update: move function

src/py/mat3ra/made/tools/utils/__init__.py

@@ -1,11 +1,9 @@
 from functools import wraps
-from typing import Any, Callable, List, Optional, Tuple
+from typing import Callable, List, Optional
 
 import numpy as np
-from mat3ra.made.material import Material
 from mat3ra.utils.matrix import convert_2x2_to_3x3
 
-from ...utils import ArrayWithIds
 from ..third_party import PymatgenStructure
 
 DEFAULT_SCALING_FACTOR = np.array([3, 3, 3])
@@ -129,72 +127,3 @@ def transform_coordinate_to_supercell(
     if reverse:
         converted_array = (np_coordinate - np_translation_vector) * np_scaling_factor
     return converted_array.tolist()
-
-
-def decorator_handle_periodic_boundary_conditions(cutoff):
-    """
-    Decorator to handle periodic boundary conditions.
-
-    Copies atoms near boundaries within the cutoff distance beyond the opposite side of the cell
-    creating the effect of periodic boundary conditions for edge atoms.
-
-    Results of the function are filtered to remove atoms or coordinates outside the original cell.
-
-    Args:
-        cutoff (float): The cutoff distance for a border slice in crystal coordinates.
-
-    Returns:
-        Callable: The decorated function.
-    """
-
-    def decorator(func):
-        @wraps(func)
-        def wrapper(material, *args, **kwargs):
-            augmented_material, last_id = augment_material_with_periodic_images(material, cutoff)
-            result = func(augmented_material, *args, **kwargs)
-            original_ids = material.basis.coordinates.ids
-            if isinstance(result, ArrayWithIds):
-                result.filter_by_ids(original_ids)
-            if isinstance(result, list):
-                if all(isinstance(x, int) for x in result):
-                    result = [id for id in result if id <= last_id]
-                elif all(isinstance(x, list) and len(x) == 3 for x in result):
-                    result = [coord for coord in result if all(0 <= c < 1 for c in coord)]
-            return result
-
-        return wrapper
-
-    return decorator
-
-
-def augment_material_with_periodic_images(material: Material, cutoff: float = 1.0):
-    """
-    Augment the material's dataset by adding atoms from periodic images within a cutoff distance from the boundaries by
-    copying them to the opposite side of the cell, translated by the cell vector beyond the boundary.
-
-    Args:
-        material (Material): The material to augment.
-        cutoff (float): The cutoff value for filtering atoms near boundaries, in crystal coordinates.
-
-    Returns:
-        Tuple[Material, int]: The augmented material and the original count of atoms.
-    """
-    last_id = material.basis.coordinates.ids[-1]
-    coordinates = np.array(material.basis.coordinates.values)
-    elements = np.array(material.basis.elements.values)
-    augmented_material = material.clone()
-    new_basis = augmented_material.basis.copy()
-
-    for axis in range(3):
-        for direction in [-1, 1]:
-            mask = (coordinates[:, axis] < cutoff) if direction == 1 else (coordinates[:, axis] > (1 - cutoff))
-            filtered_coordinates = coordinates[mask]
-            filtered_elements = elements[mask]
-            translation_vector = np.zeros(3)
-            translation_vector[axis] = direction
-            translated_coordinates = filtered_coordinates + translation_vector
-            for coord, elem in zip(translated_coordinates, filtered_elements):
-                new_basis.add_atom(elem, coord)
-
-    augmented_material.basis = new_basis
-    return augmented_material, last_id