@mat3ra/made 2026.8.7-0 → 2026.8.18-0

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/configuration.py

@@ -1,19 +0,0 @@
-from typing import Tuple, Union
-
-from mat3ra.made.material import Material
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseConfigurationPydantic
-
-from ..... import MaterialWithBuildMetadata
-
-
-class CrystalLatticeLinesConfiguration(BaseConfigurationPydantic):
-    """
-    Configuration for creating crystal lattice lines from a material.
-
-    Args:
-        crystal: The monolayer material to create the lattice lines from.
-        miller_indices_2d: The (u,v) Miller indices for the line direction.
-    """
-
-    crystal: Union[Material, MaterialWithBuildMetadata]
-    miller_indices_2d: Tuple[int, int]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/edge_types.py

@@ -1,51 +0,0 @@
-from enum import Enum
-from typing import Tuple
-
-
-class EdgeTypesEnum(str, Enum):
-    """
-    Enum for nanoribbon/nanotape edge types.
-    """
-
-    zigzag = "zigzag"
-    armchair = "armchair"
-
-
-MILLER_INDICES_TO_EDGE_TYPE_MAP = {
-    (0, 1): EdgeTypesEnum.zigzag,
-    (1, 1): EdgeTypesEnum.armchair,
-}
-
-
-def get_miller_indices_from_edge_type(edge_type: EdgeTypesEnum) -> Tuple[int, int]:
-    """
-    Convert edge type shorthand to (u,v) Miller indices.
-
-    Args:
-        edge_type: "zigzag" or "armchair"
-
-    Returns:
-        Tuple of (u,v) Miller indices.
-    """
-    for miller_indices, mapped_edge_type in MILLER_INDICES_TO_EDGE_TYPE_MAP.items():
-        if mapped_edge_type == edge_type:
-            return miller_indices
-    raise ValueError(f"Unknown edge type: {edge_type}. Use 'zigzag' or 'armchair'.")
-
-
-def get_edge_type_from_miller_indices(miller_indices_2d: Tuple[int, int]) -> str:
-    """
-    Convert (u,v) Miller indices to edge type string.
-
-    Args:
-        miller_indices_2d: Tuple of (u,v) Miller indices
-
-    Returns:
-        Edge type string: "Zigzag", "Armchair", or "(uv)" for other indices
-    """
-    edge_type = MILLER_INDICES_TO_EDGE_TYPE_MAP.get(miller_indices_2d)
-    if edge_type:
-        return edge_type.value.capitalize()
-    else:
-        miller_str = f"{miller_indices_2d[0]}{miller_indices_2d[1]}"
-        return f"({miller_str})"

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines/helpers.py

@@ -1,58 +0,0 @@
-from typing import Optional, Tuple, Union
-
-from mat3ra.made.material import Material
-
-from ......analyze.lattice_lines import CrystalLatticeLinesMaterialAnalyzer
-from ......build.pristine_structures.two_dimensional.slab.termination_utils import select_slab_termination
-from ..... import MaterialWithBuildMetadata
-from ..crystal_lattice_lines_unique_repeated.configuration import CrystalLatticeLinesUniqueRepeatedConfiguration
-from .edge_types import EdgeTypesEnum, get_miller_indices_from_edge_type
-
-
-def create_lattice_lines_config_and_material(
-    material: Union[Material, MaterialWithBuildMetadata],
-    miller_indices_2d: Optional[Tuple[int, int]],
-    edge_type: Optional[EdgeTypesEnum],
-    width: int,
-    length: int,
-    termination_formula: Optional[str] = None,
-):
-    """
-    Create a lattice lines configuration from a material.
-
-    Args:
-        material: The monolayer material to create the lattice lines from.
-        miller_indices_2d: The (u,v) Miller indices for the line direction.
-        edge_type: Edge type ("zigzag" or "armchair") - alternative to miller_indices_2d.
-        width: Number of repetitions in width direction.
-        length: Number of repetitions in length direction.
-        termination_formula: Formula of the termination to use.
-
-    Returns:
-        CrystalLatticeLinesUniqueRepeatedConfiguration: The configuration object.
-    """
-    if miller_indices_2d is None and edge_type is None:
-        raise ValueError("Either miller_indices_2d or edge_type must be provided")
-
-    resolved_miller_indices: Tuple[int, int]
-    if miller_indices_2d is not None:
-        resolved_miller_indices = miller_indices_2d
-    elif edge_type is not None:
-        resolved_miller_indices = get_miller_indices_from_edge_type(edge_type)
-    else:
-        raise ValueError("Either miller_indices_2d or edge_type must be provided")
-
-    lattice_lines_analyzer = CrystalLatticeLinesMaterialAnalyzer(
-        material=material, miller_indices_2d=resolved_miller_indices
-    )
-    terminations = lattice_lines_analyzer.terminations
-    termination = select_slab_termination(terminations, termination_formula)
-
-    lattice_lines_config = CrystalLatticeLinesUniqueRepeatedConfiguration(
-        crystal=material,
-        miller_indices_2d=resolved_miller_indices,
-        termination_top=termination,
-        number_of_repetitions_width=width,
-        number_of_repetitions_length=length,
-    )
-    return lattice_lines_config

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated/__init__.py

@@ -1,4 +0,0 @@
-from .builder import CrystalLatticeLinesRepeatedBuilder
-from .configuration import CrystalLatticeLinesUniqueRepeatedConfiguration
-
-__all__ = ["CrystalLatticeLinesRepeatedBuilder", "CrystalLatticeLinesUniqueRepeatedConfiguration"]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated/builder.py

@@ -1,42 +0,0 @@
-from typing import Type
-
-from mat3ra.made.material import Material
-
-from ......analyze.lattice_lines import CrystalLatticeLinesMaterialAnalyzer
-from ......modify import wrap_to_unit_cell
-from ......operations.core.unary import supercell, translate
-from ..crystal_lattice_lines.builder import CrystalLatticeLinesBuilder
-from .configuration import CrystalLatticeLinesUniqueRepeatedConfiguration
-
-
-class CrystalLatticeLinesRepeatedBuilder(CrystalLatticeLinesBuilder):
-    """
-    Builder for creating repeated crystal lattice lines with termination.
-    This is similar to AtomicLayersUniqueRepeatedBuilder but for 1D lines.
-    """
-
-    _ConfigurationType: Type[
-        CrystalLatticeLinesUniqueRepeatedConfiguration
-    ] = CrystalLatticeLinesUniqueRepeatedConfiguration
-
-    def _generate(self, configuration: CrystalLatticeLinesUniqueRepeatedConfiguration) -> Material:
-        crystal_lattice_lines_material = super()._generate(configuration)
-
-        crystal_lattice_lines_analyzer = CrystalLatticeLinesMaterialAnalyzer(
-            material=configuration.crystal, miller_indices_2d=configuration.miller_indices_2d
-        )
-        translation_vector = crystal_lattice_lines_analyzer.get_translation_vector_for_termination_without_vacuum(
-            configuration.termination_top
-        )
-        material_translated = translate(crystal_lattice_lines_material, translation_vector)
-        material_translated_wrapped = wrap_to_unit_cell(material_translated)
-
-        material_translated_wrapped_repeated = supercell(
-            material_translated_wrapped,
-            [
-                [configuration.number_of_repetitions_length, 0, 0],
-                [0, configuration.number_of_repetitions_width, 0],
-                [0, 0, 1],
-            ],
-        )
-        return material_translated_wrapped_repeated

package/src/py/mat3ra/made/tools/build_components/entities/reusable/one_dimensional/crystal_lattice_lines_unique_repeated/configuration.py

@@ -1,21 +0,0 @@
-from typing import Optional
-
-from ....auxiliary.two_dimensional.termination import Termination
-from ..crystal_lattice_lines.configuration import CrystalLatticeLinesConfiguration
-
-
-class CrystalLatticeLinesUniqueRepeatedConfiguration(CrystalLatticeLinesConfiguration):
-    """
-    Configuration for creating repeated crystal lattice lines with termination.
-
-    Args:
-        crystal: The monolayer material to create the lattice lines from.
-        miller_indices_2d: The (u,v) Miller indices for the line direction.
-        termination_top: The termination to use for the lattice lines.
-    """
-
-    # TODO: right and left for x terminations
-    termination_top: Termination
-    termination_bottom: Optional[Termination] = None
-    number_of_repetitions_width: int = 1
-    number_of_repetitions_length: int = 1

package/src/py/mat3ra/made/tools/build_components/entities/reusable/three_dimensional/supercell/configuration.py

@@ -1,11 +0,0 @@
-import numpy as np
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.three_dimensional.supercell_matrix_3d import (
-    SupercellMatrix3DSchema,
-)
-
-from ...base_builder import BaseConfigurationPydantic
-
-
-class SupercellConfiguration(BaseConfigurationPydantic):
-    type: str = "SupercellConfiguration"
-    supercell_matrix: SupercellMatrix3DSchema = SupercellMatrix3DSchema(root=np.eye(3).tolist())

package/src/py/mat3ra/made/tools/build_components/entities/reusable/three_dimensional/supercell/helpers.py

@@ -1,38 +0,0 @@
-from typing import List, Optional, Union
-
-import numpy as np
-from mat3ra.made.material import Material
-
-from ......operations.core.unary import supercell
-from ..... import MaterialWithBuildMetadata
-from .configuration import SupercellConfiguration
-
-
-def create_supercell(
-    material: Union[Material, MaterialWithBuildMetadata],
-    supercell_matrix: Optional[List[List[int]]] = None,
-    scaling_factor: Optional[List[int]] = None,
-) -> Material:
-    """
-    Create a supercell of the atoms.
-
-    Args:
-        material (Material): The atoms to create a supercell of.
-        supercell_matrix (List[List[int]]): The supercell matrix (e.g. [[3,0,0],[0,3,0],[0,0,1]]).
-        scaling_factor (List[int], optional): The scaling factor instead of matrix (e.g. [3,3,1]).
-            If provided, supercell_matrix is ignored.
-
-    Returns:
-        Material: The supercell material.
-    """
-    if scaling_factor is not None:
-        supercell_matrix = np.multiply(scaling_factor, np.eye(3)).tolist()
-    new_material = supercell(material, supercell_matrix)
-
-    # Convert to MaterialWithBuildMetadata and set metadata
-    material_with_metadata = MaterialWithBuildMetadata.create(new_material.to_dict())
-    configuration = SupercellConfiguration(supercell_matrix=supercell_matrix)
-    material_with_metadata.metadata.add_build_metadata_step(
-        configuration=configuration.to_dict(), build_parameters={"supercell_matrix": supercell_matrix}
-    )
-    return material_with_metadata

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/__init__.py

@@ -1,24 +0,0 @@
-from .atomic_layers_unique_repeated import AtomicLayersUniqueRepeatedBuilder, AtomicLayersUniqueRepeatedConfiguration
-from .crystal_lattice_planes import CrystalLatticePlanesBuilder, CrystalLatticePlanesConfiguration
-
-# from .slab_stack import (
-#     SlabStackBuilder,
-#     SlabStackConfiguration,
-#     create_slab_stack,
-#     recreate_slab_with_fractional_layers,
-# )
-
-__all__ = [
-    # atomic_layers
-    # atomic_layers_unique_repeated
-    "AtomicLayersUniqueRepeatedBuilder",
-    "AtomicLayersUniqueRepeatedConfiguration",
-    # crystal_lattice_planes
-    "CrystalLatticePlanesBuilder",
-    "CrystalLatticePlanesConfiguration",
-    # slab_stack
-    # "SlabStackBuilder",
-    # "SlabStackConfiguration",
-    # "create_slab_stack",
-    # "recreate_slab_with_fractional_layers",
-]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/__init__.py

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

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/builder.py

@@ -1,62 +0,0 @@
-from typing import Type
-
-from ......analyze import BaseMaterialAnalyzer
-from ......modify import wrap_to_unit_cell
-from ......operations.core.unary import rotate, supercell, translate
-from ..... import MaterialWithBuildMetadata
-from ....auxiliary.two_dimensional.miller_indices import MillerIndices
-from ..crystal_lattice_planes.builder import CrystalLatticePlanesBuilder
-from .configuration import AtomicLayersUniqueRepeatedConfiguration
-
-
-class AtomicLayersUniqueRepeatedBuilder(CrystalLatticePlanesBuilder):
-    _ConfigurationType: Type[AtomicLayersUniqueRepeatedConfiguration] = AtomicLayersUniqueRepeatedConfiguration
-
-    def _generate(self, configuration: AtomicLayersUniqueRepeatedConfiguration) -> MaterialWithBuildMetadata:
-        crystal_lattice_planes_material = super()._generate(configuration)
-
-        crystal_lattice_planes_material_analyzer = self.get_analyzer(configuration)
-
-        if configuration.termination_top is not None:
-            termination = configuration.termination_top
-            should_rotate = False
-        elif configuration.termination_bottom is not None:
-            termination = configuration.termination_bottom
-            should_rotate = True
-        else:
-            raise ValueError(
-                "Either termination_top or termination_bottom is required for AtomicLayersUniqueRepeatedBuilder"
-            )
-
-        translation_vector = (
-            crystal_lattice_planes_material_analyzer.get_translation_vector_for_termination_without_vacuum(termination)
-        )
-        material_translated = translate(crystal_lattice_planes_material, translation_vector)
-        material_translated_wrapped = wrap_to_unit_cell(material_translated)
-
-        if should_rotate:
-            # Rotation of basis around [1,0,0] yielded the same material, probably due to the symmetry of unit cell.
-            # rotation around X and Z simultaneously gives the mirroring effect. (x,y,z) ⟶ (z,−y,x)
-            material_translated_wrapped = rotate(material_translated_wrapped, angle=180, axis=[1, 0, 1])
-        material_translated_wrapped_layered = supercell(
-            material_translated_wrapped, [[1, 0, 0], [0, 1, 0], [0, 0, configuration.number_of_repetitions]]
-        )
-        return material_translated_wrapped_layered
-
-    def _update_material_name(
-        self, material: MaterialWithBuildMetadata, configuration: AtomicLayersUniqueRepeatedConfiguration
-    ) -> MaterialWithBuildMetadata:
-        material_analyzer = BaseMaterialAnalyzer(material=material)
-        material.formula = material_analyzer.formula
-        miller_indices_str = str(MillerIndices(root=configuration.miller_indices))
-
-        if configuration.termination_top is not None:
-            termination_str = f"termination {configuration.termination_top}"
-        elif configuration.termination_bottom is not None:
-            termination_str = f"bottom termination {configuration.termination_bottom}"
-        else:
-            termination_str = ""
-
-        new_name = f"{material.formula}{miller_indices_str}, {termination_str}"
-        material.name = new_name
-        return material

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/configuration.py

@@ -1,14 +0,0 @@
-from typing import Optional
-
-from mat3ra.esse.models.materials_category.defective_structures.two_dimensional.base_configuration import (
-    AtomicLayersUniqueRepeatedSchema,
-)
-
-from ....auxiliary.two_dimensional.termination import Termination
-from ..crystal_lattice_planes.configuration import CrystalLatticePlanesConfiguration
-
-
-class AtomicLayersUniqueRepeatedConfiguration(CrystalLatticePlanesConfiguration, AtomicLayersUniqueRepeatedSchema):
-    termination_top: Optional[Termination] = None
-    termination_bottom: Optional[Termination] = None
-    number_of_repetitions: int

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/helpers.py

@@ -1,42 +0,0 @@
-from typing import Optional, Tuple, Union
-
-from mat3ra.made.material import Material
-
-from ..... import MaterialWithBuildMetadata
-from ....auxiliary.two_dimensional.termination import Termination
-from .. import AtomicLayersUniqueRepeatedBuilder, AtomicLayersUniqueRepeatedConfiguration
-
-
-def create_atomic_layers(
-    material: Union[Material, MaterialWithBuildMetadata],
-    miller_indices: Tuple[int, int, int] = (0, 0, 1),
-    termination: Optional[Termination] = None,
-    number_of_layers: int = 1,
-) -> Material:
-    """
-    Creates a material composed of repeated unique atomic layers from a given crystal.
-
-    This function identifies the sequence of unique atomic layers for the given Miller
-    indices and then constructs the material by repeating this sequence, starting
-    with a given surface termination.
-
-    Args:
-        material (Material): The crystal material to create atomic layers from.
-        miller_indices (Tuple[int, int, int]): Miller indices for the atomic layers.
-        termination (Termination): The termination to use for the atomic layers.
-        number_of_layers (int): Number of times to repeat the sequence of unique atomic layers.
-    Returns:
-        Material: The atomic layers material.
-
-    """
-    atomic_layers_config = AtomicLayersUniqueRepeatedConfiguration(
-        crystal=material,
-        miller_indices=miller_indices,
-        termination_top=termination,
-        number_of_repetitions=number_of_layers,
-    )
-
-    atomic_layers_builder = AtomicLayersUniqueRepeatedBuilder()
-    atomic_layers_material = atomic_layers_builder.get_material(atomic_layers_config)
-
-    return atomic_layers_material

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/__init__.py

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

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/builder.py

@@ -1,39 +0,0 @@
-from typing import Any, Optional
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseSingleBuilder, TypeConfiguration
-
-from ......analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer
-from ......build_components import MaterialWithBuildMetadata
-from ......modify import translate_to_z_level
-from ......operations.core.unary import supercell
-from .configuration import CrystalLatticePlanesConfiguration
-
-
-class CrystalLatticePlanesBuilder(BaseSingleBuilder):
-    _PostProcessParametersType: Any = None
-    use_enforce_convention: bool = True
-
-    def get_analyzer(self, configuration: CrystalLatticePlanesConfiguration) -> CrystalLatticePlanesMaterialAnalyzer:
-        return CrystalLatticePlanesMaterialAnalyzer(
-            material=configuration.crystal, miller_indices=configuration.miller_indices
-        )
-
-    def _generate(self, configuration: CrystalLatticePlanesConfiguration) -> MaterialWithBuildMetadata:
-        crystal_lattice_planes_analyzer = self.get_analyzer(configuration)
-        miller_supercell_matrix = crystal_lattice_planes_analyzer.miller_supercell_matrix
-        miller_supercell_material = supercell(configuration.crystal, miller_supercell_matrix)
-        return miller_supercell_material
-
-    def _enforce_convention(self, material: MaterialWithBuildMetadata) -> MaterialWithBuildMetadata:
-        if not self.use_enforce_convention:
-            return material
-        return translate_to_z_level(material, "bottom")
-
-    def _post_process(
-        self,
-        item: MaterialWithBuildMetadata,
-        post_process_parameters: Optional[Any] = None,
-        configuration: Optional[TypeConfiguration] = None,
-    ) -> MaterialWithBuildMetadata:
-        item = super()._post_process(item, post_process_parameters, configuration)
-        return self._enforce_convention(item)

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/configuration.py

@@ -1,24 +0,0 @@
-from typing import Union
-
-from mat3ra.esse.models.materials_category_components.entities.reusable.two_dimensional.crystal_lattice_planes import (
-    CrystalLatticePlanesSchema,
-)
-from mat3ra.made.material import Material
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseConfigurationPydantic
-
-from ......build_components import MaterialWithBuildMetadata
-from ....auxiliary.two_dimensional.miller_indices import MillerIndices
-
-
-class CrystalLatticePlanesConfiguration(CrystalLatticePlanesSchema, BaseConfigurationPydantic):
-    crystal: Union[Material, MaterialWithBuildMetadata]
-
-    @property
-    def in_plane_vectors(self):
-        # Two vectors in the plane of the Miller indices
-        return self.crystal.lattice.vector_arrays[:2, :2]
-
-    @property
-    def miller_indices_as_string(self) -> str:
-        miller_indices_cls_instance = MillerIndices(root=self.miller_indices)
-        return str(miller_indices_cls_instance)

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/__init__.py

@@ -1,10 +0,0 @@
-from .builder import SlabStackBuilder
-from .configuration import SlabStackConfiguration
-from .helpers import create_slab_stack, recreate_slab_with_fractional_layers
-
-__all__ = [
-    "SlabStackBuilder",
-    "SlabStackConfiguration",
-    "create_slab_stack",
-    "recreate_slab_with_fractional_layers",
-]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/builder.py

@@ -1,36 +0,0 @@
-from typing import Type
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import TypeConfiguration
-
-from ......build.pristine_structures.two_dimensional.slab import SlabBuilder
-from ......build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
-from ..... import MaterialWithBuildMetadata
-from .....operations.core.combinations.stack.builder import StackNComponentsBuilder
-from .configuration import SlabStackConfiguration
-
-
-class SlabStackBuilder(StackNComponentsBuilder):
-    _ConfigurationType: Type[SlabStackConfiguration] = SlabStackConfiguration
-
-    @property
-    def stack_component_types_conversion_map(self):
-        return {
-            **super().stack_component_types_conversion_map,
-            SlabConfiguration: SlabBuilder,
-        }
-
-    @property
-    def name_suffix(self) -> str:
-        return "Slab Stack"
-
-    def get_name_suffix(self, configuration: SlabStackConfiguration) -> str:
-        return self.name_suffix
-
-    def _update_material_name(
-        self, material: MaterialWithBuildMetadata, configuration: TypeConfiguration
-    ) -> MaterialWithBuildMetadata:
-        name_suffix = self.get_name_suffix(configuration) or self.name_suffix
-        base_name = material.name
-        name = f"{base_name}, {name_suffix}"
-        material.name = name
-        return material

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/configuration.py

@@ -1,31 +0,0 @@
-from mat3ra.esse.models.materials_category_components.entities.reusable.two_dimensional.slab_stack_configuration import (  # noqa: E501
-    SlabStackConfigurationSchema,
-)
-from mat3ra.made.material import Material
-
-from .....operations.core.combinations.stack.configuration import StackConfiguration
-from ....core.two_dimensional.vacuum.configuration import VacuumConfiguration
-
-
-class SlabStackConfiguration(StackConfiguration, SlabStackConfigurationSchema):
-    """
-    Configuration for stacking a slab, an isolated defect and a vacuum layer.
-
-    Args:
-        stack_components: List containing [slab, slab_component, vacuum].
-        direction: Direction of stacking (default: z).
-    """
-
-    type: str = "SlabStackConfiguration"
-
-    @property
-    def slab(self) -> Material:
-        return self.stack_components[0]
-
-    @property
-    def added_component(self) -> Material:
-        return self.stack_components[1]
-
-    @property
-    def vacuum_configuration(self) -> VacuumConfiguration:
-        return self.stack_components[2]

package/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/helpers.py

@@ -1,80 +0,0 @@
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from sympy import ceiling
-
-from ......analyze.slab import SlabMaterialAnalyzer
-from ......build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
-from ......build.pristine_structures.two_dimensional.slab.helpers import create_slab
-from ......modify import filter_by_box
-from ..... import MaterialWithBuildMetadata
-from ....core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .builder import SlabStackBuilder
-from .configuration import SlabStackConfiguration
-
-
-def create_slab_stack(
-    slab: MaterialWithBuildMetadata, added_component: MaterialWithBuildMetadata
-) -> MaterialWithBuildMetadata:
-    """
-    Create a slab stack by stacking a slab, a slab component, and a vacuum layer.
-
-    Args:
-        slab: The original slab material.
-        added_component: The material to be stacked on top of the slab.
-    Returns:
-        Material: The new slab stack material.
-    """
-    analyzer = SlabMaterialAnalyzer(material=slab)
-
-    slab_without_vacuum_configuration = analyzer.slab_configuration_with_no_vacuum
-    slab_build_parameters = analyzer.build_parameters
-
-    new_slab = SlabBuilder(build_parameters=slab_build_parameters).get_material(slab_without_vacuum_configuration)
-
-    original_vacuum_config = analyzer.get_slab_vacuum_configuration()
-    vacuum_config = VacuumConfiguration(
-        size=original_vacuum_config.size, crystal=new_slab, direction=original_vacuum_config.direction
-    )
-
-    slab_stack_config = SlabStackConfiguration(
-        stack_components=[new_slab, added_component, vacuum_config], direction=AxisEnum.z
-    )
-
-    slab_stack_builder = SlabStackBuilder()
-    return slab_stack_builder.get_material(slab_stack_config)
-
-
-def recreate_slab_with_fractional_layers(
-    slab: MaterialWithBuildMetadata, number_of_layers: float
-) -> MaterialWithBuildMetadata:
-    """
-    Create a slab with a specified number of fractional layers.
-
-    Args:
-        slab: The original slab material.
-        number_of_layers: The total number of layers in the new slab.
-    Returns:
-        Material: The new slab material with the specified number of layers and vacuum if needed.
-    """
-    analyzer = SlabMaterialAnalyzer(material=slab)
-    slab_without_vacuum = analyzer.slab_configuration_with_no_vacuum
-    build_parameters = analyzer.build_parameters
-
-    ceiling_number_of_layers = int(ceiling(number_of_layers))
-    slab_with_int_layers_without_vacuum = create_slab(
-        crystal=slab_without_vacuum.atomic_layers.crystal,
-        miller_indices=slab_without_vacuum.atomic_layers.miller_indices,
-        termination_top_formula=slab_without_vacuum.atomic_layers.termination_top.formula
-        if slab_without_vacuum.atomic_layers.termination_top
-        else None,
-        termination_bottom_formula=None,
-        number_of_layers=ceiling_number_of_layers,
-        vacuum=0,
-        xy_supercell_matrix=build_parameters.xy_supercell_matrix,
-    )
-
-    max_z_crystal_coordinate = number_of_layers / ceiling_number_of_layers
-    return filter_by_box(
-        slab_with_int_layers_without_vacuum,
-        max_coordinate=[1, 1, max_z_crystal_coordinate],
-        reset_ids=True,
-    )

package/src/py/mat3ra/made/tools/build_components/entities/reusable/zero_dimensional/coordinates_shape_enum.py

@@ -1,8 +0,0 @@
-from enum import Enum
-
-
-class CoordinatesShapeEnum(str, Enum):
-    SPHERE = "sphere"
-    CYLINDER = "cylinder"
-    BOX = "rectangle"
-    TRIANGULAR_PRISM = "triangular_prism"

package/src/py/mat3ra/made/tools/build_components/metadata/__init__.py

@@ -1,2 +0,0 @@
-from .material_build_metadata import BuildMetadata, MaterialBuildMetadata
-from .material_with_build_metadata import MaterialWithBuildMetadata