@mat3ra/made 2026.8.7-0 → 2026.8.18-0

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanoribbon/helpers.py

@@ -1,76 +0,0 @@
-from typing import Optional, Tuple, Union
-from typing import TypeVar
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-
-from mat3ra.made.material import Material
-from . import NanoribbonConfiguration
-from .builders import NanoribbonBuilder, NanoribbonBuilderParameters
-from ..nanotape import NanoTapeConfiguration
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .....build_components.entities.reusable.base_builder import BaseBuilderParameters
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines.edge_types import EdgeTypesEnum
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines.helpers import (
-    create_lattice_lines_config_and_material,
-)
-
-P = TypeVar("P", bound=BaseBuilderParameters)
-
-
-def create_nanoribbon(
-    material: Union[Material, MaterialWithBuildMetadata],
-    miller_indices_2d: Optional[Tuple[int, int]] = None,
-    edge_type: EdgeTypesEnum = EdgeTypesEnum.zigzag,
-    width: int = 2,
-    length: int = 2,
-    vacuum_width: float = 10.0,
-    vacuum_length: float = 10.0,
-    use_rectangular_lattice: bool = True,
-    termination_formula: Optional[str] = None,
-) -> Material:
-    """
-    Creates a nanoribbon material from a monolayer material.
-
-    Args:
-        material: The monolayer material to create the nanoribbon from (assumes vacuum is present).
-        miller_indices_2d: The (u,v) Miller indices for the nanoribbon direction.
-        edge_type: Edge type string ("zigzag"/"armchair"). Optional if miller_indices_2d is provided.
-        width: The width of the nanoribbon in number of unit cells.
-        length: The length of the nanoribbon in number of unit cells.
-        vacuum_width: The width of the vacuum region in Angstroms (cartesian).
-        vacuum_length: The length of the vacuum region in Angstroms (cartesian).
-        use_rectangular_lattice: Whether the nanoribbon is rectangular.
-        termination_formula: The termination formula to use for the nanoribbon (e.g., "Si").
-
-    Returns:
-        Material: The generated nanoribbon material.
-    """
-    lattice_lines_config = create_lattice_lines_config_and_material(
-        material=material,
-        miller_indices_2d=miller_indices_2d,
-        edge_type=edge_type,
-        width=width,
-        length=length,
-        termination_formula=termination_formula,
-    )
-    nanotape_vacuum_config = VacuumConfiguration(
-        size=vacuum_width,
-        direction=AxisEnum.y,
-    )
-    nanotape_config = NanoTapeConfiguration(
-        stack_components=[lattice_lines_config, nanotape_vacuum_config],
-        direction=AxisEnum.y,
-    )
-    vacuum_config = VacuumConfiguration(
-        size=vacuum_length,
-        direction=AxisEnum.x,
-    )
-    config = NanoribbonConfiguration(
-        stack_components=[nanotape_config, vacuum_config],
-        direction=AxisEnum.x,
-    )
-    builder = NanoribbonBuilder(
-        build_parameters=NanoribbonBuilderParameters(use_rectangular_lattice=use_rectangular_lattice)
-    )
-    return builder.get_material(config)

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/__init__.py

@@ -1,11 +0,0 @@
-from .build_parameters import NanoTapeBuilderParameters
-from .configuration import NanoTapeConfiguration
-from .builders import NanoTapeBuilder
-from .helpers import create_nanotape
-
-__all__ = [
-    "NanoTapeConfiguration",
-    "NanoTapeBuilder",
-    "NanoTapeBuilderParameters",
-    "create_nanotape",
-]

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/build_parameters.py

@@ -1,9 +0,0 @@
-from pydantic import Field
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseBuilderParameters
-
-
-class NanoTapeBuilderParameters(BaseBuilderParameters):
-    use_rectangular_lattice: bool = Field(
-        True, description="If True, set the XY lattice to be rectangular after stacking."
-    )

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/builders.py

@@ -1,83 +0,0 @@
-from typing import Any, Optional, Union, Type
-
-from mat3ra.made.lattice import Lattice
-from mat3ra.made.material import Material
-
-from . import NanoTapeBuilderParameters
-from .configuration import NanoTapeConfiguration
-from .....build_components import MaterialWithBuildMetadata, TypeConfiguration
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines.edge_types import (
-    get_edge_type_from_miller_indices,
-)
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines_unique_repeated import (
-    CrystalLatticeLinesUniqueRepeatedConfiguration,
-)
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines_unique_repeated.builder import (
-    CrystalLatticeLinesRepeatedBuilder,
-)
-from .....build_components.operations.core.combinations.stack.builder import StackNComponentsBuilder
-from .....modify import wrap_to_unit_cell
-
-
-class NanoTapeBuilder(StackNComponentsBuilder):
-    _ConfigurationType: Type[NanoTapeConfiguration] = NanoTapeConfiguration
-    _GeneratedItemType: Type[Material] = Material
-    _BuildParametersType: Type[NanoTapeBuilderParameters] = NanoTapeBuilderParameters
-    _DefaultBuildParameters: NanoTapeBuilderParameters = NanoTapeBuilderParameters(
-        use_rectangular_lattice=True,
-    )
-
-    @property
-    def stack_component_types_conversion_map(self):
-        return {
-            **super().stack_component_types_conversion_map,
-            CrystalLatticeLinesUniqueRepeatedConfiguration: CrystalLatticeLinesRepeatedBuilder,
-        }
-
-    def _make_rectangular_lattice(self, item: Material) -> Material:
-        lattice_vectors = item.lattice.vector_arrays
-        new_lattice_vectors = [
-            [lattice_vectors[0][0], 0.0, 0.0],
-            [0.0, lattice_vectors[1][1], 0.0],
-            [0.0, 0.0, lattice_vectors[2][2]],
-        ]
-        new_lattice = Lattice.from_vectors_array(vectors=new_lattice_vectors)
-        item.set_lattice(new_lattice)
-        return item
-
-    def _update_material_name_with_edge_type(
-        self,
-        material: Union[Material, MaterialWithBuildMetadata],
-        crystal_name: str,
-        miller_indices_2d: tuple,
-        structure_type: str,
-    ) -> Material:
-        edge_type = get_edge_type_from_miller_indices(miller_indices_2d)
-        miller_str = f"{miller_indices_2d[0]}{miller_indices_2d[1]}"
-        material.name = f"{crystal_name} - {edge_type} {structure_type} ({miller_str})"
-        return material
-
-    def _update_material_name(
-        self, material: Union[Material, MaterialWithBuildMetadata], configuration: Any
-    ) -> Material:
-        if isinstance(configuration, NanoTapeConfiguration):
-            lattice_lines = configuration.lattice_lines
-            material = self._update_material_name_with_edge_type(
-                material, lattice_lines.crystal.name, lattice_lines.miller_indices_2d, "Nanotape"
-            )
-            return material
-        return super()._update_material_name(material, configuration)
-
-    def _post_process(
-        self,
-        item: Material,
-        post_process_parameters: Optional[Any] = None,
-        configuration: Optional[TypeConfiguration] = None,
-    ) -> Material:
-        item = super()._post_process(item, post_process_parameters, configuration)
-        # wrapping before changing lattice to avoid singular atoms beyond the boundaries
-        item = wrap_to_unit_cell(item)
-        params = self.build_parameters or self._DefaultBuildParameters
-        if params.use_rectangular_lattice:
-            item = self._make_rectangular_lattice(item)
-        return wrap_to_unit_cell(item)

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/configuration.py

@@ -1,35 +0,0 @@
-from typing import List, Union
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.esse.models.materials_category.pristine_structures.two_dimensional.nanotape import (
-    NanoTapeConfigurationSchema,
-)
-
-from .....build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .....build_components.operations.core.combinations.stack.configuration import StackConfiguration
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines_unique_repeated import (
-    CrystalLatticeLinesUniqueRepeatedConfiguration,
-)
-
-
-class NanoTapeConfiguration(StackConfiguration, NanoTapeConfigurationSchema):
-    """
-    Configuration for building a nanotape from crystal lattice lines.
-    NanoTape = [CrystalLatticeLinesUniqueRepeatedConfiguration, vacuum] stacked in X or Y direction.
-
-    Args:
-        stack_components: List of configuration objects for nanotape components.
-        direction: Direction along which to stack components.
-    """
-
-    type: str = "NanoTapeConfiguration"
-    stack_components: List[Union[CrystalLatticeLinesUniqueRepeatedConfiguration, VacuumConfiguration]]
-    direction: AxisEnum = AxisEnum.y
-
-    @property
-    def lattice_lines(self):
-        return self.stack_components[0]
-
-    @property
-    def vacuum_configuration(self) -> VacuumConfiguration:
-        return self.stack_components[1]

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/nanotape/helpers.py

@@ -1,62 +0,0 @@
-from typing import Optional, Tuple, Union
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-
-from mat3ra.made.material import Material
-from . import NanoTapeConfiguration
-from .builders import NanoTapeBuilder, NanoTapeBuilderParameters
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines.edge_types import EdgeTypesEnum
-from .....build_components.entities.reusable.one_dimensional.crystal_lattice_lines.helpers import (
-    create_lattice_lines_config_and_material,
-)
-
-
-def create_nanotape(
-    material: Union[Material, MaterialWithBuildMetadata],
-    miller_indices_2d: Optional[Tuple[int, int]] = None,
-    edge_type: EdgeTypesEnum = EdgeTypesEnum.zigzag,
-    width: int = 2,
-    length: int = 2,
-    vacuum_width: float = 10.0,
-    use_rectangular_lattice: bool = True,
-    termination_formula: Optional[str] = None,
-) -> Material:
-    """
-    Creates a nanotape material from a monolayer material.
-
-    Args:
-        material: The monolayer material to create the nanotape from (assumes vacuum is present).
-        miller_indices_2d: The (u,v) Miller indices for the nanotape direction.
-        edge_type: Edge type string ("zigzag"/"armchair"). Optional if miller_indices_2d is provided.
-        width: The width of the nanotape in number of unit cells.
-        length: The length of the nanotape in number of unit cells.
-        vacuum_width: The width of the vacuum region in Angstroms (cartesian).
-        use_rectangular_lattice: Whether the nanotape is rectangular.
-        termination_formula: The termination formula to use for the nanotape (e.g., "Si").
-
-    Returns:
-        Material: The generated nanotape material.
-    """
-    lattice_lines_config = create_lattice_lines_config_and_material(
-        material=material,
-        miller_indices_2d=miller_indices_2d,
-        edge_type=edge_type,
-        width=width,
-        length=length,
-        termination_formula=termination_formula,
-    )
-    vacuum_config = VacuumConfiguration(
-        size=vacuum_width,
-        crystal=material,
-        direction=AxisEnum.y,
-    )
-    config = NanoTapeConfiguration(
-        stack_components=[lattice_lines_config, vacuum_config],
-        direction=AxisEnum.y,
-    )
-    builder = NanoTapeBuilder(
-        build_parameters=NanoTapeBuilderParameters(use_rectangular_lattice=use_rectangular_lattice)
-    )
-    return builder.get_material(config)

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/__init__.py

@@ -1,9 +0,0 @@
-from .build_parameters import SlabBuilderParameters
-from .builder import SlabBuilder
-from .configuration import SlabConfiguration
-
-__all__ = [
-    "SlabBuilderParameters",
-    "SlabBuilder",
-    "SlabConfiguration",
-]

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/build_parameters.py

@@ -1,8 +0,0 @@
-from typing import List
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseBuilderParameters
-
-
-class SlabBuilderParameters(BaseBuilderParameters):
-    use_orthogonal_c: bool = True
-    xy_supercell_matrix: List[List[int]] = [[1, 0], [0, 1]]

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/builder.py

@@ -1,42 +0,0 @@
-from typing import Type, cast
-
-from .build_parameters import SlabBuilderParameters
-from .configuration import SlabConfiguration
-from .utils import get_orthogonal_c_slab
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.reusable.two_dimensional import (
-    AtomicLayersUniqueRepeatedConfiguration,
-    AtomicLayersUniqueRepeatedBuilder,
-)
-
-from .....build_components.operations.core.combinations.stack.builder import StackNComponentsBuilder
-from .....operations.core.unary import supercell
-
-
-class SlabBuilder(StackNComponentsBuilder):
-    _BuildParametersType: Type[SlabBuilderParameters] = SlabBuilderParameters
-    _DefaultBuildParameters: SlabBuilderParameters = SlabBuilderParameters()
-
-    @property
-    def stack_component_types_conversion_map(self):
-        return {
-            **super().stack_component_types_conversion_map,
-            AtomicLayersUniqueRepeatedConfiguration: AtomicLayersUniqueRepeatedBuilder,
-        }
-
-    def _generate(self, configuration: SlabConfiguration) -> MaterialWithBuildMetadata:
-        stack_as_material = super()._generate(configuration)
-        build_params = cast(SlabBuilderParameters, self.build_parameters)
-        supercell_slab = supercell(stack_as_material, build_params.xy_supercell_matrix)
-        if build_params.use_orthogonal_c:
-            supercell_slab = get_orthogonal_c_slab(supercell_slab)
-        return supercell_slab
-
-    def _update_material_name(
-        self, material: MaterialWithBuildMetadata, configuration: SlabConfiguration
-    ) -> MaterialWithBuildMetadata:
-        # for example: "Si(001), termination Si_P4/mmm_1, Slab"
-        material = AtomicLayersUniqueRepeatedBuilder()._update_material_name(material, configuration.atomic_layers)
-        new_name = f"{material.name}, Slab"
-        material.name = new_name
-        return material

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/configuration.py

@@ -1,99 +0,0 @@
-from typing import List, Optional, Tuple, Union
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.esse.models.materials_category.pristine_structures.two_dimensional.slab import SlabConfigurationSchema
-from mat3ra.made.material import Material
-from .termination_utils import select_slab_termination
-
-from .....analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer
-from .....build_components.entities.reusable.two_dimensional.atomic_layers_unique_repeated.configuration import (
-    AtomicLayersUniqueRepeatedConfiguration,
-)
-from .....build_components.metadata import MaterialWithBuildMetadata
-from .....build_components.operations.core.combinations.stack.configuration import StackConfiguration
-from .....build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .....build_components.entities.auxiliary.two_dimensional.termination import Termination
-
-
-class SlabConfiguration(StackConfiguration, SlabConfigurationSchema):
-    type: str = "SlabConfiguration"
-    stack_components: List[Union[AtomicLayersUniqueRepeatedConfiguration, VacuumConfiguration]]  # No Materials!
-    direction: AxisEnum = AxisEnum.z
-
-    termination_top: Optional[Termination] = None
-    termination_bottom: Optional[Termination] = None
-
-    @property
-    def number_of_layers(self):
-        return self.atomic_layers.number_of_repetitions
-
-    @property
-    def vacuum(self):
-        return self.vacuum_configuration.size
-
-    @property
-    def atomic_layers(self):
-        return self.stack_components[0]
-
-    @property
-    def vacuum_configuration(self) -> VacuumConfiguration:
-        return self.stack_components[1]
-
-    def set_vacuum(self, vacuum: float) -> None:
-        vacuum_configuration = self.vacuum_configuration
-        vacuum_configuration.size = vacuum
-        self.stack_components[1] = vacuum_configuration
-
-    @classmethod
-    def from_parameters(
-        cls,
-        material_or_dict: Union[Material, dict],
-        miller_indices: Tuple[int, int, int],
-        number_of_layers: int,
-        termination_top_formula: Optional[str] = None,
-        termination_bottom_formula: Optional[str] = None,
-        vacuum: float = 10.0,
-        use_conventional_cell: bool = True,
-    ) -> "SlabConfiguration":
-        """
-        Creates a SlabConfiguration from the given parameters.
-        Args:
-            material_or_dict (Union[Material, dict]): Material or dictionary representation of the material.
-            miller_indices (Tuple[int, int, int]): Miller indices for the slab surface.
-            number_of_layers (int): Number of atomic layers in the slab, in the number of unit cells.
-            termination_top_formula (Optional[str]): Formula of the top termination to use for the slab (i.e. "SrTiO").
-            termination_bottom_formula (Optional[str]): Formula of the bottom termination to use for the slab.
-
-            vacuum (float): Size of the vacuum layer in Angstroms.
-
-        Returns:
-            SlabConfiguration: The created slab configuration.
-        """
-        if isinstance(material_or_dict, dict):
-            material = MaterialWithBuildMetadata.create(material_or_dict)
-        else:
-            material = material_or_dict
-
-        crystal_lattice_planes_analyzer = CrystalLatticePlanesMaterialAnalyzer(
-            material=material, miller_indices=miller_indices
-        )
-        terminations = crystal_lattice_planes_analyzer.terminations
-        termination_top = select_slab_termination(terminations, termination_top_formula)
-        termination_bottom = select_slab_termination(terminations, termination_bottom_formula)
-
-        if use_conventional_cell:
-            material = crystal_lattice_planes_analyzer.material_with_conventional_lattice
-        atomic_layers_repeated_configuration = AtomicLayersUniqueRepeatedConfiguration(
-            crystal=material,
-            miller_indices=miller_indices,
-            termination_top=termination_top,
-            termination_bottom=termination_bottom,
-            number_of_repetitions=number_of_layers,
-        )
-
-        vacuum_configuration = VacuumConfiguration(size=vacuum, crystal=None, direction=AxisEnum.z)
-
-        return cls(
-            stack_components=[atomic_layers_repeated_configuration, vacuum_configuration],
-            direction=AxisEnum.z,
-        )

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/helpers.py

@@ -1,95 +0,0 @@
-from typing import List, Tuple, Union, Optional
-
-from mat3ra.made.material import Material
-from . import SlabBuilderParameters, SlabConfiguration, SlabBuilder
-from .....analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.auxiliary.two_dimensional.termination import Termination
-
-
-DEFAULT_XY_SUPERCELL_MATRIX = ([1, 0], [0, 1])
-
-
-def create_slab(
-    crystal: Union[Material, MaterialWithBuildMetadata],
-    miller_indices: Tuple[int, int, int] = (0, 0, 1),
-    use_conventional_cell=True,
-    use_orthogonal_c: bool = True,
-    termination_top: Optional[Termination] = None,
-    termination_bottom: Optional[Termination] = None,
-    termination_top_formula: Optional[str] = None,
-    termination_bottom_formula: Optional[str] = None,
-    number_of_layers=1,
-    vacuum=10.0,
-    xy_supercell_matrix=DEFAULT_XY_SUPERCELL_MATRIX,
-) -> MaterialWithBuildMetadata:
-    """
-    Creates a slab material from a crystal material with specified Miller indices and other parameters.
-
-    Args:
-        crystal (Material): The crystal material to create the slab from.
-        miller_indices (Tuple[int, int, int]): Miller indices for the slab surface.
-        use_conventional_cell (bool): Whether to use the conventional cell for the crystal to apply Miller indices.
-        use_orthogonal_c (bool): Whether to make slab with c-lattice orthogonal to miller indices plane, along z-axis.
-        termination (Termination): The termination to use for the slab, supply a class instance of Termination.
-        termination_formula (str): The stoichiometric formula of the termination, e.g. "Si", "TiO", "SrTiO", "Hf2O".
-        number_of_layers (int): Number of atomic layers in the slab, in the number of unit cells.
-        vacuum (float): Size of the vacuum layer in Angstroms.
-        xy_supercell_matrix (List[List[int]]): Supercell matrix for the xy plane to apply to the generated slab.
-
-    Returns:
-        Material: The generated slab material.
-    """
-    if termination_top is not None:
-        termination_top_formula = termination_top.formula
-    if termination_bottom is not None:
-        termination_bottom_formula = termination_bottom.formula
-
-    slab_builder_parameters = SlabBuilderParameters(
-        xy_supercell_matrix=xy_supercell_matrix,
-        use_orthogonal_c=use_orthogonal_c,
-    )
-    slab_configuration = SlabConfiguration.from_parameters(
-        material_or_dict=crystal,
-        miller_indices=miller_indices,
-        number_of_layers=number_of_layers,
-        termination_top_formula=termination_top_formula,
-        termination_bottom_formula=termination_bottom_formula,
-        vacuum=vacuum,
-        use_conventional_cell=use_conventional_cell,
-    )
-    builder = SlabBuilder(build_parameters=slab_builder_parameters)
-    return builder.get_material(slab_configuration)
-
-
-def create_slab_if_not(
-    material: MaterialWithBuildMetadata, default_slab_configuration: SlabConfiguration
-) -> MaterialWithBuildMetadata:
-    slab = material
-    build_metadata_slab = slab.metadata.get_build_metadata_of_type("SlabConfiguration")
-    if build_metadata_slab is None:
-        print("The material is not a slab. Creating a new slab...")
-        slab = SlabBuilder().get_material(default_slab_configuration)
-    return slab
-
-
-def get_slab_terminations(
-    material: Union[Material, MaterialWithBuildMetadata], miller_indices: Tuple[int, int, int] = (0, 0, 1)
-) -> List[Termination]:
-    crystal_lattice_planes_analyzer = CrystalLatticePlanesMaterialAnalyzer(
-        material=material, miller_indices=miller_indices
-    )
-    return crystal_lattice_planes_analyzer.terminations
-
-
-def get_slab_material_in_standard_representation(slab_material: Union[Material, MaterialWithBuildMetadata]) -> Material:
-    """
-    Get the slab material in a standard representation.
-
-    Args:
-        slab_material (Material): The slab material to convert.
-
-    Returns:
-        Material: The slab material in standard representation.
-    """
-    pass

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/termination_utils.py

@@ -1,14 +0,0 @@
-from typing import List, Optional
-
-from mat3ra.made.tools.build_components.entities.auxiliary.two_dimensional.termination import Termination
-
-
-def select_slab_termination(terminations: List[Termination], formula: Optional[str] = None) -> Termination:
-    if not terminations:
-        raise ValueError("No terminations available.")
-    if formula is None:
-        return terminations[0]
-    for termination in terminations:
-        if termination.formula == formula:
-            return termination
-    raise ValueError(f"Termination with formula {formula} not found in available terminations: {terminations}")

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/utils.py

@@ -1,61 +0,0 @@
-from typing import Union, Optional, List
-
-import numpy as np
-
-from mat3ra.made.lattice import Lattice
-from mat3ra.made.material import Material
-from .....build_components import MaterialWithBuildMetadata
-from .....build_components.entities.auxiliary.two_dimensional.termination import Termination
-from .....modify import wrap_to_unit_cell
-from .....operations.core.unary import edit_cell
-
-
-def select_slab_termination(terminations: List[Termination], formula: Optional[str] = None) -> Termination:
-    if not terminations:
-        raise ValueError("No terminations available.")
-    if formula is None:
-        return terminations[0]
-    for termination in terminations:
-        if termination.formula == formula:
-            return termination
-    raise ValueError(f"Termination with formula {formula} not found in available terminations: {terminations}")
-
-
-def get_orthogonal_c_slab(material: Union[Material, MaterialWithBuildMetadata]) -> Material:
-    """
-    Make the c-vector orthogonal to the ab plane and update the basis.
-
-    This function calculates a new c-vector that is orthogonal to the a and b vectors
-    of the lattice. It then computes the transformation matrix between the old and new
-    lattice vectors and applies this transformation to the atomic coordinates.
-
-    A new material is returned with an updated lattice and basis, where the new
-    lattice is defined by its parameters (a, b, c, alpha, beta, gamma) to avoid
-    storing raw vectors, preserving a standard representation.
-
-    Args:
-        material (Material): The input material object.
-
-    Returns:
-        Material: A new material object with an orthogonalized c-vector and
-                  updated basis.
-    """
-    new_material = material.clone()
-    current_vectors = np.array(new_material.lattice.vector_arrays)
-    a_vec, b_vec, c_old_vec = current_vectors
-
-    normal = np.cross(a_vec, b_vec)
-    n_hat = normal / np.linalg.norm(normal)
-    height = float(np.dot(c_old_vec, n_hat))
-    c_new_vec = n_hat * height
-
-    new_vectors = np.array([a_vec, b_vec, c_new_vec])
-    transform_matrix = np.dot(current_vectors, np.linalg.inv(new_vectors))
-
-    new_basis = new_material.basis.clone()
-    new_basis.transform_by_matrix(transform_matrix)
-    new_lattice_from_vectors = Lattice.from_vectors_array(new_vectors.tolist())
-    new_material = edit_cell(new_material, new_lattice_from_vectors.vector_arrays)
-    new_material.basis = new_basis
-    new_material = wrap_to_unit_cell(new_material)
-    return new_material

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab_strained_supercell/builder.py

@@ -1,22 +0,0 @@
-from typing import Type
-
-from .configuration import SlabStrainedSupercellConfiguration
-from ..slab import SlabBuilder
-from .....build_components import MaterialWithBuildMetadata
-from .....operations.core.unary import strain, supercell
-
-
-class SlabStrainedSupercellBuilder(SlabBuilder):
-    _ConfigurationType: Type[SlabStrainedSupercellConfiguration] = SlabStrainedSupercellConfiguration
-
-    def _generate(self, configuration: SlabStrainedSupercellConfiguration) -> MaterialWithBuildMetadata:
-        slab_material = super()._generate(configuration)
-        if configuration.xy_supercell_matrix:
-            slab_material = supercell(slab_material, configuration.xy_supercell_matrix)
-
-        strained_slab_material = strain(
-            slab_material,
-            configuration.strain_matrix,
-        )
-
-        return strained_slab_material

package/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab_strained_supercell/configuration.py

@@ -1,17 +0,0 @@
-from typing import Optional
-
-import numpy as np
-from mat3ra.esse.models.core.abstract.matrix_3x3 import Matrix3x3Schema
-from mat3ra.esse.models.materials_category.pristine_structures.two_dimensional.slab_strained_supercell import (
-    SlabStrainedSupercellConfigurationSchema,
-)
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.two_dimensional.supercell_matrix_2d import (
-    SupercellMatrix2DSchema,
-)
-
-from ..slab.configuration import SlabConfiguration
-
-
-class SlabStrainedSupercellConfiguration(SlabConfiguration, SlabStrainedSupercellConfigurationSchema):
-    strain_matrix: Matrix3x3Schema = Matrix3x3Schema(root=np.eye(3).tolist())
-    xy_supercell_matrix: Optional[SupercellMatrix2DSchema] = SupercellMatrix2DSchema(root=[[1, 0], [0, 1]])