feature/SOF 7397

src/py/mat3ra/made/basis.py

@@ -24,14 +24,14 @@ def from_dict(
         coordinates: List[Dict],
         units: str,
         labels: Optional[List[Dict]] = None,
-        cell: Optional[Dict] = None,
+        cell: Optional[List[List[float]]] = None,
         constraints: Optional[List[Dict]] = None,
     ) -> "Basis":
         return Basis(
             elements=ArrayWithIds.from_list_of_dicts(elements),
             coordinates=ArrayWithIds.from_list_of_dicts(coordinates),
             units=units,
-            cell=Cell.from_nested_array(cell),
+            cell=Cell.from_vectors_array(cell),
             labels=ArrayWithIds.from_list_of_dicts(labels) if labels else ArrayWithIds(values=[]),
             constraints=ArrayWithIds.from_list_of_dicts(constraints) if constraints else ArrayWithIds(values=[]),
         )

src/py/mat3ra/made/cell.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional
 
 import numpy as np
 from mat3ra.utils.mixins import RoundNumericValuesMixin
@@ -13,13 +13,13 @@ class Cell(RoundNumericValuesMixin, BaseModel):
     __round_precision__ = 6
 
     @classmethod
-    def from_nested_array(cls, nested_array):
-        if nested_array is None:
-            nested_array = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
-        return cls(vector1=nested_array[0], vector2=nested_array[1], vector3=nested_array[2])
+    def from_vectors_array(cls, vectors_array: Optional[List[List[float]]] = None) -> "Cell":
+        if vectors_array is None:
+            vectors_array = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+        return cls(vector1=vectors_array[0], vector2=vectors_array[1], vector3=vectors_array[2])
 
     @property
-    def vectors_as_nested_array(self, skip_rounding=False) -> List[List[float]]:
+    def vectors_as_array(self, skip_rounding=False) -> List[List[float]]:
         if skip_rounding:
             return [self.vector1, self.vector2, self.vector3]
         return self.round_array_or_number([self.vector1, self.vector2, self.vector3])
@@ -32,22 +32,22 @@ def to_json(self, skip_rounding=False):
             self.vector3 if skip_rounding else _(self.vector3),
         ]
 
-    def clone(self):
-        return self.from_nested_array(self.vectors_as_nested_array)
+    def clone(self) -> "Cell":
+        return self.from_vectors_array(self.vectors_as_array)
 
-    def clone_and_scale_by_matrix(self, matrix):
+    def clone_and_scale_by_matrix(self, matrix: List[List[float]]) -> "Cell":
         new_cell = self.clone()
         new_cell.scale_by_matrix(matrix)
         return new_cell
 
-    def convert_point_to_cartesian(self, point):
-        np_vector = np.array(self.vectors_as_nested_array)
+    def convert_point_to_cartesian(self, point: List[float]) -> List[float]:
+        np_vector = np.array(self.vectors_as_array)
         return np.dot(point, np_vector)
 
-    def convert_point_to_crystal(self, point):
-        np_vector = np.array(self.vectors_as_nested_array)
+    def convert_point_to_crystal(self, point: List[float]) -> List[float]:
+        np_vector = np.array(self.vectors_as_array)
         return np.dot(point, np.linalg.inv(np_vector))
 
-    def scale_by_matrix(self, matrix):
-        np_vector = np.array(self.vectors_as_nested_array)
-        self.vector1, self.vector2, self.vector3 = np.dot(matrix, np_vector).tolist()
+    def scale_by_matrix(self, matrix: List[List[float]]):
+        np_vector = np.array(self.vectors_as_array)
+        self.vector1, self.vector2, self.vector3 = np.dot(np.array(matrix), np_vector).tolist()

src/py/mat3ra/made/lattice.py

@@ -8,6 +8,8 @@
 from .cell import Cell
 
 HASH_TOLERANCE = 3
+DEFAULT_UNITS = {"length": "angstrom", "angle": "degree"}
+DEFAULT_TYPE = "TRI"
 
 
 class Lattice(RoundNumericValuesMixin, BaseModel):
@@ -17,11 +19,8 @@ class Lattice(RoundNumericValuesMixin, BaseModel):
     alpha: float = 90.0
     beta: float = 90.0
     gamma: float = 90.0
-    units: Dict[str, str] = {
-        "length": "angstrom",
-        "angle": "degree",
-    }
-    type: str = "TRI"
+    units: Dict[str, str] = DEFAULT_UNITS
+    type: str = DEFAULT_TYPE
 
     @property
     def vectors(self) -> List[List[float]]:
@@ -52,6 +51,29 @@ def vectors(self) -> List[List[float]]:
             [0.0, 0.0, c],
         ]
 
+    @classmethod
+    def from_vectors_array(
+        cls, vectors: List[List[float]], units: Optional[Dict[str, str]] = None, type: Optional[str] = None
+    ) -> "Lattice":
+        """
+        Create a Lattice object from a nested array of vectors.
+        Args:
+            vectors (List[List[float]]): A nested array of vectors.
+        Returns:
+            Lattice: A Lattice object.
+        """
+        a = np.linalg.norm(vectors[0])
+        b = np.linalg.norm(vectors[1])
+        c = np.linalg.norm(vectors[2])
+        alpha = np.degrees(np.arccos(np.dot(vectors[1], vectors[2]) / (b * c)))
+        beta = np.degrees(np.arccos(np.dot(vectors[0], vectors[2]) / (a * c)))
+        gamma = np.degrees(np.arccos(np.dot(vectors[0], vectors[1]) / (a * b)))
+        if units is None:
+            units = DEFAULT_UNITS
+        if type is None:
+            type = DEFAULT_TYPE
+        return cls(a=float(a), b=float(b), c=float(c), alpha=alpha, beta=beta, gamma=gamma, units=units, type=type)
+
     def to_json(self, skip_rounding: bool = False) -> Dict[str, Any]:
         __round__ = RoundNumericValuesMixin.round_array_or_number
         round_func = __round__ if not skip_rounding else lambda x: x
@@ -78,7 +100,7 @@ def vector_arrays(self) -> List[List[float]]:
 
     @property
     def cell(self) -> Cell:
-        return Cell.from_nested_array(self.vector_arrays)
+        return Cell.from_vectors_array(self.vector_arrays)
 
     def volume(self) -> float:
         np_vector = np.array(self.vector_arrays)

src/py/mat3ra/made/material.py

@@ -90,3 +90,8 @@ def to_crystal(self) -> None:
         new_basis = self.basis.copy()
         new_basis.to_crystal()
         self.basis = new_basis
+
+    def set_coordinates(self, coordinates: List[List[float]]) -> None:
+        new_basis = self.basis.copy()
+        new_basis.coordinates.values = coordinates
+        self.basis = new_basis

src/py/mat3ra/made/tools/build/defect/builders.py

@@ -30,7 +30,8 @@
     get_closest_site_id_from_coordinate_and_element,
 )
 from ....utils import get_center_of_coordinates
-from ...utils import transform_coordinate_to_supercell, CoordinateConditionBuilder
+from ...utils import transform_coordinate_to_supercell
+from ...utils import coordinate as CoordinateCondition
 from ..utils import merge_materials
 from ..slab import SlabConfiguration, create_slab, Termination
 from ..supercell import create_supercell
@@ -436,7 +437,7 @@ def condition(coordinate: List[float]):
         return self.merge_slab_and_defect(island_material, new_material)
 
     def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
-        condition_callable, _ = configuration.condition
+        condition_callable = configuration.condition.condition
         return [
             self.create_island(
                 material=configuration.crystal,
@@ -463,7 +464,7 @@ def _calculate_cut_direction_vector(self, material: Material, cut_direction: Lis
             The normalized cut direction vector in Cartesian coordinates.
         """
         np_cut_direction = np.array(cut_direction)
-        direction_vector = np.dot(np.array(material.basis.cell.vectors_as_nested_array), np_cut_direction)
+        direction_vector = np.dot(np.array(material.basis.cell.vectors_as_array), np_cut_direction)
         normalized_direction_vector = direction_vector / np.linalg.norm(direction_vector)
         return normalized_direction_vector
 
@@ -499,7 +500,7 @@ def _calculate_rotation_parameters(
         """
         height_cartesian = self._calculate_height_cartesian(original_material, new_material)
         cut_direction_xy_proj_cart = np.linalg.norm(
-            np.dot(np.array(new_material.basis.cell.vectors_as_nested_array), normalized_direction_vector)
+            np.dot(np.array(new_material.basis.cell.vectors_as_array), normalized_direction_vector)
         )
         # Slope of the terrace along the cut direction
         hypotenuse = np.linalg.norm([height_cartesian, cut_direction_xy_proj_cart])
@@ -592,10 +593,10 @@ def create_terrace(
         )
 
         normalized_direction_vector = self._calculate_cut_direction_vector(material, cut_direction)
-        condition, _ = CoordinateConditionBuilder.plane(
+        condition = CoordinateCondition.PlaneCoordinateCondition(
             plane_normal=normalized_direction_vector,
             plane_point_coordinate=pivot_coordinate,
-        )
+        ).condition
         atoms_within_terrace = filter_by_condition_on_coordinates(
             material=material_with_additional_layers,
             condition=condition,

src/py/mat3ra/made/tools/build/defect/configuration.py

@@ -1,17 +1,25 @@
-from typing import Optional, List, Any, Callable, Dict, Tuple, Union
+from typing import Optional, List, Union
 from pydantic import BaseModel
 
 from mat3ra.code.entity import InMemoryEntity
 from mat3ra.made.material import Material
 
 from ...analyze import get_closest_site_id_from_coordinate, get_atomic_coordinates_extremum
-from ...utils import CoordinateConditionBuilder
+from ...utils.coordinate import (
+    CylinderCoordinateCondition,
+    SphereCoordinateCondition,
+    BoxCoordinateCondition,
+    TriangularPrismCoordinateCondition,
+    PlaneCoordinateCondition,
+)
 from .enums import PointDefectTypeEnum, SlabDefectTypeEnum, AtomPlacementMethodEnum, ComplexDefectTypeEnum
 
 
 class BaseDefectConfiguration(BaseModel):
-    # TODO: fix arbitrary_types_allowed error and set Material class type
-    crystal: Any = None
+    crystal: Material = None
+
+    class Config:
+        arbitrary_types_allowed = True
 
     @property
     def _json(self):
@@ -169,16 +177,21 @@ class IslandSlabDefectConfiguration(SlabDefectConfiguration):
     """
 
     defect_type: SlabDefectTypeEnum = SlabDefectTypeEnum.ISLAND
-    condition: Optional[Tuple[Callable[[List[float]], bool], Dict]] = CoordinateConditionBuilder().cylinder()
+    condition: Union[
+        CylinderCoordinateCondition,
+        SphereCoordinateCondition,
+        BoxCoordinateCondition,
+        TriangularPrismCoordinateCondition,
+        PlaneCoordinateCondition,
+    ] = CylinderCoordinateCondition()
 
     @property
     def _json(self):
-        _, condition_json = self.condition
         return {
             **super()._json,
             "type": self.get_cls_name(),
             "defect_type": self.defect_type.name,
-            "condition": condition_json,
+            "condition": self.condition.get_json(),
         }
 
 

src/py/mat3ra/made/tools/build/interface/builders.py

@@ -1,6 +1,7 @@
 from typing import Any, List, Optional
 
 import numpy as np
+from mat3ra.made.tools.modify import translate_to_z_level
 from pydantic import BaseModel
 from ase.build.tools import niggli_reduce
 from pymatgen.analysis.interfaces.coherent_interfaces import (
@@ -144,9 +145,13 @@ class ZSLStrainMatchingInterfaceBuilder(ConvertGeneratedItemsPymatgenStructureMi
 
     def _generate(self, configuration: InterfaceConfiguration) -> List[PymatgenInterface]:
         generator = ZSLGenerator(**self.build_parameters.strain_matching_parameters.dict())
+        substrate_with_atoms_translated_to_bottom = translate_to_z_level(
+            configuration.substrate_configuration.bulk, "bottom"
+        )
+        film_with_atoms_translated_to_bottom = translate_to_z_level(configuration.film_configuration.bulk, "bottom")
         builder = CoherentInterfaceBuilder(
-            substrate_structure=to_pymatgen(configuration.substrate_configuration.bulk),
-            film_structure=to_pymatgen(configuration.film_configuration.bulk),
+            substrate_structure=to_pymatgen(substrate_with_atoms_translated_to_bottom),
+            film_structure=to_pymatgen(film_with_atoms_translated_to_bottom),
             substrate_miller=configuration.substrate_configuration.miller_indices,
             film_miller=configuration.film_configuration.miller_indices,
             zslgen=generator,

src/py/mat3ra/made/tools/build/perturbation/__init__.py

@@ -0,0 +1,37 @@
+from typing import Union, Optional
+
+from mat3ra.made.material import Material
+from .builders import (
+    SlabPerturbationBuilder,
+    DistancePreservingSlabPerturbationBuilder,
+    CellMatchingDistancePreservingSlabPerturbationBuilder,
+)
+from .configuration import PerturbationConfiguration
+
+
+def create_perturbation(
+    configuration: PerturbationConfiguration,
+    preserve_distance: Optional[bool] = False,
+    builder: Union[
+        SlabPerturbationBuilder,
+        DistancePreservingSlabPerturbationBuilder,
+        CellMatchingDistancePreservingSlabPerturbationBuilder,
+        None,
+    ] = None,
+) -> Material:
+    """
+    Return a material with a perturbation applied.
+
+    Args:
+        configuration: The configuration of the perturbation to be applied.
+        preserve_distance: If True, the builder that preserves the distance between atoms is used.
+        builder: The builder to be used to create the perturbation.
+
+    Returns:
+        The material with the perturbation applied.
+    """
+    if builder is None:
+        builder = SlabPerturbationBuilder()
+    if preserve_distance:
+        builder = CellMatchingDistancePreservingSlabPerturbationBuilder()
+    return builder.get_material(configuration)