@mat3ra/made 2026.8.13-0 → 2026.8.26-0

package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/build_parameters.py

@@ -1,10 +0,0 @@
-from typing import List, Optional
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseBuilderParameters
-
-
-class TerraceBuildParameters(BaseBuilderParameters):
-    rotate_to_match_pbc: bool = True
-    axis: List[int] = [0, 1, 0]
-    angle: float = 0.0
-    new_lattice_vectors: Optional[List[List[float]]] = None

package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/builder.py

@@ -1,30 +0,0 @@
-from typing import Type
-
-from .build_parameters import TerraceBuildParameters
-from .configuration import TerraceDefectConfiguration
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.reusable.two_dimensional.slab_stack.builder import SlabStackBuilder
-from .....modify import translate_to_z_level
-from .....operations.core.unary import edit_cell, rotate
-
-
-class TerraceDefectBuilder(SlabStackBuilder):
-    _ConfigurationType: Type[TerraceDefectConfiguration] = TerraceDefectConfiguration
-    _BuildParametersType: Type[TerraceBuildParameters] = TerraceBuildParameters
-    _DefaultBuildParameters: TerraceBuildParameters = TerraceBuildParameters()
-
-    def get_name_suffix(self, configuration: TerraceDefectConfiguration) -> str:
-        return f"Terrace {configuration.cut_direction}"
-
-    def _generate(self, configuration: TerraceDefectConfiguration) -> MaterialWithBuildMetadata:
-        material = super()._generate(configuration)
-        build_params = self.build_parameters if self.build_parameters else self._DefaultBuildParameters
-        if build_params.rotate_to_match_pbc:
-            axis = build_params.axis
-            angle = build_params.angle
-            new_lattice_vectors = build_params.new_lattice_vectors
-            translated_material = translate_to_z_level(material, "center")
-            adjusted_material = edit_cell(translated_material, new_lattice_vectors)
-            material = rotate(adjusted_material, axis, angle)
-
-        return material

package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/configuration.py

@@ -1,11 +0,0 @@
-from typing import List
-
-from mat3ra.esse.models.materials_category.defective_structures.two_dimensional.terrace.configuration import (
-    TerraceDefectConfigurationSchema,
-)
-
-from .....build_components.entities.reusable.two_dimensional.slab_stack.configuration import SlabStackConfiguration
-
-
-class TerraceDefectConfiguration(SlabStackConfiguration, TerraceDefectConfigurationSchema):
-    cut_direction: List[int] = [1, 0, 0]

package/src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/terrace/helpers.py

@@ -1,78 +0,0 @@
-from typing import Optional, List
-
-from .build_parameters import TerraceBuildParameters
-from .builder import TerraceDefectBuilder
-from .configuration import TerraceDefectConfiguration
-from .....analyze.terrace import TerraceMaterialAnalyzer
-from .....build_components import MaterialWithBuildMetadata
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
-from .....build_components.entities.reusable.two_dimensional.slab_stack.helpers import (
-    recreate_slab_with_fractional_layers,
-)
-from .....entities.coordinate import PlaneCoordinateCondition
-from .....modify import filter_by_condition_on_coordinates
-
-
-def create_defect_terrace(
-    slab: MaterialWithBuildMetadata,
-    cut_direction: Optional[List[int]] = None,
-    pivot_coordinate: Optional[List[float]] = None,
-    number_of_added_layers: float = 1.0,
-    use_cartesian_coordinates: bool = False,
-    rotate_to_match_pbc: bool = True,
-) -> MaterialWithBuildMetadata:
-    """
-    Create a terrace at the specified position on the surface of the material.
-
-    Args:
-        slab: The original slab material to which the terrace will be added.
-        cut_direction: The direction of the cut in lattice directions, Miller indices.
-        pivot_coordinate: The center position of the terrace.
-        number_of_added_layers: The number of added layers to the slab which will form the terrace
-        use_cartesian_coordinates: Whether to use Cartesian coordinates for the center position.
-        rotate_to_match_pbc: Whether to rotate the material to match the periodic boundary conditions.
-    Returns:
-        The material with the terrace added.
-    """
-    if cut_direction is None:
-        cut_direction = [0, 0, 1]
-    if pivot_coordinate is None:
-        pivot_coordinate = [0.5, 0.5, 0.5]
-
-    terrace_analyzer = TerraceMaterialAnalyzer(
-        material=slab, cut_direction=cut_direction, number_of_added_layers=number_of_added_layers
-    )
-
-    additional_slab_material = recreate_slab_with_fractional_layers(slab, number_of_added_layers)
-
-    normalized_direction_vector = terrace_analyzer.cut_direction_vector
-
-    condition = PlaneCoordinateCondition(
-        plane_normal=normalized_direction_vector,
-        plane_point_coordinate=pivot_coordinate,
-    ).condition
-
-    slab_in_stack_config = terrace_analyzer.slab_configuration_with_no_vacuum
-    slab_build_parameters = terrace_analyzer.build_parameters
-
-    slab_in_stack = SlabBuilder(build_parameters=slab_build_parameters).get_material(slab_in_stack_config)
-    isolated_defect = filter_by_condition_on_coordinates(
-        material=additional_slab_material,
-        condition=condition,
-        use_cartesian_coordinates=use_cartesian_coordinates,
-    )
-    vacuum = terrace_analyzer.get_slab_vacuum_configuration()
-
-    terrace_configuration = TerraceDefectConfiguration(
-        stack_components=[slab_in_stack, isolated_defect, vacuum], cut_direction=cut_direction
-    )
-
-    angle = terrace_analyzer.angle
-    axis = terrace_analyzer.rotation_axis
-    new_lattice_vectors = terrace_analyzer.new_lattice_vectors
-    parameters = TerraceBuildParameters(
-        rotate_to_match_pbc=rotate_to_match_pbc, angle=angle, axis=axis, new_lattice_vectors=new_lattice_vectors
-    )
-    terrace = TerraceDefectBuilder(build_parameters=parameters).get_material(terrace_configuration)
-
-    return terrace

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/builder.py

@@ -1,31 +0,0 @@
-from typing import Type, Union
-
-from mat3ra.made.material import Material
-from .configuration import PairDefectConfiguration
-from ..point_defect.base.builder import PointDefectBuilder
-from ..point_defect.vacancy.builder import VacancyDefectBuilder
-from .....build_components import MaterialWithBuildMetadata, TypeConfiguration
-
-
-class PairDefectBuilder(VacancyDefectBuilder, PointDefectBuilder):
-    _ConfigurationType: Type[PairDefectConfiguration] = PairDefectConfiguration
-
-    def _update_material_name(
-        self, material: Union[Material, MaterialWithBuildMetadata], configuration: TypeConfiguration
-    ) -> Material:
-        host_material = configuration.merge_components[0]
-
-        primary_defect_name = (
-            configuration.merge_components[1].element.chemical_element.value
-            if hasattr(configuration.merge_components[1].element.chemical_element, "value")
-            else configuration.merge_components[1].element.chemical_element
-        )
-        secondary_defect_name = (
-            configuration.merge_components[2].element.chemical_element.value
-            if hasattr(configuration.merge_components[2].element.chemical_element, "value")
-            else configuration.merge_components[2].element.chemical_element
-        )
-        if host_material:
-            material.name = f"{host_material.name}, Pair Defect: {primary_defect_name} + {secondary_defect_name}"
-
-        return material

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/configuration.py

@@ -1,45 +0,0 @@
-from typing import List, Union
-
-# fmt: off
-from mat3ra.esse.models.materials_category.defective_structures.zero_dimensional. \
-    point_defect.base_configuration import (
-    PointDefectBaseConfigurationSchema,
-)
-# fmt: on
-from mat3ra.esse.models.materials_category_components.operations.core.combinations.merge import MergeMethodsEnum
-
-from mat3ra.made.material import Material
-from ..point_defect.base.configuration import PointDefectConfiguration
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.auxiliary.zero_dimensional.point_defect_site.configuration import (
-    PointDefectSiteConfiguration,
-)
-from .....build_components.operations.core.combinations.merge.configuration import MergeConfiguration
-
-
-class PairDefectConfiguration(MergeConfiguration, PointDefectBaseConfigurationSchema):
-    """
-    Configuration for building a pair defect by merging materials.
-
-    Args:
-        merge_components: List containing [crystal, primary_defect_configuration, secondary_defect_configuration].
-        merge_method: Method to use for merging.
-    """
-
-    type: str = "PairDefectConfiguration"
-    merge_components: List[Union[Material, PointDefectSiteConfiguration]]
-    merge_method: MergeMethodsEnum = MergeMethodsEnum.REPLACE
-
-    @classmethod
-    def from_parameters(
-        cls,
-        crystal: Union[Material, MaterialWithBuildMetadata],
-        primary_defect_configuration: PointDefectConfiguration,
-        secondary_defect_configuration: PointDefectConfiguration,
-        **kwargs,
-    ):
-        primary_defect_site_configuration = primary_defect_configuration.merge_components[1]
-        secondary_defect_site_configuration = secondary_defect_configuration.merge_components[1]
-        return cls(
-            merge_components=[crystal, primary_defect_site_configuration, secondary_defect_site_configuration], **kwargs
-        )

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/pair_defect/helpers.py

@@ -1,80 +0,0 @@
-from typing import List, Optional, Union
-
-from mat3ra.made.material import Material
-from .builder import PairDefectBuilder
-from .configuration import PairDefectConfiguration
-from ..point_defect import (
-    PointDefectTypeEnum,
-    VacancyPlacementMethodEnum,
-    SubstitutionPlacementMethodEnum,
-    InterstitialPlacementMethodEnum,
-    AtomPlacementMethodEnum,
-    create_defect_configuration,
-)
-from .....build_components import MaterialWithBuildMetadata
-
-
-def create_defect_pair(
-    material: Union[Material, MaterialWithBuildMetadata],
-    defect_type_1: Optional[PointDefectTypeEnum] = None,
-    coordinate_1: Optional[List[float]] = None,
-    element_1: Optional[str] = None,
-    placement_method_1: Union[
-        VacancyPlacementMethodEnum,
-        SubstitutionPlacementMethodEnum,
-        InterstitialPlacementMethodEnum,
-        AtomPlacementMethodEnum,
-    ] = AtomPlacementMethodEnum.EXACT_COORDINATE,
-    defect_type_2: Optional[PointDefectTypeEnum] = None,
-    coordinate_2: Optional[List[float]] = None,
-    element_2: Optional[str] = None,
-    placement_method_2: Union[
-        VacancyPlacementMethodEnum,
-        SubstitutionPlacementMethodEnum,
-        InterstitialPlacementMethodEnum,
-        AtomPlacementMethodEnum,
-    ] = AtomPlacementMethodEnum.EXACT_COORDINATE,
-    use_cartesian_coordinates: bool = False,
-) -> Material:
-    """
-    Create a pair defect in the given material.
-
-    Args:
-        material: The host material.
-        defect_type_1: Type of the first defect.
-        coordinate_1: Coordinate for the first defect.
-        element_1: Element for substitution/interstitial defects.
-        placement_method_1: Method to resolve the final coordinate for the first defect.
-        defect_type_2: Type of the second defect.
-        coordinate_2: Coordinate for the second defect.
-        element_2: Element for substitution/interstitial defects.
-        placement_method_2: Method to resolve the final coordinate for the second defect.
-        use_cartesian_coordinates: Whether the coordinates are in Cartesian units.
-
-    Returns:
-        material: Union[Material, MaterialWithBuildMetadata] with the pair defect applied.
-    """
-    if not defect_type_1 or not coordinate_1:
-        raise ValueError("defect_type_1 and coordinate_1 must be provided.")
-    configuration_1 = create_defect_configuration(
-        material,
-        defect_type_1,
-        coordinate_1,
-        element_1,
-        placement_method_1,
-        use_cartesian_coordinates,
-    )
-    if not defect_type_2 or not coordinate_2:
-        raise ValueError("defect_type_2 and coordinate_2 must be provided.")
-    configuration_2 = create_defect_configuration(
-        material, defect_type_2, coordinate_2, element_2, placement_method_2, use_cartesian_coordinates
-    )
-
-    pair_config = PairDefectConfiguration.from_parameters(
-        crystal=material,
-        primary_defect_configuration=configuration_1,
-        secondary_defect_configuration=configuration_2,
-    )
-
-    builder = PairDefectBuilder()
-    return builder.get_material(pair_config)

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/__init__.py

@@ -1,40 +0,0 @@
-from .atom_placement_method_enum import AtomPlacementMethodEnum
-from .base.builder import PointDefectBuilder
-from .base.configuration import PointDefectConfiguration
-from .complex_defect_type_enum import ComplexDefectTypeEnum
-from .factories import PointDefectConfigurationFactory, create_defect_configuration, resolve_coordinate
-from .helpers import create_multiple_defects
-from .interstitial.configuration import InterstitialDefectConfiguration
-from .interstitial.helpers import create_defect_point_interstitial
-from .interstitial.interstitial_placement_method_enum import InterstitialPlacementMethodEnum
-from .point_defect_type_enum import PointDefectTypeEnum
-from .substitutional.configuration import SubstitutionalDefectConfiguration
-from .substitutional.helpers import create_defect_point_substitution
-from .substitutional.substitution_placement_method_enum import SubstitutionPlacementMethodEnum
-from .vacancy.configuration import VacancyDefectConfiguration
-from .vacancy.helpers import create_defect_point_vacancy
-from .vacancy.vacancy_placement_method_enum import VacancyPlacementMethodEnum
-
-__all__ = [
-    # Enums
-    "AtomPlacementMethodEnum",
-    "ComplexDefectTypeEnum",
-    "InterstitialPlacementMethodEnum",
-    "PointDefectTypeEnum",
-    "SubstitutionPlacementMethodEnum",
-    "VacancyPlacementMethodEnum",
-    # Classes
-    "PointDefectBuilder",
-    "PointDefectConfiguration",
-    "PointDefectConfigurationFactory",
-    "InterstitialDefectConfiguration",
-    "SubstitutionalDefectConfiguration",
-    "VacancyDefectConfiguration",
-    # Functions
-    "create_defect_configuration",
-    "resolve_coordinate",
-    "create_multiple_defects",
-    "create_defect_point_interstitial",
-    "create_defect_point_substitution",
-    "create_defect_point_vacancy",
-]

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/atom_placement_method_enum.py

@@ -1,14 +0,0 @@
-from enum import Enum
-
-
-class AtomPlacementMethodEnum(str, Enum):
-    # Places the atom at the exact given coordinate.
-    EXACT_COORDINATE = "exact_coordinate"
-    # Among existing atoms, selects the closest one to the given coordinate.
-    CLOSEST_SITE = "closest_site"
-    # Places the atom at the equal distance from the closest atoms to the given coordinate.
-    EQUIDISTANT = "equidistant"
-    # Places the atom at the existing or extrapolated crystal site closest to the given coordinate.
-    NEW_CRYSTAL_SITE = "new_crystal_site"
-    # Places the atom at Voronoi site closest to the given coordinate.
-    VORONOI_SITE = "voronoi_site"

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/__init__.py

@@ -1,7 +0,0 @@
-from .builder import PointDefectBuilder
-from .configuration import PointDefectConfiguration
-
-__all__ = [
-    "PointDefectBuilder",
-    "PointDefectConfiguration",
-]

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/builder.py

@@ -1,42 +0,0 @@
-from typing import Type, Dict, Union
-
-from mat3ra.made.material import Material
-from .configuration import PointDefectConfiguration
-from ..interstitial.configuration import InterstitialDefectConfiguration
-from ..substitutional.configuration import SubstitutionalDefectConfiguration
-from ..vacancy.configuration import VacancyDefectConfiguration
-from ......build_components import MaterialWithBuildMetadata, TypeConfiguration
-from ......build_components.entities.auxiliary.zero_dimensional.point_defect_site.builder import PointDefectSiteBuilder
-from ......build_components.entities.auxiliary.zero_dimensional.point_defect_site.configuration import (
-    PointDefectSiteConfiguration,
-)
-from ......build_components.operations.core.combinations.merge.builder import MergeBuilder
-
-
-class PointDefectBuilder(MergeBuilder):
-    _ConfigurationType: Type[PointDefectConfiguration] = PointDefectConfiguration
-
-    @property
-    def merge_component_types_conversion_map(self) -> Dict[Type, Type]:
-        return {
-            VacancyDefectConfiguration: PointDefectSiteBuilder,
-            SubstitutionalDefectConfiguration: PointDefectSiteBuilder,
-            InterstitialDefectConfiguration: PointDefectSiteBuilder,
-            PointDefectSiteConfiguration: PointDefectSiteBuilder,
-        }
-
-    def _update_material_name(
-        self, material: Union[Material, MaterialWithBuildMetadata], configuration: TypeConfiguration
-    ) -> MaterialWithBuildMetadata:
-        host_material = None
-        for component in configuration.merge_components:
-            if isinstance(component, Material):
-                host_material = component
-                break
-
-        if host_material:
-            defect_type = configuration.__class__.__name__.lower()
-            defect_type = defect_type.replace("defectconfiguration", "").replace("configuration", "")
-            material.name = f"{host_material.name} with {defect_type} defect"
-
-        return material

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/configuration.py

@@ -1,27 +0,0 @@
-from typing import Union, List
-
-# fmt: off
-from mat3ra.esse.models.materials_category.defective_structures.zero_dimensional.\
-    point_defect.base_configuration import (
-    PointDefectBaseConfigurationSchema,
-)
-# fmt: on
-
-from mat3ra.made.material import Material
-from mat3ra.made.tools.build_components.entities.auxiliary.zero_dimensional.point_defect_site.configuration import (
-    PointDefectSiteConfiguration,
-)
-from mat3ra.made.tools.build_components.operations.core.combinations.merge.configuration import MergeConfiguration
-
-
-class PointDefectConfiguration(MergeConfiguration, PointDefectBaseConfigurationSchema):
-    """
-    Configuration for building a point defect by merging materials.
-
-    Args:
-        merge_components: List of materials or configurations to merge.
-        merge_method: Method to use for merging.
-    """
-
-    type: str = "PointDefectConfiguration"
-    merge_components: List[Union[Material, PointDefectSiteConfiguration]]

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/complex_defect_type_enum.py

@@ -1,5 +0,0 @@
-from enum import Enum
-
-
-class ComplexDefectTypeEnum(str, Enum):
-    PAIR = "pair"

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/factories.py

@@ -1,69 +0,0 @@
-from typing import List, Dict, Union, Type, Optional
-
-from mat3ra.made.material import Material
-from .....analyze.crystal_site.crystal_site_analyzer import CrystalSiteAnalyzer
-from .....analyze.crystal_site.voronoi_crystal_site_analyzer import VoronoiCrystalSiteAnalyzer
-from .....build_components import MaterialWithBuildMetadata
-from .atom_placement_method_enum import AtomPlacementMethodEnum
-from .base.configuration import PointDefectConfiguration
-from .interstitial.configuration import InterstitialDefectConfiguration
-from .interstitial.interstitial_placement_method_enum import InterstitialPlacementMethodEnum
-from .point_defect_type_enum import PointDefectTypeEnum
-from .substitutional.configuration import SubstitutionalDefectConfiguration
-from .substitutional.substitution_placement_method_enum import SubstitutionPlacementMethodEnum
-from .vacancy.configuration import VacancyDefectConfiguration
-from .vacancy.vacancy_placement_method_enum import VacancyPlacementMethodEnum
-
-
-def resolve_coordinate(
-    material: Union[Material, MaterialWithBuildMetadata],
-    coordinate: List[float],
-    placement_method,
-    use_cartesian_coordinates: bool = False,
-) -> List[float]:
-    if use_cartesian_coordinates:
-        coordinate = material.basis.cell.convert_point_to_crystal(coordinate)
-
-    if placement_method in [VacancyPlacementMethodEnum.CLOSEST_SITE, SubstitutionPlacementMethodEnum.CLOSEST_SITE]:
-        analyzer = CrystalSiteAnalyzer(material=material, coordinate=coordinate)
-        return analyzer.closest_site_coordinate
-    elif placement_method == InterstitialPlacementMethodEnum.VORONOI_SITE:
-        analyzer = VoronoiCrystalSiteAnalyzer(material=material, coordinate=coordinate)
-        return analyzer.voronoi_site_coordinate
-    else:
-        analyzer = CrystalSiteAnalyzer(material=material, coordinate=coordinate)
-        return analyzer.exact_coordinate
-
-
-class PointDefectConfigurationFactory:
-    _type_to_configuration_map: Dict[PointDefectTypeEnum, Type[PointDefectConfiguration]] = {
-        PointDefectTypeEnum.VACANCY: VacancyDefectConfiguration,
-        PointDefectTypeEnum.SUBSTITUTION: SubstitutionalDefectConfiguration,
-        PointDefectTypeEnum.INTERSTITIAL: InterstitialDefectConfiguration,
-    }
-
-    @classmethod
-    def get_constructor(cls, defect_type: PointDefectTypeEnum) -> Type[PointDefectConfiguration]:
-        try:
-            return cls._type_to_configuration_map[defect_type]
-        except KeyError:
-            raise ValueError(f"Unsupported defect type: {defect_type}")
-
-
-def create_defect_configuration(
-    material: Union[Material, MaterialWithBuildMetadata],
-    defect_type: PointDefectTypeEnum,
-    coordinate: List[float],
-    element: Optional[str] = None,
-    placement_method: Union[
-        VacancyPlacementMethodEnum,
-        SubstitutionPlacementMethodEnum,
-        InterstitialPlacementMethodEnum,
-        AtomPlacementMethodEnum,
-    ] = AtomPlacementMethodEnum.EXACT_COORDINATE,
-    use_cartesian_coordinates: bool = False,
-) -> PointDefectConfiguration:
-    resolved_coordinate = resolve_coordinate(material, coordinate, placement_method, use_cartesian_coordinates)
-    config_class = PointDefectConfigurationFactory.get_constructor(defect_type=defect_type)
-
-    return config_class.from_parameters(crystal=material, coordinate=resolved_coordinate, element=element)

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/helpers.py

@@ -1,92 +0,0 @@
-from typing import List, Union
-
-from mat3ra.made.material import Material
-from .interstitial.helpers import create_defect_point_interstitial
-from .interstitial.interstitial_placement_method_enum import InterstitialPlacementMethodEnum
-from .point_defect_type_enum import PointDefectTypeEnum
-from .substitutional.helpers import create_defect_point_substitution
-from .substitutional.substitution_placement_method_enum import SubstitutionPlacementMethodEnum
-from .types import PointDefectDict
-from .vacancy.helpers import create_defect_point_vacancy
-from .vacancy.vacancy_placement_method_enum import VacancyPlacementMethodEnum
-from .....build_components import MaterialWithBuildMetadata
-
-DEFECT_TYPE_MAPPING = {
-    PointDefectTypeEnum.VACANCY: {
-        "create_func": "create_point_defect_vacancy",
-        "placement_enum": VacancyPlacementMethodEnum,
-        "default_method": VacancyPlacementMethodEnum.CLOSEST_SITE,
-    },
-    PointDefectTypeEnum.SUBSTITUTION: {
-        "create_func": "create_point_defect_substitution",
-        "placement_enum": SubstitutionPlacementMethodEnum,
-        "default_method": SubstitutionPlacementMethodEnum.CLOSEST_SITE,
-    },
-    PointDefectTypeEnum.INTERSTITIAL: {
-        "create_func": "create_point_defect_interstitial",
-        "placement_enum": InterstitialPlacementMethodEnum,
-        "default_method": InterstitialPlacementMethodEnum.EXACT_COORDINATE,
-    },
-}
-
-
-def create_multiple_defects(
-    material: Union[Material, MaterialWithBuildMetadata],
-    defect_dicts: List[PointDefectDict],
-) -> Material:
-    """
-    Create multiple point defects from a list of PointDefectDict.
-
-    Args:
-        material (Material): The host material.
-        defect_dicts (List[PointDefectDict]): List of defect dictionaries with keys:
-            - type: str ("vacancy", "substitution", "interstitial")
-            - coordinate: List[float]
-            - element: str (required for substitution and interstitial)
-            - placement_method: str or enum (optional)
-                - For vacancy/substitution: "CLOSEST_SITE"
-                - For interstitial:  "EXACT_COORDINATE", "VORONOI_SITE"
-                Defaults to "closest_site" for vacancy/substitution and "exact_coordinate" for interstitial.
-            - use_cartesian_coordinates: bool (optional, defaults to False)
-                Whether the input coordinates are in Cartesian units.
-
-    Returns:
-        Material: A new material with all defects applied.
-    """
-    current_material = material
-
-    for defect_dict in defect_dicts:
-        defect_type = defect_dict.type
-
-        if defect_type not in [e.value for e in PointDefectTypeEnum]:
-            raise ValueError(f"Unsupported defect type: {defect_dict.type}")
-
-        use_cartesian = getattr(defect_dict, "use_cartesian_coordinates", False)
-
-        if defect_type == "vacancy":
-            current_material = create_defect_point_vacancy(
-                current_material,
-                coordinate=defect_dict.coordinate,
-                placement_method=defect_dict.placement_method or VacancyPlacementMethodEnum.CLOSEST_SITE.value,
-                use_cartesian_coordinates=use_cartesian,
-            )
-
-        elif defect_type == "substitution":
-            current_material = create_defect_point_substitution(
-                current_material,
-                coordinate=defect_dict.coordinate,
-                element=defect_dict.element,  # type: ignore # Pydantic validates this at creation
-                placement_method=defect_dict.placement_method or SubstitutionPlacementMethodEnum.CLOSEST_SITE.value,
-                use_cartesian_coordinates=use_cartesian,
-            )
-
-        elif defect_type == "interstitial":
-            current_material = create_defect_point_interstitial(
-                current_material,
-                coordinate=defect_dict.coordinate,
-                element=defect_dict.element,  # type: ignore # Pydantic validates this at creation
-                placement_method=defect_dict.placement_method or InterstitialPlacementMethodEnum.EXACT_COORDINATE.value,
-                use_cartesian_coordinates=use_cartesian,
-            )
-
-    return current_material

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/__init__.py

@@ -1,7 +0,0 @@
-from .configuration import InterstitialDefectConfiguration
-from .interstitial_placement_method_enum import InterstitialPlacementMethodEnum
-
-__all__ = [
-    "InterstitialDefectConfiguration",
-    "InterstitialPlacementMethodEnum",
-]

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/builder.py

@@ -1,8 +0,0 @@
-from ..base.builder import PointDefectBuilder
-from .configuration import (
-    InterstitialDefectConfiguration,
-)
-
-
-class InterstitialDefectBuilder(PointDefectBuilder):
-    _ConfigurationType = InterstitialDefectConfiguration

package/src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/configuration.py

@@ -1,29 +0,0 @@
-from typing import List, Union
-
-from mat3ra.esse.models.materials_category.defective_structures.zero_dimensional.point_defect.interstitial import (
-    InterstitialPointDefectSchema,
-)
-from mat3ra.esse.models.materials_category_components.entities.core.zero_dimensional.atom import AtomSchema
-from mat3ra.esse.models.materials_category_components.operations.core.combinations.merge import MergeMethodsEnum
-
-from mat3ra.made.material import Material
-from ......build_components import MaterialWithBuildMetadata
-from ..base.configuration import PointDefectConfiguration
-from ......build_components.entities.auxiliary.zero_dimensional.point_defect_site.configuration import (
-    PointDefectSiteConfiguration,
-)
-
-
-class InterstitialDefectConfiguration(PointDefectConfiguration, InterstitialPointDefectSchema):
-    type: str = "InterstitialDefectConfiguration"
-
-    @classmethod
-    def from_parameters(
-        cls, crystal: Union[Material, MaterialWithBuildMetadata], coordinate: List[float], element: str, **kwargs
-    ):
-        interstitial_site = PointDefectSiteConfiguration(
-            crystal=crystal,
-            element=AtomSchema(chemical_element=element),
-            coordinate=coordinate,
-        )
-        return cls(merge_components=[crystal, interstitial_site], merge_method=MergeMethodsEnum.ADD, **kwargs)