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_components/entities/auxiliary/two_dimensional/__init__.py

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

mat3ra/esse/models/materials_category_components/entities/auxiliary/two_dimensional/miller_indices.py

@@ -0,0 +1,16 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category_components/entities/auxiliary/two_dimensional/miller_indices.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import List, Optional
+
+from pydantic import Field, RootModel
+
+
+class MillerIndicesSchema(RootModel[Optional[List[int]]]):
+    root: Optional[List[int]] = Field([0, 0, 1], max_length=3, min_length=3, title="Miller Indices Schema")
+    """
+    Miller indices [h, k, l] defining crystallographic planes
+    """

mat3ra/esse/models/materials_category_components/entities/auxiliary/two_dimensional/supercell_matrix_2d.py

@@ -0,0 +1,25 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category_components/entities/auxiliary/two_dimensional/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/materials_category_components/entities/auxiliary/two_dimensional/termination.py

@@ -0,0 +1,144 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category_components/entities/auxiliary/two_dimensional/termination.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Union
+
+from pydantic import BaseModel, Field, constr
+
+
+class ChemicalElements(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 TerminationSchema(BaseModel):
+    chemical_elements: Union[ChemicalElements, constr(pattern=r"^[A-Z][a-z]?([A-Z][a-z]?)*$")] = Field(
+        ..., title="Chemical Elements"
+    )
+    """
+    Chemical elements at the termination. Can be a single element (e.g. 'Si') or a compound (e.g. 'SiO')
+    """
+    space_group_symmetry_label: str = Field(..., title="Space Group Symmetry Label")
+    """
+    Space group symmetry designation for the termination
+    """

mat3ra/esse/models/materials_category_components/entities/auxiliary/zero_dimensional/__init__.py

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

mat3ra/esse/models/materials_category_components/entities/auxiliary/zero_dimensional/crystal_site.py

@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category_components/entities/auxiliary/zero_dimensional/crystal_site.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from typing import List
+
+from pydantic import BaseModel, Field
+
+
+class CrystalSiteSchema(BaseModel):
+    coordinate: List[float] = Field(..., max_length=3, min_length=3, title="coordinate 3d schema")

mat3ra/esse/models/materials_category_components/entities/core/three_dimensional/__init__.py

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

mat3ra/esse/models/{materials_category/defects/zero_dimensional/slab/configuration.py → materials_category_components/entities/core/three_dimensional/crystal.py}

@@ -1,5 +1,5 @@
 # generated by datamodel-codegen:
-#   filename:  materials_category/defects/zero_dimensional/slab/configuration.json
+#   filename:  materials_category_components/entities/core/three_dimensional/crystal.json
 #   version:   0.28.5
 
 from __future__ import annotations
@@ -10,10 +10,136 @@ 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 Value15(Enum):
+    X = "X"
+    Vac = "Vac"
+
+
 class AtomicElementSchema(BaseModel):
-    value: str
+    value: Union[Value, Value15]
     """
-    value of this entry
+    All elements, including extra elements
     """
     id: int
     """
@@ -159,30 +285,30 @@ class VolumeSchema(BaseModel):
     value: float
 
 
-class Name48(Enum):
+class Name33(Enum):
     density = "density"
 
 
-class Units25(Enum):
+class Units19(Enum):
     g_cm_3 = "g/cm^3"
 
 
 class DensitySchema(BaseModel):
     name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
-    units: Optional[Units25] = None
+    units: Optional[Units19] = None
     value: float
 
 
-class Units26(Enum):
+class Units20(Enum):
     angstrom = "angstrom"
 
 
 class ScalarSchema(BaseModel):
-    units: Optional[Units26] = None
+    units: Optional[Units20] = None
     value: float
 
 
-class Name49(Enum):
+class Name34(Enum):
     symmetry = "symmetry"
 
 
@@ -202,7 +328,7 @@ class SymmetrySchema(BaseModel):
     name: Literal["2#-datamodel-code-generator-#-object-#-special-#"]
 
 
-class Name50(Enum):
+class Name35(Enum):
     elemental_ratio = "elemental_ratio"
 
 
@@ -215,7 +341,7 @@ class ElementalRatio(BaseModel):
     """
 
 
-class Name51(Enum):
+class Name36(Enum):
     p_norm = "p-norm"
 
 
@@ -228,7 +354,7 @@ class PNorm(BaseModel):
     value: float
 
 
-class Name52(Enum):
+class Name37(Enum):
     inchi = "inchi"
 
 
@@ -237,7 +363,7 @@ class InChIRepresentationSchema(BaseModel):
     value: str
 
 
-class Name53(Enum):
+class Name38(Enum):
     inchi_key = "inchi_key"
 
 
@@ -316,7 +442,7 @@ class FileSourceSchema(BaseModel):
     """
 
 
-class Name54(Enum):
+class Name39(Enum):
     default = "default"
     atomsTooClose = "atomsTooClose"
     atomsOverlap = "atomsOverlap"
@@ -329,7 +455,7 @@ class Severity(Enum):
 
 
 class MaterialConsistencyCheckSchema(BaseModel):
-    name: Name54
+    name: Name39
     """
     Name of the consistency check that is performed, which is listed in an enum.
     """
@@ -347,7 +473,7 @@ class MaterialConsistencyCheckSchema(BaseModel):
     """
 
 
-class MaterialSchema(BaseModel):
+class CrystalSchema(BaseModel):
     formula: Optional[str] = None
     """
     reduced chemical formula
@@ -402,33 +528,3 @@ class MaterialSchema(BaseModel):
     Identifies that entity is defaultable
     """
     metadata: Optional[Dict[str, Any]] = None
-
-
-class DefectType(Enum):
-    vacancy = "vacancy"
-    substitution = "substitution"
-    interstitial = "interstitial"
-    adatom = "adatom"
-
-
-class SlabPointDefectConfigurationSchema(BaseModel):
-    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
-    """
-    number_of_added_layers: Optional[conint(ge=1)] = Field(1, title="Number of Layers Schema")
-    """
-    Number of atomic layers in a structural component
-    """
-    crystal: MaterialSchema = Field(..., title="material schema")
-    defect_type: DefectType
-    coordinate: List[float] = Field(..., max_length=3, min_length=3, title="coordinate 3d schema")
-    chemical_element: Optional[str] = None
-    """
-    The chemical element for substitution or interstitial defects
-    """
-    use_cartesian_coordinates: Optional[bool] = False
-    """
-    Whether coordinates are in cartesian rather than fractional coordinates
-    """

mat3ra/esse/models/materials_category_components/entities/core/three_dimensional/void.py

@@ -0,0 +1,32 @@
+# generated by datamodel-codegen:
+#   filename:  materials_category_components/entities/core/three_dimensional/void.json
+#   version:   0.28.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import List, Literal
+
+from pydantic import BaseModel, Field
+
+
+class CoordinateShapeEnum(Enum):
+    cylinder = "cylinder"
+    sphere = "sphere"
+    box = "box"
+    triangular_prism = "triangular_prism"
+    plane = "plane"
+
+
+class BoxCoordinateConditionSchema(BaseModel):
+    shape: Literal["box"] = Field(..., title="Coordinate Shape Enum")
+    min_coordinate: List[float] = Field(..., max_length=3, min_length=3, title="coordinate 3d schema")
+    max_coordinate: List[float] = Field(..., max_length=3, min_length=3, title="coordinate 3d schema")
+
+
+class VoidSchema(BaseModel):
+    center_coordinate: List[float] = Field(..., max_length=3, min_length=3, title="coordinate 3d schema")
+    shape: BoxCoordinateConditionSchema = Field(..., title="Coordinate Conditions Schema")
+    """
+    Combined schema for all coordinate condition types
+    """

mat3ra/esse/models/materials_category_components/entities/core/two_dimensional/__init__.py

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