mat3ra-esse 2025.7.29.post0__py3-none-any.whl → 2025.8.6.post0__py3-none-any.whl

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  1. mat3ra/esse/data/examples.py +1 -1
  2. mat3ra/esse/data/schemas.py +1 -1
  3. mat3ra/esse/models/apse/file/applications/espresso/7.2/pw_x.py +6 -6
  4. mat3ra/esse/models/core/reusable/energy.py +2 -2
  5. mat3ra/esse/models/element.py +6 -6
  6. mat3ra/esse/models/material/__init__.py +14 -14
  7. mat3ra/esse/models/materials_category/compound_pristine_structures/two_dimensional/interface/configuration.py +549 -2319
  8. mat3ra/esse/models/materials_category/defective_structures/one_dimensional/grain_boundary_linear/configuration.py +537 -2307
  9. mat3ra/esse/models/materials_category/defective_structures/two_dimensional/adatom/configuration.py +206 -190
  10. mat3ra/esse/models/materials_category/defective_structures/two_dimensional/grain_boundary_planar/configuration.py +56 -1826
  11. mat3ra/esse/models/materials_category/defective_structures/two_dimensional/island/configuration.py +331 -311
  12. mat3ra/esse/models/materials_category/defective_structures/two_dimensional/terrace/configuration.py +331 -311
  13. mat3ra/esse/models/materials_category/defective_structures/zero_dimensional/point_defect/interstitial.py +72 -72
  14. mat3ra/esse/models/materials_category/defective_structures/zero_dimensional/point_defect/substitutional.py +72 -72
  15. mat3ra/esse/models/materials_category/defective_structures/zero_dimensional/point_defect/vacancy.py +14 -14
  16. mat3ra/esse/models/materials_category/pristine_structures/three_dimensional/ideal_crystal.py +14 -14
  17. mat3ra/esse/models/materials_category/pristine_structures/two_dimensional/nanoribbon.py +150 -134
  18. mat3ra/esse/models/materials_category/pristine_structures/two_dimensional/nanotape.py +86 -74
  19. mat3ra/esse/models/materials_category/pristine_structures/two_dimensional/slab.py +84 -72
  20. mat3ra/esse/models/materials_category/pristine_structures/two_dimensional/slab_strained_supercell.py +84 -72
  21. mat3ra/esse/models/materials_category/processed_structures/two_dimensional/passivation/configuration.py +70 -70
  22. mat3ra/esse/models/materials_category_components/entities/auxiliary/zero_dimensional/crystal_site.py +14 -14
  23. mat3ra/esse/models/materials_category_components/entities/auxiliary/zero_dimensional/point_defect_site.py +14 -14
  24. mat3ra/esse/models/materials_category_components/entities/auxiliary/zero_dimensional/void_region.py +14 -14
  25. mat3ra/esse/models/materials_category_components/entities/core/three_dimensional/crystal.py +14 -14
  26. mat3ra/esse/models/materials_category_components/entities/core/two_dimensional/vacuum.py +14 -14
  27. mat3ra/esse/models/materials_category_components/entities/reusable/one_dimensional/crystal_lattice_lines.py +14 -14
  28. mat3ra/esse/models/materials_category_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated.py +16 -16
  29. mat3ra/esse/models/materials_category_components/entities/reusable/three_dimensional/crystal_lattice_base.py +14 -14
  30. mat3ra/esse/models/materials_category_components/entities/reusable/{repetitions.py → three_dimensional/repetitions.py} +1 -1
  31. mat3ra/esse/models/materials_category_components/entities/reusable/three_dimensional/strained_non_uniform.py +14 -14
  32. mat3ra/esse/models/materials_category_components/entities/reusable/three_dimensional/strained_uniform.py +14 -14
  33. mat3ra/esse/models/materials_category_components/entities/reusable/three_dimensional/supercell.py +14 -14
  34. mat3ra/esse/models/materials_category_components/entities/reusable/two_dimensional/crystal_lattice_planes.py +14 -14
  35. mat3ra/esse/models/materials_category_components/entities/reusable/two_dimensional/slab_stack_configuration.py +148 -132
  36. mat3ra/esse/models/materials_category_components/operations/core/combinations/stack.py +14 -2
  37. mat3ra/esse/models/materials_category_components/operations/core/modifications/perturb.py +14 -14
  38. mat3ra/esse/models/properties_directory/derived_properties.py +11 -11
  39. mat3ra/esse/models/properties_directory/non_scalar/density_of_states.py +2 -2
  40. mat3ra/esse/models/properties_directory/non_scalar/phonon_dispersions.py +2 -2
  41. mat3ra/esse/models/properties_directory/non_scalar/phonon_dos.py +2 -2
  42. mat3ra/esse/models/properties_directory/non_scalar/total_energy_contributions.py +50 -50
  43. mat3ra/esse/models/properties_directory/non_scalar/vibrational_spectrum.py +2 -2
  44. mat3ra/esse/models/properties_directory/scalar/electron_affinity.py +2 -2
  45. mat3ra/esse/models/properties_directory/scalar/fermi_energy.py +2 -2
  46. mat3ra/esse/models/properties_directory/scalar/formation_energy.py +2 -2
  47. mat3ra/esse/models/properties_directory/scalar/ionization_potential.py +2 -2
  48. mat3ra/esse/models/properties_directory/scalar/reaction_energy_barrier.py +2 -2
  49. mat3ra/esse/models/properties_directory/scalar/surface_energy.py +2 -2
  50. mat3ra/esse/models/properties_directory/scalar/total_energy.py +2 -2
  51. mat3ra/esse/models/properties_directory/scalar/valence_band_offset.py +2 -2
  52. mat3ra/esse/models/properties_directory/scalar/zero_point_energy.py +2 -2
  53. mat3ra/esse/models/properties_directory/structural/molecular_pattern.py +4 -4
  54. mat3ra/esse/models/properties_directory/workflow/convergence/ionic.py +2 -2
  55. {mat3ra_esse-2025.7.29.post0.dist-info → mat3ra_esse-2025.8.6.post0.dist-info}/METADATA +1 -1
  56. {mat3ra_esse-2025.7.29.post0.dist-info → mat3ra_esse-2025.8.6.post0.dist-info}/RECORD +59 -60
  57. mat3ra/esse/models/materials_category/pristine_structures/two_dimensional/slab_strained_supercell_with_gap.py +0 -1151
  58. {mat3ra_esse-2025.7.29.post0.dist-info → mat3ra_esse-2025.8.6.post0.dist-info}/WHEEL +0 -0
  59. {mat3ra_esse-2025.7.29.post0.dist-info → mat3ra_esse-2025.8.6.post0.dist-info}/licenses/LICENSE.md +0 -0
  60. {mat3ra_esse-2025.7.29.post0.dist-info → mat3ra_esse-2025.8.6.post0.dist-info}/top_level.txt +0 -0
@@ -273,13 +273,13 @@ class Value(Enum):
273
273
  Og = "Og"
274
274
 
275
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276
- class Value181(Enum):
276
+ class Value157(Enum):
277
277
  X = "X"
278
278
  Vac = "Vac"
279
279
 
280
280
 
281
281
  class AtomicElementSchema(BaseModel):
282
- value: Union[Value, Value181]
282
+ value: Union[Value, Value157]
283
283
  """
284
284
  All elements, including extra elements
285
285
  """
@@ -427,30 +427,30 @@ class VolumeSchema(BaseModel):
427
427
  value: float
428
428
 
429
429
 
430
- class Name725(Enum):
430
+ class Name629(Enum):
431
431
  density = "density"
432
432
 
433
433
 
434
- class Units294(Enum):
434
+ class Units258(Enum):
435
435
  g_cm_3 = "g/cm^3"
436
436
 
437
437
 
438
438
  class DensitySchema(BaseModel):
439
439
  name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
440
- units: Optional[Units294] = None
440
+ units: Optional[Units258] = None
441
441
  value: float
442
442
 
443
443
 
444
- class Units295(Enum):
444
+ class Units259(Enum):
445
445
  angstrom = "angstrom"
446
446
 
447
447
 
448
448
  class ScalarSchema(BaseModel):
449
- units: Optional[Units295] = None
449
+ units: Optional[Units259] = None
450
450
  value: float
451
451
 
452
452
 
453
- class Name726(Enum):
453
+ class Name630(Enum):
454
454
  symmetry = "symmetry"
455
455
 
456
456
 
@@ -470,7 +470,7 @@ class SymmetrySchema(BaseModel):
470
470
  name: Literal["2#-datamodel-code-generator-#-object-#-special-#"]
471
471
 
472
472
 
473
- class Name727(Enum):
473
+ class Name631(Enum):
474
474
  elemental_ratio = "elemental_ratio"
475
475
 
476
476
 
@@ -483,7 +483,7 @@ class ElementalRatio(BaseModel):
483
483
  """
484
484
 
485
485
 
486
- class Name728(Enum):
486
+ class Name632(Enum):
487
487
  p_norm = "p-norm"
488
488
 
489
489
 
@@ -496,7 +496,7 @@ class PNorm(BaseModel):
496
496
  value: float
497
497
 
498
498
 
499
- class Name729(Enum):
499
+ class Name633(Enum):
500
500
  inchi = "inchi"
501
501
 
502
502
 
@@ -505,7 +505,7 @@ class InChIRepresentationSchema(BaseModel):
505
505
  value: str
506
506
 
507
507
 
508
- class Name730(Enum):
508
+ class Name634(Enum):
509
509
  inchi_key = "inchi_key"
510
510
 
511
511
 
@@ -584,7 +584,7 @@ class FileSourceSchema(BaseModel):
584
584
  """
585
585
 
586
586
 
587
- class Name731(Enum):
587
+ class Name635(Enum):
588
588
  default = "default"
589
589
  atomsTooClose = "atomsTooClose"
590
590
  atomsOverlap = "atomsOverlap"
@@ -597,7 +597,7 @@ class Severity(Enum):
597
597
 
598
598
 
599
599
  class MaterialConsistencyCheckSchema(BaseModel):
600
- name: Name731
600
+ name: Name635
601
601
  """
602
602
  Name of the consistency check that is performed, which is listed in an enum.
603
603
  """
@@ -701,7 +701,7 @@ class AxisEnum(Enum):
701
701
  z = "z"
702
702
 
703
703
 
704
- class Value182(Enum):
704
+ class Value158(Enum):
705
705
  H = "H"
706
706
  He = "He"
707
707
  Li = "Li"
@@ -822,13 +822,13 @@ class Value182(Enum):
822
822
  Og = "Og"
823
823
 
824
824
 
825
- class Value183(Enum):
825
+ class Value159(Enum):
826
826
  X = "X"
827
827
  Vac = "Vac"
828
828
 
829
829
 
830
- class AtomicElementSchema87(BaseModel):
831
- value: Union[Value182, Value183]
830
+ class AtomicElementSchema75(BaseModel):
831
+ value: Union[Value158, Value159]
832
832
  """
833
833
  All elements, including extra elements
834
834
  """
@@ -838,8 +838,8 @@ class AtomicElementSchema87(BaseModel):
838
838
  """
839
839
 
840
840
 
841
- class BasisSchema85(BaseModel):
842
- elements: List[AtomicElementSchema87] = Field(..., title="atomic elements schema")
841
+ class BasisSchema73(BaseModel):
842
+ elements: List[AtomicElementSchema75] = Field(..., title="atomic elements schema")
843
843
  """
844
844
  atomic elements schema
845
845
  """
@@ -854,7 +854,7 @@ class BasisSchema85(BaseModel):
854
854
  """
855
855
 
856
856
 
857
- class LatticeVectorsSchema85(BaseModel):
857
+ class LatticeVectorsSchema73(BaseModel):
858
858
  a: List[float] = Field(..., max_length=3, min_length=3, title="vector 3d schema")
859
859
  b: List[float] = Field(..., max_length=3, min_length=3, title="vector 3d schema")
860
860
  c: List[float] = Field(..., max_length=3, min_length=3, title="vector 3d schema")
@@ -865,12 +865,12 @@ class LatticeVectorsSchema85(BaseModel):
865
865
  units: Optional[LatticeVectorsUnitsEnum] = Field("angstrom", title="lattice vectors units enum")
866
866
 
867
867
 
868
- class LatticeUnitsSchema86(BaseModel):
868
+ class LatticeUnitsSchema74(BaseModel):
869
869
  length: Optional[LatticeUnitsLengthEnum] = Field("angstrom", title="lattice units length enum")
870
870
  angle: Optional[LatticeUnitsAngleEnum] = Field("degree", title="lattice units angle enum")
871
871
 
872
872
 
873
- class LatticeSchema85(BaseModel):
873
+ class LatticeSchema73(BaseModel):
874
874
  a: float
875
875
  """
876
876
  length of the first lattice vector
@@ -895,56 +895,56 @@ class LatticeSchema85(BaseModel):
895
895
  """
896
896
  angle between first and third lattice vector
897
897
  """
898
- vectors: Optional[LatticeVectorsSchema85] = Field(None, title="lattice vectors schema")
898
+ vectors: Optional[LatticeVectorsSchema73] = Field(None, title="lattice vectors schema")
899
899
  type: Optional[LatticeTypeEnum] = Field("TRI", title="lattice type enum")
900
- units: Optional[LatticeUnitsSchema86] = Field(
901
- default_factory=lambda: LatticeUnitsSchema86.model_validate({"length": "angstrom", "angle": "degree"}),
900
+ units: Optional[LatticeUnitsSchema74] = Field(
901
+ default_factory=lambda: LatticeUnitsSchema74.model_validate({"length": "angstrom", "angle": "degree"}),
902
902
  title="Lattice units schema",
903
903
  )
904
904
 
905
905
 
906
- class Name732(Enum):
906
+ class Name636(Enum):
907
907
  volume = "volume"
908
908
 
909
909
 
910
- class Units296(Enum):
910
+ class Units260(Enum):
911
911
  angstrom_3 = "angstrom^3"
912
912
 
913
913
 
914
- class VolumeSchema85(BaseModel):
914
+ class VolumeSchema73(BaseModel):
915
915
  name: Literal["0#-datamodel-code-generator-#-object-#-special-#"]
916
- units: Optional[Units296] = None
916
+ units: Optional[Units260] = None
917
917
  value: float
918
918
 
919
919
 
920
- class Name733(Enum):
920
+ class Name637(Enum):
921
921
  density = "density"
922
922
 
923
923
 
924
- class Units297(Enum):
924
+ class Units261(Enum):
925
925
  g_cm_3 = "g/cm^3"
926
926
 
927
927
 
928
- class DensitySchema86(BaseModel):
928
+ class DensitySchema74(BaseModel):
929
929
  name: Literal["1#-datamodel-code-generator-#-object-#-special-#"]
930
- units: Optional[Units297] = None
930
+ units: Optional[Units261] = None
931
931
  value: float
932
932
 
933
933
 
934
- class Units298(Enum):
934
+ class Units262(Enum):
935
935
  angstrom = "angstrom"
936
936
 
937
937
 
938
- class ScalarSchema87(BaseModel):
939
- units: Optional[Units298] = None
938
+ class ScalarSchema75(BaseModel):
939
+ units: Optional[Units262] = None
940
940
  value: float
941
941
 
942
942
 
943
- class Name734(Enum):
943
+ class Name638(Enum):
944
944
  symmetry = "symmetry"
945
945
 
946
946
 
947
- class SymmetrySchema85(BaseModel):
947
+ class SymmetrySchema73(BaseModel):
948
948
  pointGroupSymbol: Optional[str] = None
949
949
  """
950
950
  point group symbol in Schoenflies notation
@@ -953,18 +953,18 @@ class SymmetrySchema85(BaseModel):
953
953
  """
954
954
  space group symbol in Hermann–Mauguin notation
955
955
  """
956
- tolerance: Optional[ScalarSchema87] = Field(None, title="scalar schema")
956
+ tolerance: Optional[ScalarSchema75] = Field(None, title="scalar schema")
957
957
  """
958
958
  tolerance used for symmetry calculation
959
959
  """
960
960
  name: Literal["2#-datamodel-code-generator-#-object-#-special-#"]
961
961
 
962
962
 
963
- class Name735(Enum):
963
+ class Name639(Enum):
964
964
  elemental_ratio = "elemental_ratio"
965
965
 
966
966
 
967
- class ElementalRatio86(BaseModel):
967
+ class ElementalRatio74(BaseModel):
968
968
  name: Literal["3#-datamodel-code-generator-#-object-#-special-#"]
969
969
  value: confloat(ge=0.0, le=1.0)
970
970
  element: Optional[str] = None
@@ -973,11 +973,11 @@ class ElementalRatio86(BaseModel):
973
973
  """
974
974
 
975
975
 
976
- class Name736(Enum):
976
+ class Name640(Enum):
977
977
  p_norm = "p-norm"
978
978
 
979
979
 
980
- class PNorm86(BaseModel):
980
+ class PNorm74(BaseModel):
981
981
  name: Literal["4#-datamodel-code-generator-#-object-#-special-#"]
982
982
  degree: Optional[int] = None
983
983
  """
@@ -986,56 +986,56 @@ class PNorm86(BaseModel):
986
986
  value: float
987
987
 
988
988
 
989
- class Name737(Enum):
989
+ class Name641(Enum):
990
990
  inchi = "inchi"
991
991
 
992
992
 
993
- class InChIRepresentationSchema86(BaseModel):
993
+ class InChIRepresentationSchema74(BaseModel):
994
994
  name: Literal["5#-datamodel-code-generator-#-object-#-special-#"]
995
995
  value: str
996
996
 
997
997
 
998
- class Name738(Enum):
998
+ class Name642(Enum):
999
999
  inchi_key = "inchi_key"
1000
1000
 
1001
1001
 
1002
- class InChIKeyRepresentationSchema86(BaseModel):
1002
+ class InChIKeyRepresentationSchema74(BaseModel):
1003
1003
  name: Literal["6#-datamodel-code-generator-#-object-#-special-#"]
1004
1004
  value: str
1005
1005
 
1006
1006
 
1007
- class DerivedPropertiesSchema86(
1007
+ class DerivedPropertiesSchema74(
1008
1008
  RootModel[
1009
1009
  Union[
1010
- VolumeSchema85,
1011
- DensitySchema86,
1012
- SymmetrySchema85,
1013
- ElementalRatio86,
1014
- PNorm86,
1015
- InChIRepresentationSchema86,
1016
- InChIKeyRepresentationSchema86,
1010
+ VolumeSchema73,
1011
+ DensitySchema74,
1012
+ SymmetrySchema73,
1013
+ ElementalRatio74,
1014
+ PNorm74,
1015
+ InChIRepresentationSchema74,
1016
+ InChIKeyRepresentationSchema74,
1017
1017
  ]
1018
1018
  ]
1019
1019
  ):
1020
1020
  root: Union[
1021
- VolumeSchema85,
1022
- DensitySchema86,
1023
- SymmetrySchema85,
1024
- ElementalRatio86,
1025
- PNorm86,
1026
- InChIRepresentationSchema86,
1027
- InChIKeyRepresentationSchema86,
1021
+ VolumeSchema73,
1022
+ DensitySchema74,
1023
+ SymmetrySchema73,
1024
+ ElementalRatio74,
1025
+ PNorm74,
1026
+ InChIRepresentationSchema74,
1027
+ InChIKeyRepresentationSchema74,
1028
1028
  ] = Field(..., discriminator="name")
1029
1029
 
1030
1030
 
1031
- class Name739(Enum):
1031
+ class Name643(Enum):
1032
1032
  default = "default"
1033
1033
  atomsTooClose = "atomsTooClose"
1034
1034
  atomsOverlap = "atomsOverlap"
1035
1035
 
1036
1036
 
1037
- class MaterialConsistencyCheckSchema85(BaseModel):
1038
- name: Name739
1037
+ class MaterialConsistencyCheckSchema73(BaseModel):
1038
+ name: Name643
1039
1039
  """
1040
1040
  Name of the consistency check that is performed, which is listed in an enum.
1041
1041
  """
@@ -1053,7 +1053,7 @@ class MaterialConsistencyCheckSchema85(BaseModel):
1053
1053
  """
1054
1054
 
1055
1055
 
1056
- class CrystalSchema80(BaseModel):
1056
+ class CrystalSchema68(BaseModel):
1057
1057
  formula: Optional[str] = None
1058
1058
  """
1059
1059
  reduced chemical formula
@@ -1062,9 +1062,9 @@ class CrystalSchema80(BaseModel):
1062
1062
  """
1063
1063
  chemical formula based on the number of atoms of each element in the supercell
1064
1064
  """
1065
- basis: BasisSchema85 = Field(..., title="basis schema")
1066
- lattice: LatticeSchema85 = Field(..., title="lattice schema")
1067
- derivedProperties: Optional[List[DerivedPropertiesSchema86]] = Field(None, title="derived properties schema")
1065
+ basis: BasisSchema73 = Field(..., title="basis schema")
1066
+ lattice: LatticeSchema73 = Field(..., title="lattice schema")
1067
+ derivedProperties: Optional[List[DerivedPropertiesSchema74]] = Field(None, title="derived properties schema")
1068
1068
  external: Optional[DatabaseSourceSchema] = Field(None, title="database source schema")
1069
1069
  """
1070
1070
  information about a database source
@@ -1085,7 +1085,7 @@ class CrystalSchema80(BaseModel):
1085
1085
  """
1086
1086
  Whether to work in the finite molecular picture (usually with atomic orbital basis)
1087
1087
  """
1088
- consistencyChecks: Optional[List[MaterialConsistencyCheckSchema85]] = None
1088
+ consistencyChecks: Optional[List[MaterialConsistencyCheckSchema73]] = None
1089
1089
  field_id: Optional[str] = Field(None, alias="_id")
1090
1090
  """
1091
1091
  entity identity
@@ -1119,12 +1119,20 @@ class VacuumConfigurationSchema(BaseModel):
1119
1119
  """
1120
1120
  Size of the vacuum slab in angstroms
1121
1121
  """
1122
- crystal: CrystalSchema80 = Field(..., title="Crystal Schema")
1122
+ crystal: CrystalSchema68 = Field(..., title="Crystal Schema")
1123
1123
  """
1124
1124
  A crystal structure, referencing the base material schema
1125
1125
  """
1126
1126
 
1127
1127
 
1128
+ class ObjectWithId(BaseModel):
1129
+ value: Optional[confloat(ge=0.0)] = None
1130
+ id: int
1131
+ """
1132
+ integer id of this entry
1133
+ """
1134
+
1135
+
1128
1136
  class SlabStrainedSupercellConfigurationSchema(BaseModel):
1129
1137
  xy_supercell_matrix: Optional[List[SupercellMatrix2DSchemaItem]] = Field(
1130
1138
  default_factory=lambda: [SupercellMatrix2DSchemaItem.model_validate(v) for v in [[1, 0], [0, 1]]],
@@ -1145,3 +1153,7 @@ class SlabStrainedSupercellConfigurationSchema(BaseModel):
1145
1153
  """
1146
1154
  Enum for axis types
1147
1155
  """
1156
+ gaps: Optional[List[ObjectWithId]] = None
1157
+ """
1158
+ Gap distances between stack components as an array of objects with id and value
1159
+ """