From c4125b1447123d554d85d2fa26c0c0f414d846ab Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 28 Aug 2024 19:28:21 -0700
Subject: [PATCH 1/8] feat: add PBC handler decorator

---
 src/py/mat3ra/made/tools/analyze.py        |  2 +
 src/py/mat3ra/made/tools/utils/__init__.py | 52 ++++++++++++++++++++++
 2 files changed, 54 insertions(+)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 889b6a88..7b5ec8a4 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -1,6 +1,7 @@
 from typing import Callable, List, Literal, Optional
 
 import numpy as np
+from .utils import decorator_handle_periodic_boundary_conditions
 from scipy.spatial import cKDTree
 
 from ..material import Material
@@ -415,6 +416,7 @@ def get_coordination_numbers(
     return coordination_numbers
 
 
+@decorator_handle_periodic_boundary_conditions(cutoff=3.0)
 def get_undercoordinated_atom_indices(
     material: Material,
     indices: List[int],
diff --git a/src/py/mat3ra/made/tools/utils/__init__.py b/src/py/mat3ra/made/tools/utils/__init__.py
index 95c961eb..ece960b1 100644
--- a/src/py/mat3ra/made/tools/utils/__init__.py
+++ b/src/py/mat3ra/made/tools/utils/__init__.py
@@ -106,3 +106,55 @@ 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):
+    def decorator(func):
+        @wraps(func)
+        def wrapper(material, *args, **kwargs):
+            # Augment material with periodic images
+            augmented_material, original_count = augment_material_with_periodic_images(material, cutoff)
+
+            # Call the original function with augmented material
+            result = func(augmented_material, *args, **kwargs)
+
+            # Filter results to include only original atoms
+            if isinstance(result, list):  # Assuming result is a list of indices
+                result = [idx for idx in result if idx < original_count]
+            return result
+
+        return wrapper
+
+    return decorator
+
+
+def augment_material_with_periodic_images(material, cutoff):
+    """Augment the material's dataset by adding atoms from periodic images near boundaries."""
+    from ..build.utils import merge_materials
+    from ..modify import filter_by_box, translate_by_vector
+
+    material = material.clone()
+    original_count = len(material.basis.coordinates.values)
+    material_slice_x1 = filter_by_box(material, [0, 0, 0], [cutoff, 1, 1])
+    material_slice_x2 = filter_by_box(material, [1 - cutoff, 0, 0], [1, 1, 1])
+    translated_material_slice_x1 = translate_by_vector(material_slice_x1, [1, 0, 0])
+    translated_material_slice_x2 = translate_by_vector(material_slice_x2, [-1, 0, 0])
+    augmented_material_x = merge_materials([material, translated_material_slice_x1, translated_material_slice_x2])
+
+    material_slice_y1 = filter_by_box(augmented_material_x, [-cutoff, 0, 0], [1 + cutoff, cutoff, 1])
+    material_slice_y2 = filter_by_box(augmented_material_x, [-cutoff, 1 - cutoff, 0], [1 + cutoff, 1, 1])
+    translated_material_slice_y1 = translate_by_vector(material_slice_y1, [0, 1, 0])
+    translated_material_slice_y2 = translate_by_vector(material_slice_y2, [0, -1, 0])
+    augmented_material_y = merge_materials(
+        [augmented_material_x, translated_material_slice_y1, translated_material_slice_y2]
+    )
+
+    material_slice_z1 = filter_by_box(augmented_material_y, [-cutoff, -cutoff, 0], [1 + cutoff, 1 + cutoff, cutoff])
+    material_slice_z2 = filter_by_box(augmented_material_y, [-cutoff, -cutoff, 1 - cutoff], [1 + cutoff, 1 + cutoff, 1])
+    translated_material_slice_z1 = translate_by_vector(material_slice_z1, [0, 0, 1])
+    translated_material_slice_z2 = translate_by_vector(material_slice_z2, [0, 0, -1])
+    augmented_material = merge_materials(
+        [augmented_material_y, translated_material_slice_z1, translated_material_slice_z2]
+    )
+
+    return augmented_material, original_count

From 8e1e69263e1823583c95b1187618f706323b814b Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 28 Aug 2024 19:56:23 -0700
Subject: [PATCH 2/8] udpate: optimize performance and deps

---
 src/py/mat3ra/made/tools/analyze.py        |  3 +-
 src/py/mat3ra/made/tools/utils/__init__.py | 83 ++++++++++++++--------
 2 files changed, 57 insertions(+), 29 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 7b5ec8a4..d3ae305f 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -350,6 +350,7 @@ def shadowing_check(z: float, neighbors_indices: List[int], surface: SurfaceType
     )
 
 
+@decorator_handle_periodic_boundary_conditions(cutoff=3.0)
 def get_surface_atom_indices(
     material: Material, surface: SurfaceTypes = SurfaceTypes.TOP, shadowing_radius: float = 2.5, depth: float = 5
 ) -> List[int]:
@@ -416,7 +417,7 @@ def get_coordination_numbers(
     return coordination_numbers
 
 
-@decorator_handle_periodic_boundary_conditions(cutoff=3.0)
+@decorator_handle_periodic_boundary_conditions(cutoff=0.1)
 def get_undercoordinated_atom_indices(
     material: Material,
     indices: List[int],
diff --git a/src/py/mat3ra/made/tools/utils/__init__.py b/src/py/mat3ra/made/tools/utils/__init__.py
index ece960b1..c3fd325d 100644
--- a/src/py/mat3ra/made/tools/utils/__init__.py
+++ b/src/py/mat3ra/made/tools/utils/__init__.py
@@ -2,6 +2,7 @@
 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 ..third_party import PymatgenStructure
@@ -119,7 +120,7 @@ def wrapper(material, *args, **kwargs):
             result = func(augmented_material, *args, **kwargs)
 
             # Filter results to include only original atoms
-            if isinstance(result, list):  # Assuming result is a list of indices
+            if isinstance(result, list):
                 result = [idx for idx in result if idx < original_count]
             return result
 
@@ -128,33 +129,59 @@ def wrapper(material, *args, **kwargs):
     return decorator
 
 
-def augment_material_with_periodic_images(material, cutoff):
-    """Augment the material's dataset by adding atoms from periodic images near boundaries."""
-    from ..build.utils import merge_materials
-    from ..modify import filter_by_box, translate_by_vector
+def filter_and_translate(coordinates: np.ndarray, elements: np.ndarray, axis: int, cutoff: float, direction: int):
+    """
+    Filter and translate atom coordinates based on the axis and direction.
+
+    Args:
+        coordinates (np.ndarray): The coordinates of the atoms.
+        elements (np.ndarray): The elements of the atoms.
+        axis (int): The axis to filter and translate.
+        cutoff (float): The cutoff value for filtering.
+        direction (int): The direction to translate.
+
+    Returns:
+        Tuple[np.ndarray, np.ndarray]: The filtered and translated coordinates and elements.
+    """
+    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
+    return translated_coordinates, filtered_elements
 
-    material = material.clone()
-    original_count = len(material.basis.coordinates.values)
-    material_slice_x1 = filter_by_box(material, [0, 0, 0], [cutoff, 1, 1])
-    material_slice_x2 = filter_by_box(material, [1 - cutoff, 0, 0], [1, 1, 1])
-    translated_material_slice_x1 = translate_by_vector(material_slice_x1, [1, 0, 0])
-    translated_material_slice_x2 = translate_by_vector(material_slice_x2, [-1, 0, 0])
-    augmented_material_x = merge_materials([material, translated_material_slice_x1, translated_material_slice_x2])
-
-    material_slice_y1 = filter_by_box(augmented_material_x, [-cutoff, 0, 0], [1 + cutoff, cutoff, 1])
-    material_slice_y2 = filter_by_box(augmented_material_x, [-cutoff, 1 - cutoff, 0], [1 + cutoff, 1, 1])
-    translated_material_slice_y1 = translate_by_vector(material_slice_y1, [0, 1, 0])
-    translated_material_slice_y2 = translate_by_vector(material_slice_y2, [0, -1, 0])
-    augmented_material_y = merge_materials(
-        [augmented_material_x, translated_material_slice_y1, translated_material_slice_y2]
-    )
-
-    material_slice_z1 = filter_by_box(augmented_material_y, [-cutoff, -cutoff, 0], [1 + cutoff, 1 + cutoff, cutoff])
-    material_slice_z2 = filter_by_box(augmented_material_y, [-cutoff, -cutoff, 1 - cutoff], [1 + cutoff, 1 + cutoff, 1])
-    translated_material_slice_z1 = translate_by_vector(material_slice_z1, [0, 0, 1])
-    translated_material_slice_z2 = translate_by_vector(material_slice_z2, [0, 0, -1])
-    augmented_material = merge_materials(
-        [augmented_material_y, translated_material_slice_z1, translated_material_slice_z2]
-    )
 
+def augment_material_with_periodic_images(material: Material, cutoff: float = 0.1):
+    """
+    Augment the material's dataset by adding atoms from periodic images near boundaries.
+
+    Args:
+        material (Material): The material to augment.
+        cutoff (float): The cutoff value for filtering atoms near boundaries.
+
+    Returns:
+        Tuple[Material, int]: The augmented material and the original count of atoms.
+    """
+    original_count = len(material.basis.coordinates.values)
+    coordinates = np.array(material.basis.coordinates.values)
+    elements = np.array(material.basis.elements.values)
+    augmented_coords = []
+    augmented_elems = []
+
+    for axis in range(3):
+        for direction in [-1, 1]:
+            translated_coords, translated_elems = filter_and_translate(coordinates, elements, axis, cutoff, direction)
+            augmented_coords.append(translated_coords)
+            augmented_elems.append(translated_elems)
+
+    augmented_coords = np.vstack(augmented_coords).tolist()
+    augmented_elems = np.concatenate(augmented_elems).tolist()
+    augmented_material = material.clone()
+
+    new_basis = material.basis.copy()
+    for i, coord in enumerate(augmented_coords):
+        new_basis.add_atom(augmented_elems[i], coord)
+
+    augmented_material.basis = new_basis
     return augmented_material, original_count

From e908fe6e5284ba5cefbc6cea96cfbae4f2b567d8 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 28 Aug 2024 20:24:38 -0700
Subject: [PATCH 3/8] update: some fixes for tests to pass

---
 src/py/mat3ra/made/tools/analyze.py        |  3 ++-
 src/py/mat3ra/made/tools/utils/__init__.py | 10 +++++-----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index d3ae305f..afb3c41c 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -350,7 +350,7 @@ def shadowing_check(z: float, neighbors_indices: List[int], surface: SurfaceType
     )
 
 
-@decorator_handle_periodic_boundary_conditions(cutoff=3.0)
+@decorator_handle_periodic_boundary_conditions(cutoff=0.1)
 def get_surface_atom_indices(
     material: Material, surface: SurfaceTypes = SurfaceTypes.TOP, shadowing_radius: float = 2.5, depth: float = 5
 ) -> List[int]:
@@ -417,6 +417,7 @@ def get_coordination_numbers(
     return coordination_numbers
 
 
+# TODO: fix decorator removal of added atoms and uncomment
 @decorator_handle_periodic_boundary_conditions(cutoff=0.1)
 def get_undercoordinated_atom_indices(
     material: Material,
diff --git a/src/py/mat3ra/made/tools/utils/__init__.py b/src/py/mat3ra/made/tools/utils/__init__.py
index c3fd325d..392ee17b 100644
--- a/src/py/mat3ra/made/tools/utils/__init__.py
+++ b/src/py/mat3ra/made/tools/utils/__init__.py
@@ -113,15 +113,15 @@ def decorator_handle_periodic_boundary_conditions(cutoff):
     def decorator(func):
         @wraps(func)
         def wrapper(material, *args, **kwargs):
-            # Augment material with periodic images
             augmented_material, original_count = augment_material_with_periodic_images(material, cutoff)
-
-            # Call the original function with augmented material
             result = func(augmented_material, *args, **kwargs)
 
-            # Filter results to include only original atoms
             if isinstance(result, list):
                 result = [idx for idx in result if idx < original_count]
+
+            if isinstance(result, list) and all(isinstance(coord, float) for coord in result):
+                result = [coordinate for coordinate in result if 0 <= coordinate <= 1]
+
             return result
 
         return wrapper
@@ -179,7 +179,7 @@ def augment_material_with_periodic_images(material: Material, cutoff: float = 0.
     augmented_elems = np.concatenate(augmented_elems).tolist()
     augmented_material = material.clone()
 
-    new_basis = material.basis.copy()
+    new_basis = augmented_material.basis.copy()
     for i, coord in enumerate(augmented_coords):
         new_basis.add_atom(augmented_elems[i], coord)
 

From e7df9f42e7341fa266f3a5fd9883f9f18abb7f13 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 29 Aug 2024 10:52:43 -0700
Subject: [PATCH 4/8] update: correctly handle diagonal cells

---
 src/py/mat3ra/made/tools/analyze.py        |  1 -
 src/py/mat3ra/made/tools/utils/__init__.py | 13 ++++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index afb3c41c..15f49ad6 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -417,7 +417,6 @@ def get_coordination_numbers(
     return coordination_numbers
 
 
-# TODO: fix decorator removal of added atoms and uncomment
 @decorator_handle_periodic_boundary_conditions(cutoff=0.1)
 def get_undercoordinated_atom_indices(
     material: Material,
diff --git a/src/py/mat3ra/made/tools/utils/__init__.py b/src/py/mat3ra/made/tools/utils/__init__.py
index 392ee17b..4c3dbd0b 100644
--- a/src/py/mat3ra/made/tools/utils/__init__.py
+++ b/src/py/mat3ra/made/tools/utils/__init__.py
@@ -166,19 +166,18 @@ def augment_material_with_periodic_images(material: Material, cutoff: float = 0.
     original_count = len(material.basis.coordinates.values)
     coordinates = np.array(material.basis.coordinates.values)
     elements = np.array(material.basis.elements.values)
-    augmented_coords = []
-    augmented_elems = []
+    augmented_coords = coordinates.tolist()
+    augmented_elems = elements.tolist()
 
     for axis in range(3):
         for direction in [-1, 1]:
             translated_coords, translated_elems = filter_and_translate(coordinates, elements, axis, cutoff, direction)
-            augmented_coords.append(translated_coords)
-            augmented_elems.append(translated_elems)
+            augmented_coords.extend(translated_coords)
+            augmented_elems.extend(translated_elems)
+            coordinates = np.array(augmented_coords)
+            elements = np.array(augmented_elems)
 
-    augmented_coords = np.vstack(augmented_coords).tolist()
-    augmented_elems = np.concatenate(augmented_elems).tolist()
     augmented_material = material.clone()
-
     new_basis = augmented_material.basis.copy()
     for i, coord in enumerate(augmented_coords):
         new_basis.add_atom(augmented_elems[i], coord)

From cbc413163857657122006110501c44f1aafe7284 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 29 Aug 2024 13:30:08 -0700
Subject: [PATCH 5/8] update: fix exessive after decorator

---
 src/py/mat3ra/made/tools/utils/__init__.py | 47 +++++++++++++---------
 1 file changed, 28 insertions(+), 19 deletions(-)

diff --git a/src/py/mat3ra/made/tools/utils/__init__.py b/src/py/mat3ra/made/tools/utils/__init__.py
index 4c3dbd0b..1ac833cc 100644
--- a/src/py/mat3ra/made/tools/utils/__init__.py
+++ b/src/py/mat3ra/made/tools/utils/__init__.py
@@ -3,6 +3,7 @@
 
 import numpy as np
 from mat3ra.made.material import Material
+from mat3ra.made.utils import ArrayWithIds
 from mat3ra.utils.matrix import convert_2x2_to_3x3
 
 from ..third_party import PymatgenStructure
@@ -110,18 +111,32 @@ def transform_coordinate_to_supercell(
 
 
 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, original_count = augment_material_with_periodic_images(material, cutoff)
+            augmented_material, last_id = augment_material_with_periodic_images(material, cutoff)
             result = func(augmented_material, *args, **kwargs)
 
             if isinstance(result, list):
-                result = [idx for idx in result if idx < original_count]
-
-            if isinstance(result, list) and all(isinstance(coord, float) for coord in result):
-                result = [coordinate for coordinate in result if 0 <= coordinate <= 1]
-
+                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
@@ -163,24 +178,18 @@ def augment_material_with_periodic_images(material: Material, cutoff: float = 0.
     Returns:
         Tuple[Material, int]: The augmented material and the original count of atoms.
     """
-    original_count = len(material.basis.coordinates.values)
+    last_id = material.basis.coordinates.ids[-1]
     coordinates = np.array(material.basis.coordinates.values)
     elements = np.array(material.basis.elements.values)
-    augmented_coords = coordinates.tolist()
-    augmented_elems = elements.tolist()
+    augmented_material = material.clone()
+    new_basis = augmented_material.basis.copy()
 
     for axis in range(3):
         for direction in [-1, 1]:
             translated_coords, translated_elems = filter_and_translate(coordinates, elements, axis, cutoff, direction)
-            augmented_coords.extend(translated_coords)
-            augmented_elems.extend(translated_elems)
-            coordinates = np.array(augmented_coords)
-            elements = np.array(augmented_elems)
-
-    augmented_material = material.clone()
-    new_basis = augmented_material.basis.copy()
-    for i, coord in enumerate(augmented_coords):
-        new_basis.add_atom(augmented_elems[i], coord)
+            for coord, elem in zip(translated_coords, translated_elems):
+                if not any(np.allclose(coord, existing_coord) for existing_coord in new_basis.coordinates.values):
+                    new_basis.add_atom(elem, coord)
 
     augmented_material.basis = new_basis
-    return augmented_material, original_count
+    return augmented_material, last_id

From 499d8ae779d832bef2d0c9f4b4f281751ac74a8a Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 29 Aug 2024 20:09:36 -0700
Subject: [PATCH 6/8] update: add try for faulty nn

---
 src/py/mat3ra/made/tools/analyze.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 15f49ad6..a209f07c 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -300,8 +300,10 @@ def get_nearest_neighbors_atom_indices(
         site_index = len(structure.sites) - 1
 
         remove_dummy_atom = True
-
-    neighbors = voronoi_nn.get_nn_info(structure, site_index)
+    try:
+        neighbors = voronoi_nn.get_nn_info(structure, site_index)
+    except:
+        return None
     neighboring_atoms_pymatgen_ids = [n["site_index"] for n in neighbors]
     if remove_dummy_atom:
         structure.remove_sites([-1])

From bd996d5cb8eedaf191cd49506f3b37e4263c02ab Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 29 Aug 2024 20:09:55 -0700
Subject: [PATCH 7/8] update: don't add colliding atom

---
 src/py/mat3ra/made/basis.py                | 12 ++++++++++--
 src/py/mat3ra/made/tools/utils/__init__.py |  3 +--
 src/py/mat3ra/made/utils.py                | 17 +++++++++++++++++
 3 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/src/py/mat3ra/made/basis.py b/src/py/mat3ra/made/basis.py
index da34c13c..21c043ec 100644
--- a/src/py/mat3ra/made/basis.py
+++ b/src/py/mat3ra/made/basis.py
@@ -6,7 +6,7 @@
 from pydantic import BaseModel
 
 from .cell import Cell
-from .utils import ArrayWithIds
+from .utils import ArrayWithIds, get_overlapping_coordinates
 
 
 class Basis(RoundNumericValuesMixin, BaseModel):
@@ -76,7 +76,15 @@ def to_crystal(self):
         self.coordinates.map_array_in_place(self.cell.convert_point_to_crystal)
         self.units = AtomicCoordinateUnits.crystal
 
-    def add_atom(self, element="Si", coordinate=[0.5, 0.5, 0.5]):
+    def add_atom(self, element="Si", coordinate=None, force=False):
+        if coordinate is None:
+            coordinate = [0, 0, 0]
+        if get_overlapping_coordinates(coordinate, self.coordinates.values, threshold=0.01):
+            if force:
+                print(f"Warning: Overlapping coordinates found for {coordinate}. Adding atom anyway.")
+            else:
+                print(f"Warning: Overlapping coordinates found for {coordinate}. Not adding atom.")
+                return
         self.elements.add_item(element)
         self.coordinates.add_item(coordinate)
 
diff --git a/src/py/mat3ra/made/tools/utils/__init__.py b/src/py/mat3ra/made/tools/utils/__init__.py
index 1ac833cc..964dbfcf 100644
--- a/src/py/mat3ra/made/tools/utils/__init__.py
+++ b/src/py/mat3ra/made/tools/utils/__init__.py
@@ -188,8 +188,7 @@ def augment_material_with_periodic_images(material: Material, cutoff: float = 0.
         for direction in [-1, 1]:
             translated_coords, translated_elems = filter_and_translate(coordinates, elements, axis, cutoff, direction)
             for coord, elem in zip(translated_coords, translated_elems):
-                if not any(np.allclose(coord, existing_coord) for existing_coord in new_basis.coordinates.values):
-                    new_basis.add_atom(elem, coord)
+                new_basis.add_atom(elem, coord)
 
     augmented_material.basis = new_basis
     return augmented_material, last_id
diff --git a/src/py/mat3ra/made/utils.py b/src/py/mat3ra/made/utils.py
index 38ca10c3..cd8a7e33 100644
--- a/src/py/mat3ra/made/utils.py
+++ b/src/py/mat3ra/made/utils.py
@@ -58,6 +58,23 @@ def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
     return np.mean(np.array(coordinates), axis=0).tolist()
 
 
+def get_overlapping_coordinates(
+    coordinate: List[float], coordinates: List[List[float]], threshold: float = 0.01
+) -> List[List[float]]:
+    """
+    Find coordinates that are within a certain threshold of a given coordinate.
+
+    Args:
+        coordinate (List[float]): The coordinate.
+        coordinates (List[List[float]]): The list of coordinates.
+        threshold (float): The threshold.
+
+    Returns:
+        List[List[float]]: The list of overlapping coordinates.
+    """
+    return [c for c in coordinates if np.linalg.norm(np.array(c) - np.array(coordinate)) < threshold]
+
+
 class ValueWithId(RoundNumericValuesMixin, BaseModel):
     id: int = 0
     value: Any = None

From 008264db4f44d0a1dc2ae00d64652710f5fa8968 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 29 Aug 2024 20:18:22 -0700
Subject: [PATCH 8/8] chore: run lint fix

---
 src/py/mat3ra/made/tools/analyze.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index a209f07c..1912a88a 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -1,13 +1,13 @@
 from typing import Callable, List, Literal, Optional
 
 import numpy as np
-from .utils import decorator_handle_periodic_boundary_conditions
 from scipy.spatial import cKDTree
 
 from ..material import Material
 from .build.passivation.enums import SurfaceTypes
 from .convert import decorator_convert_material_args_kwargs_to_atoms, to_pymatgen
 from .third_party import ASEAtoms, PymatgenIStructure, PymatgenVoronoiNN
+from .utils import decorator_handle_periodic_boundary_conditions
 
 
 @decorator_convert_material_args_kwargs_to_atoms
@@ -302,7 +302,7 @@ def get_nearest_neighbors_atom_indices(
         remove_dummy_atom = True
     try:
         neighbors = voronoi_nn.get_nn_info(structure, site_index)
-    except:
+    except ValueError:
         return None
     neighboring_atoms_pymatgen_ids = [n["site_index"] for n in neighbors]
     if remove_dummy_atom: