From 6cda719aa393c68f7da9c922ec4cb5c518ed29a7 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Tue, 2 Jul 2024 11:52:34 -0400
Subject: [PATCH 01/35] feat: add neigboring atoms function

---
 src/py/mat3ra/made/tools/analyze.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index ea988646..9cc98755 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, Optional
 
 import numpy as np
+from pymatgen.analysis.local_env import VoronoiNN
 
 from ..material import Material
 from .convert import decorator_convert_material_args_kwargs_to_atoms, to_pymatgen
@@ -229,3 +230,29 @@ def get_atom_indices_with_condition_on_coordinates(
             selected_indices.append(coord.id)
 
     return selected_indices
+
+
+def get_neighboring_atoms_indices(material: Material, position: List[float] = [0, 0, 0]) -> Optional[List[int]]:
+    """
+    Returns the indices of direct neighboring atoms to a specified position in the material using Voronoi tessellation.
+
+    Args:
+        material (Material): The material object to find neighbors in.
+        position (List[float]): The position to find neighbors for.
+
+    Returns:
+        List[int]: A list of indices of neighboring atoms, or an empty list if no neighbors are found.
+    """
+    structure = to_pymatgen(material)
+
+    voronoi_nn = VoronoiNN(tol=0.5)
+    structure.append("X", position, validate_proximity=False)
+    neighbors = voronoi_nn.get_nn_info(structure, len(structure.sites) - 1)
+    neighboring_atoms_pymatgen_ids = [n["site_index"] for n in neighbors]
+    structure.remove_sites([-1])
+
+    all_coordinates = material.basis.coordinates
+    all_coordinates.filter_by_indices(neighboring_atoms_pymatgen_ids)
+    neighboring_atoms_ids = all_coordinates.ids
+
+    return neighboring_atoms_ids

From 5409ac6e76ef8928de3466e875c8b053cada3e32 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Tue, 2 Jul 2024 14:02:34 -0400
Subject: [PATCH 02/35] update: add setup for slab defects

---
 src/py/mat3ra/made/tools/build/defect/builders.py | 10 ++++++++++
 .../made/tools/build/defect/configuration.py      | 15 ++++++++++++---
 src/py/mat3ra/made/tools/build/defect/enums.py    |  4 ++++
 3 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index e1582f28..7902ebfb 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -67,3 +67,13 @@ class SubstitutionPointDefectBuilder(PointDefectBuilder):
 
 class InterstitialPointDefectBuilder(PointDefectBuilder):
     _generator: PymatgenInterstitial = PymatgenInterstitial
+
+
+class SlabDefectBuilderParameters(BaseModel):
+    add_vacuum: bool = True
+    min_vacuum_thickness: float = 5.0
+
+
+class SlabDefectBuilder(BaseBuilder):
+    _BuildParametersType = SlabDefectBuilderParameters
+    _DefaultBuildParameters = SlabDefectBuilderParameters()
diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index c0897a92..ad057e46 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -5,7 +5,7 @@
 from mat3ra.made.material import Material
 
 from ...analyze import get_closest_site_id_from_position
-from .enums import PointDefectTypeEnum
+from .enums import PointDefectTypeEnum, SlabDefectTypeEnum
 
 
 class BaseDefectConfiguration(BaseModel):
@@ -23,7 +23,7 @@ def from_site_id(
         cls, crystal: Material, defect_type: PointDefectTypeEnum, site_id: int, chemical_element: Optional[str] = None
     ):
         if not crystal:
-            RuntimeError("Crystal is not defined")
+            raise RuntimeError("Crystal is not defined")
         position = crystal.coordinates_array[site_id]
         return cls(crystal=crystal, defect_type=defect_type, position=position, chemical_element=chemical_element)
 
@@ -36,7 +36,7 @@ def from_approximate_position(
         chemical_element: Optional[str] = None,
     ):
         if not crystal:
-            RuntimeError("Crystal is not defined")
+            raise RuntimeError("Crystal is not defined")
         closest_site_id = get_closest_site_id_from_position(crystal, approximate_position)
         return cls.from_site_id(
             crystal=crystal, defect_type=defect_type, site_id=closest_site_id, chemical_element=chemical_element
@@ -50,3 +50,12 @@ def _json(self):
             "position": self.position,
             "chemical_element": self.chemical_element,
         }
+
+
+class SlabDefectConfiguration(BaseDefectConfiguration, InMemoryEntity):
+    defect_type: SlabDefectTypeEnum
+
+
+class AdatomSlabDefectConfiguration(SlabDefectConfiguration):
+    position: List[float] = [0.5, 0.5, 0.5]
+    chemical_element: str = "Si"
diff --git a/src/py/mat3ra/made/tools/build/defect/enums.py b/src/py/mat3ra/made/tools/build/defect/enums.py
index 8e9c092f..da3b92fd 100644
--- a/src/py/mat3ra/made/tools/build/defect/enums.py
+++ b/src/py/mat3ra/made/tools/build/defect/enums.py
@@ -5,3 +5,7 @@ class PointDefectTypeEnum(str, Enum):
     VACANCY = "vacancy"
     SUBSTITUTION = "substitution"
     INTERSTITIAL = "interstitial"
+
+
+class SlabDefectTypeEnum(str, Enum):
+    ADATOM = "adatom"

From 6a43b9400b4cf5c2b43b3e413cc3d75e6096ace5 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Tue, 2 Jul 2024 14:11:00 -0400
Subject: [PATCH 03/35] update: add adatom and equidistant

---
 .../made/tools/build/defect/builders.py       | 65 ++++++++++++++++++-
 1 file changed, 64 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 7902ebfb..13462bb2 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -1,7 +1,8 @@
 from typing import List, Callable
 
-from mat3ra.made.material import Material
 from pydantic import BaseModel
+from mat3ra.made.material import Material
+
 
 from ...third_party import (
     PymatgenStructure,
@@ -14,6 +15,7 @@
 from ...convert import to_pymatgen
 from ..mixins import ConvertGeneratedItemsPymatgenStructureMixin
 from .configuration import PointDefectConfiguration
+from ...analyze import get_neighboring_atoms_indices
 
 
 class PointDefectBuilderParameters(BaseModel):
@@ -77,3 +79,64 @@ class SlabDefectBuilderParameters(BaseModel):
 class SlabDefectBuilder(BaseBuilder):
     _BuildParametersType = SlabDefectBuilderParameters
     _DefaultBuildParameters = SlabDefectBuilderParameters()
+
+
+class AdatomSlabDefectBuilder(SlabDefectBuilder):
+    _GeneratedItemType: Material = Material
+
+    def add_adatom(
+        material: Material, chemical_element: str = "Si", position: List[float] = [0.5, 0.5, 0.5]
+    ) -> Material:
+        material_copy = material.clone()
+        basis = material_copy.basis
+        basis.add_atom(chemical_element, position)
+        material_copy.basis = basis
+        return [material_copy]
+
+    _generator = add_adatom
+
+
+class EquidistantAdatomSlabDefectBuilder(SlabDefectBuilder):
+    _GeneratedItemType: Material = Material
+
+    def add_adatom_equdistant(
+        material: Material,
+        chemical_element: str = "Si",
+        approximate_position: List[float] = [0.5, 0.5, 0.5],
+        distance: float = 2.0,
+    ) -> Material:
+        """
+        Adds an atom to the material at a position that is equidistant to the nearest atoms
+        (that are found within proximity to the approx position) with the specified distance.
+        """
+        material_copy: Material = material.clone()
+        basis = material_copy.basis
+
+        distance = distance / material_copy.lattice.c
+        max_z = max([coordinate[2] for coordinate in basis.coordinates.values])
+
+        # Move the appx position to the top of the slab
+        adatom_position = approximate_position.copy()
+        adatom_position[2] = max_z + distance
+
+        neighboring_atoms_ids = get_neighboring_atoms_indices(material, adatom_position)
+
+        # Find equidistant position from heighboring atoms with the set z
+        if neighboring_atoms_ids is not None:
+            neighboring_atoms_coordinates = [basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
+
+        equidistant_position = [
+            sum([coordinate[i] for coordinate in neighboring_atoms_coordinates]) / len(neighboring_atoms_coordinates)
+            for i in range(3)
+        ]
+        equidistant_position[2] = adatom_position[2]
+
+        # Check for valid position (inside the cell)
+        if equidistant_position[2] > basis.cell.vectors_as_nested_array[2][2]:
+            raise ValueError("The adatom position is outside the cell.")
+
+        basis.add_atom(chemical_element, equidistant_position)
+        material_copy.basis = basis
+        return [material_copy]
+
+    _generator = add_adatom_equdistant

From 528487974a7cf8bf13e10db9848bff020f78d780 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Wed, 3 Jul 2024 20:01:03 -0400
Subject: [PATCH 04/35] update: imports

---
 src/py/mat3ra/made/tools/analyze.py                   |  5 ++---
 .../mat3ra/made/tools/build/defect/configuration.py   | 11 +----------
 src/py/mat3ra/made/tools/third_party.py               |  2 ++
 3 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 9cc98755..38730cd0 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -1,11 +1,10 @@
 from typing import Callable, List, Optional
 
 import numpy as np
-from pymatgen.analysis.local_env import VoronoiNN
 
 from ..material import Material
 from .convert import decorator_convert_material_args_kwargs_to_atoms, to_pymatgen
-from .third_party import ASEAtoms, PymatgenIStructure
+from .third_party import ASEAtoms, PymatgenIStructure, PymatgenVoronoiNN
 
 
 @decorator_convert_material_args_kwargs_to_atoms
@@ -245,7 +244,7 @@ def get_neighboring_atoms_indices(material: Material, position: List[float] = [0
     """
     structure = to_pymatgen(material)
 
-    voronoi_nn = VoronoiNN(tol=0.5)
+    voronoi_nn = PymatgenVoronoiNN(tol=0.5)
     structure.append("X", position, validate_proximity=False)
     neighbors = voronoi_nn.get_nn_info(structure, len(structure.sites) - 1)
     neighboring_atoms_pymatgen_ids = [n["site_index"] for n in neighbors]
diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index ad057e46..eda9f804 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -5,7 +5,7 @@
 from mat3ra.made.material import Material
 
 from ...analyze import get_closest_site_id_from_position
-from .enums import PointDefectTypeEnum, SlabDefectTypeEnum
+from .enums import PointDefectTypeEnum
 
 
 class BaseDefectConfiguration(BaseModel):
@@ -50,12 +50,3 @@ def _json(self):
             "position": self.position,
             "chemical_element": self.chemical_element,
         }
-
-
-class SlabDefectConfiguration(BaseDefectConfiguration, InMemoryEntity):
-    defect_type: SlabDefectTypeEnum
-
-
-class AdatomSlabDefectConfiguration(SlabDefectConfiguration):
-    position: List[float] = [0.5, 0.5, 0.5]
-    chemical_element: str = "Si"
diff --git a/src/py/mat3ra/made/tools/third_party.py b/src/py/mat3ra/made/tools/third_party.py
index d6329e75..226627d3 100644
--- a/src/py/mat3ra/made/tools/third_party.py
+++ b/src/py/mat3ra/made/tools/third_party.py
@@ -5,6 +5,7 @@
 from pymatgen.analysis.defects.core import Interstitial as PymatgenInterstitial
 from pymatgen.analysis.defects.core import Substitution as PymatgenSubstitution
 from pymatgen.analysis.defects.core import Vacancy as PymatgenVacancy
+from pymatgen.analysis.local_env import VoronoiNN as PymatgenVoronoiNN
 from pymatgen.core import IStructure as PymatgenIStructure
 from pymatgen.core import PeriodicSite as PymatgenPeriodicSite
 from pymatgen.core.interface import Interface as PymatgenInterface
@@ -38,4 +39,5 @@
     "ase_make_supercell",
     "PymatgenAseAtomsAdaptor",
     "PymatgenPoscar",
+    "PymatgenVoronoiNN",
 ]

From b3a184166ac88030e785b44abb4569d7b5794ef2 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 5 Jul 2024 21:14:41 -0700
Subject: [PATCH 05/35] update: address pr comments

---
 src/py/mat3ra/made/tools/analyze.py           | 17 +++++-
 .../made/tools/build/defect/builders.py       | 61 +++++++++++--------
 2 files changed, 50 insertions(+), 28 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 38730cd0..9024ca85 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -211,7 +211,7 @@ def get_atom_indices_with_condition_on_coordinates(
     Args:
         material (Material): Material object
         condition (Callable[List[float], bool]): Function that checks if coordinates satisfy the condition.
-        use_cartesian (bool): Whether to use Cartesian coordinates for the condition evaluation.
+        use_cartesian_coordinates (bool): Whether to use Cartesian coordinates for the condition evaluation.
 
     Returns:
         List[int]: List of indices of atoms whose coordinates satisfy the condition.
@@ -231,7 +231,7 @@ def get_atom_indices_with_condition_on_coordinates(
     return selected_indices
 
 
-def get_neighboring_atoms_indices(material: Material, position: List[float] = [0, 0, 0]) -> Optional[List[int]]:
+def get_nearest_neighbors_atom_indices(material: Material, position: List[float] = [0, 0, 0]) -> Optional[List[int]]:
     """
     Returns the indices of direct neighboring atoms to a specified position in the material using Voronoi tessellation.
 
@@ -255,3 +255,16 @@ def get_neighboring_atoms_indices(material: Material, position: List[float] = [0
     neighboring_atoms_ids = all_coordinates.ids
 
     return neighboring_atoms_ids
+
+
+def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
+    """
+    Calculate the center of the coordinates.
+
+    Args:
+        coordinates (List[List[float]]): The list of coordinates.
+
+    Returns:
+        List[float]: The center of the coordinates.
+    """
+    return [sum([coordinate[i] for coordinate in coordinates]) / len(coordinates) for i in range(3)]
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 13462bb2..de41076f 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -15,7 +15,7 @@
 from ...convert import to_pymatgen
 from ..mixins import ConvertGeneratedItemsPymatgenStructureMixin
 from .configuration import PointDefectConfiguration
-from ...analyze import get_neighboring_atoms_indices
+from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates
 
 
 class PointDefectBuilderParameters(BaseModel):
@@ -72,8 +72,8 @@ class InterstitialPointDefectBuilder(PointDefectBuilder):
 
 
 class SlabDefectBuilderParameters(BaseModel):
-    add_vacuum: bool = True
-    min_vacuum_thickness: float = 5.0
+    auto_add_vacuum: bool = True
+    vacuum_thickness: float = 5.0
 
 
 class SlabDefectBuilder(BaseBuilder):
@@ -85,10 +85,18 @@ class AdatomSlabDefectBuilder(SlabDefectBuilder):
     _GeneratedItemType: Material = Material
 
     def add_adatom(
-        material: Material, chemical_element: str = "Si", position: List[float] = [0.5, 0.5, 0.5]
-    ) -> Material:
+        self,
+        material: Material,
+        chemical_element: str = "Si",
+        position_on_surface: List[float] = [0.5, 0.5],
+        distance_z: float = 2.0,
+    ) -> List[Material]:
         material_copy = material.clone()
         basis = material_copy.basis
+        distance_in_crystal_units = distance_z / material_copy.lattice.c
+        max_z = max([coordinate[2] for coordinate in basis.coordinates.values])
+        position = position_on_surface.copy()
+        position[2] = max_z + distance_in_crystal_units
         basis.add_atom(chemical_element, position)
         material_copy.basis = basis
         return [material_copy]
@@ -100,38 +108,39 @@ class EquidistantAdatomSlabDefectBuilder(SlabDefectBuilder):
     _GeneratedItemType: Material = Material
 
     def add_adatom_equdistant(
+        self,
         material: Material,
         chemical_element: str = "Si",
-        approximate_position: List[float] = [0.5, 0.5, 0.5],
-        distance: float = 2.0,
-    ) -> Material:
+        approximate_position_on_surface: List[float] = [0.5, 0.5],
+        distance_z: float = 2.0,
+    ) -> List[Material]:
         """
-        Adds an atom to the material at a position that is equidistant to the nearest atoms
+        Add an atom to the material at a position that is equidistant to the nearest atoms
         (that are found within proximity to the approx position) with the specified distance.
+
+        Args:
+            material (Material): The material to add the adatom to.
+            chemical_element (str): The chemical element of the adatom.
+            approximate_position_on_surface (List[float]): The approximate position of the adatom on the surface.
+            distance_z (float): The distance from the nearest atoms to the adatom.
+
+        Returns:
+            List[Material]: A list containing the material with the adatom added.
         """
         material_copy: Material = material.clone()
         basis = material_copy.basis
-
-        distance = distance / material_copy.lattice.c
+        distance_in_crystal_units = distance_z / material_copy.lattice.c
         max_z = max([coordinate[2] for coordinate in basis.coordinates.values])
+        adatom_position = approximate_position_on_surface.copy()
+        adatom_position[2] = max_z + distance_in_crystal_units
 
-        # Move the appx position to the top of the slab
-        adatom_position = approximate_position.copy()
-        adatom_position[2] = max_z + distance
-
-        neighboring_atoms_ids = get_neighboring_atoms_indices(material, adatom_position)
+        neighboring_atoms_ids = get_nearest_neighbors_atom_indices(material, adatom_position)
+        if not neighboring_atoms_ids:
+            raise ValueError("No neighboring atoms found.")
+        neighboring_atoms_coordinates = [basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
 
-        # Find equidistant position from heighboring atoms with the set z
-        if neighboring_atoms_ids is not None:
-            neighboring_atoms_coordinates = [basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
-
-        equidistant_position = [
-            sum([coordinate[i] for coordinate in neighboring_atoms_coordinates]) / len(neighboring_atoms_coordinates)
-            for i in range(3)
-        ]
+        equidistant_position = get_center_of_coordinates(neighboring_atoms_coordinates)
         equidistant_position[2] = adatom_position[2]
-
-        # Check for valid position (inside the cell)
         if equidistant_position[2] > basis.cell.vectors_as_nested_array[2][2]:
             raise ValueError("The adatom position is outside the cell.")
 

From 04403ad4ff01369811ace2c35da56d8e9c424f65 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 5 Jul 2024 21:19:07 -0700
Subject: [PATCH 06/35] chore: cleanup

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

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index de41076f..93054f73 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -13,9 +13,9 @@
 )
 from ...build import BaseBuilder
 from ...convert import to_pymatgen
+from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates, get_atomic_coordinates_max_z
 from ..mixins import ConvertGeneratedItemsPymatgenStructureMixin
 from .configuration import PointDefectConfiguration
-from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates
 
 
 class PointDefectBuilderParameters(BaseModel):
@@ -130,7 +130,7 @@ def add_adatom_equdistant(
         material_copy: Material = material.clone()
         basis = material_copy.basis
         distance_in_crystal_units = distance_z / material_copy.lattice.c
-        max_z = max([coordinate[2] for coordinate in basis.coordinates.values])
+        max_z = get_atomic_coordinates_max_z(material_copy)
         adatom_position = approximate_position_on_surface.copy()
         adatom_position[2] = max_z + distance_in_crystal_units
 

From 864ece08582c7ba5e3cc812f4b0f4730cad223d1 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sat, 6 Jul 2024 19:09:05 -0700
Subject: [PATCH 07/35] update: add adatom config

---
 .../mat3ra/made/tools/build/defect/configuration.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index eda9f804..a6e946bb 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -5,7 +5,7 @@
 from mat3ra.made.material import Material
 
 from ...analyze import get_closest_site_id_from_position
-from .enums import PointDefectTypeEnum
+from .enums import PointDefectTypeEnum, SlabDefectTypeEnum
 
 
 class BaseDefectConfiguration(BaseModel):
@@ -50,3 +50,14 @@ def _json(self):
             "position": self.position,
             "chemical_element": self.chemical_element,
         }
+
+
+class SlabDefectConfiguration(BaseDefectConfiguration):
+    pass
+
+
+class AdatomSlabDefectConfiguration(SlabDefectConfiguration):
+    defect_type: SlabDefectTypeEnum = SlabDefectTypeEnum.ADATOM
+    position_on_surface: List[float] = [0.5, 0.5]
+    distance_z: float = 2.0
+    chemical_element: str = "Si"

From a3bec27843fe257c3ef11dc7e1db5bab0be769de Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sat, 6 Jul 2024 19:09:41 -0700
Subject: [PATCH 08/35] update: adjust adatom generation

---
 .../mat3ra/made/tools/build/defect/__init__.py  | 13 +++++++------
 .../mat3ra/made/tools/build/defect/builders.py  | 17 ++++++++++++-----
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/__init__.py b/src/py/mat3ra/made/tools/build/defect/__init__.py
index d447e72c..b8f766fb 100644
--- a/src/py/mat3ra/made/tools/build/defect/__init__.py
+++ b/src/py/mat3ra/made/tools/build/defect/__init__.py
@@ -1,11 +1,11 @@
-from typing import Optional
+from typing import Optional, Union
 
 from mat3ra.utils.factory import BaseFactory
 from mat3ra.made.material import Material
 
-from .builders import PointDefectBuilderParameters
-from .configuration import PointDefectConfiguration
-from .enums import PointDefectTypeEnum
+from .builders import PointDefectBuilderParameters, SlabDefectBuilderParameters
+from .configuration import PointDefectConfiguration, AdatomSlabDefectConfiguration
+from .enums import PointDefectTypeEnum, SlabDefectTypeEnum
 
 
 class DefectBuilderFactory(BaseFactory):
@@ -13,12 +13,13 @@ class DefectBuilderFactory(BaseFactory):
         PointDefectTypeEnum.VACANCY: "mat3ra.made.tools.build.defect.builders.VacancyPointDefectBuilder",
         PointDefectTypeEnum.SUBSTITUTION: "mat3ra.made.tools.build.defect.builders.SubstitutionPointDefectBuilder",
         PointDefectTypeEnum.INTERSTITIAL: "mat3ra.made.tools.build.defect.builders.InterstitialPointDefectBuilder",
+        SlabDefectTypeEnum.ADATOM: "mat3ra.made.tools.build.defect.builders.AdatomSlabDefectBuilder",
     }
 
 
 def create_defect(
-    configuration: PointDefectConfiguration,
-    builder_parameters: Optional[PointDefectBuilderParameters] = None,
+    configuration: Union[PointDefectConfiguration, AdatomSlabDefectConfiguration],
+    builder_parameters: Union[PointDefectBuilderParameters, SlabDefectBuilderParameters, None] = None,
 ) -> Material:
     """
     Return a material with a selected defect added.
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 93054f73..16d0dfd7 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -15,7 +15,7 @@
 from ...convert import to_pymatgen
 from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates, get_atomic_coordinates_max_z
 from ..mixins import ConvertGeneratedItemsPymatgenStructureMixin
-from .configuration import PointDefectConfiguration
+from .configuration import PointDefectConfiguration, AdatomSlabDefectConfiguration
 
 
 class PointDefectBuilderParameters(BaseModel):
@@ -82,6 +82,7 @@ class SlabDefectBuilder(BaseBuilder):
 
 
 class AdatomSlabDefectBuilder(SlabDefectBuilder):
+    _ConfigurationType: type(AdatomSlabDefectConfiguration) = AdatomSlabDefectConfiguration  # type: ignore
     _GeneratedItemType: Material = Material
 
     def add_adatom(
@@ -94,14 +95,20 @@ def add_adatom(
         material_copy = material.clone()
         basis = material_copy.basis
         distance_in_crystal_units = distance_z / material_copy.lattice.c
-        max_z = max([coordinate[2] for coordinate in basis.coordinates.values])
+        max_z = get_atomic_coordinates_max_z(material_copy)
         position = position_on_surface.copy()
-        position[2] = max_z + distance_in_crystal_units
+        position.append(max_z + distance_in_crystal_units)
         basis.add_atom(chemical_element, position)
         material_copy.basis = basis
         return [material_copy]
 
-    _generator = add_adatom
+    def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
+        return self.add_adatom(
+            material=configuration.crystal,
+            chemical_element=configuration.chemical_element,
+            position_on_surface=configuration.position_on_surface,
+            distance_z=configuration.distance_z,
+        )
 
 
 class EquidistantAdatomSlabDefectBuilder(SlabDefectBuilder):
@@ -148,4 +155,4 @@ def add_adatom_equdistant(
         material_copy.basis = basis
         return [material_copy]
 
-    _generator = add_adatom_equdistant
+    _generate = add_adatom_equdistant

From 73dd8b4478397bc5e77c4faf030fd0c89d42fbb4 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sat, 6 Jul 2024 19:15:44 -0700
Subject: [PATCH 09/35] chore: cleanup

---
 src/py/mat3ra/made/tools/analyze.py           | 24 +------------------
 .../made/tools/build/defect/builders.py       | 15 ++++++++----
 2 files changed, 12 insertions(+), 27 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 14081e18..541f7a5c 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -1,4 +1,4 @@
-from typing import Callable, List, Optional, Literal
+from typing import Callable, List, Literal, Optional
 
 import numpy as np
 
@@ -270,28 +270,6 @@ def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
     return [sum([coordinate[i] for coordinate in coordinates]) / len(coordinates) for i in range(3)]
 
 
-def get_atomic_coordinates_min_z(
-    material: Material,
-    use_cartesian_coordinates: bool = False,
-) -> float:
-    """
-    Return minimum of Z coordinates in crystal or cartesian units.
-
-    Args:
-        material (Material): Material object.
-        use_cartesian_coordinates (bool): Whether to use Cartesian coordinates
-    Returns:
-        float: Minimum of Z coordinates.
-    """
-    new_material = material.clone()
-    if use_cartesian_coordinates:
-        new_basis = new_material.basis
-        new_basis.to_cartesian()
-        new_material.basis = new_basis
-    coordinates = new_material.basis.coordinates.to_array_of_values_with_ids()
-    return min([coord.value[2] for coord in coordinates])
-
-
 def get_atomic_coordinates_extremum(
     material: Material,
     extremum: Literal["max", "min"] = "max",
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 16d0dfd7..cb9f3a9a 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -13,7 +13,7 @@
 )
 from ...build import BaseBuilder
 from ...convert import to_pymatgen
-from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates, get_atomic_coordinates_max_z
+from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates, get_atomic_coordinates_extremum
 from ..mixins import ConvertGeneratedItemsPymatgenStructureMixin
 from .configuration import PointDefectConfiguration, AdatomSlabDefectConfiguration
 
@@ -95,7 +95,7 @@ def add_adatom(
         material_copy = material.clone()
         basis = material_copy.basis
         distance_in_crystal_units = distance_z / material_copy.lattice.c
-        max_z = get_atomic_coordinates_max_z(material_copy)
+        max_z = get_atomic_coordinates_extremum(material_copy)
         position = position_on_surface.copy()
         position.append(max_z + distance_in_crystal_units)
         basis.add_atom(chemical_element, position)
@@ -112,6 +112,7 @@ def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemTyp
 
 
 class EquidistantAdatomSlabDefectBuilder(SlabDefectBuilder):
+    _ConfigurationType: type(AdatomSlabDefectConfiguration) = AdatomSlabDefectConfiguration  # type: ignore
     _GeneratedItemType: Material = Material
 
     def add_adatom_equdistant(
@@ -137,7 +138,7 @@ def add_adatom_equdistant(
         material_copy: Material = material.clone()
         basis = material_copy.basis
         distance_in_crystal_units = distance_z / material_copy.lattice.c
-        max_z = get_atomic_coordinates_max_z(material_copy)
+        max_z = get_atomic_coordinates_extremum(material_copy)
         adatom_position = approximate_position_on_surface.copy()
         adatom_position[2] = max_z + distance_in_crystal_units
 
@@ -155,4 +156,10 @@ def add_adatom_equdistant(
         material_copy.basis = basis
         return [material_copy]
 
-    _generate = add_adatom_equdistant
+    def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
+        return self.add_adatom_equdistant(
+            material=configuration.crystal,
+            chemical_element=configuration.chemical_element,
+            approximate_position_on_surface=configuration.position_on_surface,
+            distance_z=configuration.distance_z,
+        )

From d2b77b50a36c2bd94de48c9b80aabd0fa3598a75 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sat, 6 Jul 2024 19:30:31 -0700
Subject: [PATCH 10/35] update: make work

---
 src/py/mat3ra/made/tools/build/__init__.py           |  9 ++++++++-
 .../mat3ra/made/tools/build/defect/configuration.py  | 12 +++++++++++-
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/__init__.py b/src/py/mat3ra/made/tools/build/__init__.py
index 99e10373..52de9f31 100644
--- a/src/py/mat3ra/made/tools/build/__init__.py
+++ b/src/py/mat3ra/made/tools/build/__init__.py
@@ -65,7 +65,14 @@ def _select(
     def _post_process(
         self, items: List[_GeneratedItemType], post_process_parameters: Optional[_PostProcessParametersType]
     ) -> List[Material]:
-        return [Material(self._convert_generated_item(item)) for item in items]
+        return [
+            (
+                self._convert_generated_item(item)
+                if isinstance(item, Material)
+                else Material(self._convert_generated_item(item))
+            )
+            for item in items
+        ]
 
     @staticmethod
     def _convert_generated_item(item: _GeneratedItemType):
diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index a6e946bb..2deff393 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -52,7 +52,7 @@ def _json(self):
         }
 
 
-class SlabDefectConfiguration(BaseDefectConfiguration):
+class SlabDefectConfiguration(BaseDefectConfiguration, InMemoryEntity):
     pass
 
 
@@ -61,3 +61,13 @@ class AdatomSlabDefectConfiguration(SlabDefectConfiguration):
     position_on_surface: List[float] = [0.5, 0.5]
     distance_z: float = 2.0
     chemical_element: str = "Si"
+
+    @property
+    def _json(self):
+        return {
+            "type": "AdatomSlabDefectConfiguration",
+            "defect_type": self.defect_type.name,
+            "position_on_surface": self.position_on_surface,
+            "distance_z": self.distance_z,
+            "chemical_element": self.chemical_element,
+        }

From 9df4ca61ce813907ac4c410e8a588e727fb6383c Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 16:14:41 -0700
Subject: [PATCH 11/35] update: use OOP

---
 .../made/tools/build/defect/builders.py       | 64 ++++++-------------
 1 file changed, 18 insertions(+), 46 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index cb9f3a9a..dcc28049 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -85,25 +85,25 @@ class AdatomSlabDefectBuilder(SlabDefectBuilder):
     _ConfigurationType: type(AdatomSlabDefectConfiguration) = AdatomSlabDefectConfiguration  # type: ignore
     _GeneratedItemType: Material = Material
 
-    def add_adatom(
+    def create_adatom(
         self,
         material: Material,
         chemical_element: str = "Si",
         position_on_surface: List[float] = [0.5, 0.5],
         distance_z: float = 2.0,
     ) -> List[Material]:
-        material_copy = material.clone()
-        basis = material_copy.basis
-        distance_in_crystal_units = distance_z / material_copy.lattice.c
-        max_z = get_atomic_coordinates_extremum(material_copy)
+        new_material = material.clone()
+        basis = new_material.basis
+        distance_in_crystal_units = distance_z / new_material.lattice.c
+        max_z = get_atomic_coordinates_extremum(new_material)
         position = position_on_surface.copy()
         position.append(max_z + distance_in_crystal_units)
         basis.add_atom(chemical_element, position)
-        material_copy.basis = basis
-        return [material_copy]
+        new_material.basis = basis
+        return [new_material]
 
     def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
-        return self.add_adatom(
+        return self.create_adatom(
             material=configuration.crystal,
             chemical_element=configuration.chemical_element,
             position_on_surface=configuration.position_on_surface,
@@ -111,55 +111,27 @@ def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemTyp
         )
 
 
-class EquidistantAdatomSlabDefectBuilder(SlabDefectBuilder):
-    _ConfigurationType: type(AdatomSlabDefectConfiguration) = AdatomSlabDefectConfiguration  # type: ignore
-    _GeneratedItemType: Material = Material
-
-    def add_adatom_equdistant(
+class EquidistantAdatomSlabDefectBuilder(AdatomSlabDefectConfiguration):
+    def create_adatom(
         self,
         material: Material,
         chemical_element: str = "Si",
-        approximate_position_on_surface: List[float] = [0.5, 0.5],
+        position_on_surface: List[float] = [0.5, 0.5],
         distance_z: float = 2.0,
     ) -> List[Material]:
-        """
-        Add an atom to the material at a position that is equidistant to the nearest atoms
-        (that are found within proximity to the approx position) with the specified distance.
-
-        Args:
-            material (Material): The material to add the adatom to.
-            chemical_element (str): The chemical element of the adatom.
-            approximate_position_on_surface (List[float]): The approximate position of the adatom on the surface.
-            distance_z (float): The distance from the nearest atoms to the adatom.
-
-        Returns:
-            List[Material]: A list containing the material with the adatom added.
-        """
-        material_copy: Material = material.clone()
-        basis = material_copy.basis
-        distance_in_crystal_units = distance_z / material_copy.lattice.c
-        max_z = get_atomic_coordinates_extremum(material_copy)
-        adatom_position = approximate_position_on_surface.copy()
-        adatom_position[2] = max_z + distance_in_crystal_units
+        equidistant_position = self.get_equidistant_position(material, position_on_surface)
+        return super().create_adatom(material, chemical_element, equidistant_position, distance_z)
 
+    def get_equidistant_position(self, material: Material, adatom_position: List[float]) -> List[float]:
+        new_basis = material.basis
         neighboring_atoms_ids = get_nearest_neighbors_atom_indices(material, adatom_position)
         if not neighboring_atoms_ids:
             raise ValueError("No neighboring atoms found.")
-        neighboring_atoms_coordinates = [basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
+        neighboring_atoms_coordinates = [new_basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
 
         equidistant_position = get_center_of_coordinates(neighboring_atoms_coordinates)
         equidistant_position[2] = adatom_position[2]
-        if equidistant_position[2] > basis.cell.vectors_as_nested_array[2][2]:
+        if equidistant_position[2] > new_basis.cell.vectors_as_nested_array[2][2]:
             raise ValueError("The adatom position is outside the cell.")
 
-        basis.add_atom(chemical_element, equidistant_position)
-        material_copy.basis = basis
-        return [material_copy]
-
-    def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
-        return self.add_adatom_equdistant(
-            material=configuration.crystal,
-            chemical_element=configuration.chemical_element,
-            approximate_position_on_surface=configuration.position_on_surface,
-            distance_z=configuration.distance_z,
-        )
+        return equidistant_position

From 46bf993a2bbda6ad637b0dd94ba4b37768c43ad2 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 16:15:41 -0700
Subject: [PATCH 12/35] update: fix conversion in base class

---
 src/py/mat3ra/made/tools/build/__init__.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/__init__.py b/src/py/mat3ra/made/tools/build/__init__.py
index 52de9f31..c1e5f2c9 100644
--- a/src/py/mat3ra/made/tools/build/__init__.py
+++ b/src/py/mat3ra/made/tools/build/__init__.py
@@ -65,14 +65,9 @@ def _select(
     def _post_process(
         self, items: List[_GeneratedItemType], post_process_parameters: Optional[_PostProcessParametersType]
     ) -> List[Material]:
-        return [
-            (
-                self._convert_generated_item(item)
-                if isinstance(item, Material)
-                else Material(self._convert_generated_item(item))
-            )
-            for item in items
-        ]
+        if self._GeneratedItemType == Material:
+            return items
+        return [Material(self._convert_generated_item(item)) for item in items]
 
     @staticmethod
     def _convert_generated_item(item: _GeneratedItemType):

From 81bbc0f91ac876d02fed7f7cc128df2908513cc8 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 16:18:26 -0700
Subject: [PATCH 13/35] chore: add docstring

---
 .../made/tools/build/defect/builders.py       | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index dcc28049..44998981 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -92,6 +92,18 @@ def create_adatom(
         position_on_surface: List[float] = [0.5, 0.5],
         distance_z: float = 2.0,
     ) -> List[Material]:
+        """
+        Create an adatom at the specified position on the surface of the material.
+
+        Args:
+            material: The material to add the adatom to.
+            chemical_element: The chemical element of the adatom.
+            position_on_surface: The position on the surface of the material.
+            distance_z: The distance of the adatom from the surface.
+
+        Returns:
+            The material with the adatom added.
+        """
         new_material = material.clone()
         basis = new_material.basis
         distance_in_crystal_units = distance_z / new_material.lattice.c
@@ -119,6 +131,18 @@ def create_adatom(
         position_on_surface: List[float] = [0.5, 0.5],
         distance_z: float = 2.0,
     ) -> List[Material]:
+        """
+        Create an adatom with an equidistant XY position among the nearest neighbors at the given distance from the surface.
+
+        Args:
+            material: The material to add the adatom to.
+            chemical_element: The chemical element of the adatom.
+            position_on_surface: The position on the surface of the material.
+            distance_z: The distance of the adatom from the surface.
+
+        Returns:
+            The material with the adatom added.
+        """
         equidistant_position = self.get_equidistant_position(material, position_on_surface)
         return super().create_adatom(material, chemical_element, equidistant_position, distance_z)
 

From e8a1320aaab3da87a07b5139f54697d10b720b8e Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 16:21:10 -0700
Subject: [PATCH 14/35] chore: fix lint

---
 src/py/mat3ra/made/tools/build/defect/builders.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 44998981..5a1f4c84 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -132,7 +132,8 @@ def create_adatom(
         distance_z: float = 2.0,
     ) -> List[Material]:
         """
-        Create an adatom with an equidistant XY position among the nearest neighbors at the given distance from the surface.
+        Create an adatom with an equidistant XY position among the nearest neighbors
+        at the given distance from the surface.
 
         Args:
             material: The material to add the adatom to.

From b1f1e48fa5ecdcfca59ce21dd85413addc4cfae6 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 16:32:18 -0700
Subject: [PATCH 15/35] update: cleanups

---
 src/py/mat3ra/made/tools/analyze.py             |  2 +-
 .../mat3ra/made/tools/build/defect/__init__.py  | 17 +++++++++++++++--
 .../mat3ra/made/tools/build/defect/builders.py  |  2 +-
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 541f7a5c..281113ee 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -267,7 +267,7 @@ def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
     Returns:
         List[float]: The center of the coordinates.
     """
-    return [sum([coordinate[i] for coordinate in coordinates]) / len(coordinates) for i in range(3)]
+    return np.mean(np.array(coordinates), axis=0)
 
 
 def get_atomic_coordinates_extremum(
diff --git a/src/py/mat3ra/made/tools/build/defect/__init__.py b/src/py/mat3ra/made/tools/build/defect/__init__.py
index b8f766fb..8d9211cf 100644
--- a/src/py/mat3ra/made/tools/build/defect/__init__.py
+++ b/src/py/mat3ra/made/tools/build/defect/__init__.py
@@ -3,7 +3,12 @@
 from mat3ra.utils.factory import BaseFactory
 from mat3ra.made.material import Material
 
-from .builders import PointDefectBuilderParameters, SlabDefectBuilderParameters
+from .builders import (
+    PointDefectBuilderParameters,
+    SlabDefectBuilderParameters,
+    AdatomSlabDefectBuilder,
+    EquidistantAdatomSlabDefectBuilder,
+)
 from .configuration import PointDefectConfiguration, AdatomSlabDefectConfiguration
 from .enums import PointDefectTypeEnum, SlabDefectTypeEnum
 
@@ -13,7 +18,6 @@ class DefectBuilderFactory(BaseFactory):
         PointDefectTypeEnum.VACANCY: "mat3ra.made.tools.build.defect.builders.VacancyPointDefectBuilder",
         PointDefectTypeEnum.SUBSTITUTION: "mat3ra.made.tools.build.defect.builders.SubstitutionPointDefectBuilder",
         PointDefectTypeEnum.INTERSTITIAL: "mat3ra.made.tools.build.defect.builders.InterstitialPointDefectBuilder",
-        SlabDefectTypeEnum.ADATOM: "mat3ra.made.tools.build.defect.builders.AdatomSlabDefectBuilder",
     }
 
 
@@ -35,3 +39,12 @@ def create_defect(
     builder = BuilderClass(builder_parameters)
 
     return builder.get_material(configuration) if builder else configuration.crystal
+
+
+def create_feature(
+    configuration: Union[AdatomSlabDefectConfiguration],
+    builder: Optional[Union[AdatomSlabDefectBuilder, EquidistantAdatomSlabDefectBuilder]] = None,
+) -> Material:
+    if builder is None:
+        builder = AdatomSlabDefectBuilder(build_parameters=SlabDefectBuilderParameters())
+    return builder.get_material(configuration)
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 5a1f4c84..2d28c8ba 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -123,7 +123,7 @@ def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemTyp
         )
 
 
-class EquidistantAdatomSlabDefectBuilder(AdatomSlabDefectConfiguration):
+class EquidistantAdatomSlabDefectBuilder(AdatomSlabDefectBuilder):
     def create_adatom(
         self,
         material: Material,

From 7778b99a3f3c72b1a82b07e150ec859a5dd1583d Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 16:49:14 -0700
Subject: [PATCH 16/35] update: rename + docstring

---
 src/py/mat3ra/made/tools/build/defect/__init__.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/__init__.py b/src/py/mat3ra/made/tools/build/defect/__init__.py
index 8d9211cf..3cc599fd 100644
--- a/src/py/mat3ra/made/tools/build/defect/__init__.py
+++ b/src/py/mat3ra/made/tools/build/defect/__init__.py
@@ -41,10 +41,20 @@ def create_defect(
     return builder.get_material(configuration) if builder else configuration.crystal
 
 
-def create_feature(
+def create_slab_defect(
     configuration: Union[AdatomSlabDefectConfiguration],
     builder: Optional[Union[AdatomSlabDefectBuilder, EquidistantAdatomSlabDefectBuilder]] = None,
 ) -> Material:
+    """
+    Return a material with a selected slab defect added.
+
+    Args:
+        configuration: The configuration of the defect to be added.
+        builder: The builder to be used to create the defect.
+
+    Returns:
+        The material with the defect added.
+    """
     if builder is None:
         builder = AdatomSlabDefectBuilder(build_parameters=SlabDefectBuilderParameters())
     return builder.get_material(configuration)

From fd36d9d7531328978a2503dfe415bcc664d1a716 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 17:38:54 -0700
Subject: [PATCH 17/35] update: fix arrays logic

---
 src/py/mat3ra/made/tools/analyze.py           |  2 +-
 .../made/tools/build/defect/builders.py       | 20 ++++++++++++++-----
 2 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 281113ee..52e7c8f4 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -267,7 +267,7 @@ def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
     Returns:
         List[float]: The center of the coordinates.
     """
-    return np.mean(np.array(coordinates), axis=0)
+    return list(np.mean(np.array(coordinates), axis=0))
 
 
 def get_atomic_coordinates_extremum(
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 2d28c8ba..e0382ccb 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -1,4 +1,4 @@
-from typing import List, Callable
+from typing import List, Callable, Optional
 
 from pydantic import BaseModel
 from mat3ra.made.material import Material
@@ -89,7 +89,7 @@ def create_adatom(
         self,
         material: Material,
         chemical_element: str = "Si",
-        position_on_surface: List[float] = [0.5, 0.5],
+        position_on_surface: Optional[List[float]] = None,
         distance_z: float = 2.0,
     ) -> List[Material]:
         """
@@ -104,6 +104,9 @@ def create_adatom(
         Returns:
             The material with the adatom added.
         """
+        if position_on_surface is None:
+            position_on_surface = [0.5, 0.5]
+        position_on_surface = position_on_surface[:2]
         new_material = material.clone()
         basis = new_material.basis
         distance_in_crystal_units = distance_z / new_material.lattice.c
@@ -128,7 +131,7 @@ def create_adatom(
         self,
         material: Material,
         chemical_element: str = "Si",
-        position_on_surface: List[float] = [0.5, 0.5],
+        position_on_surface: Optional[List[float]] = None,
         distance_z: float = 2.0,
     ) -> List[Material]:
         """
@@ -144,11 +147,18 @@ def create_adatom(
         Returns:
             The material with the adatom added.
         """
-        equidistant_position = self.get_equidistant_position(material, position_on_surface)
+        if position_on_surface is None:
+            position_on_surface = [0.5, 0.5]
+        equidistant_position = self.get_equidistant_position(material, position_on_surface, distance_z)
         return super().create_adatom(material, chemical_element, equidistant_position, distance_z)
 
-    def get_equidistant_position(self, material: Material, adatom_position: List[float]) -> List[float]:
+    def get_equidistant_position(
+        self, material: Material, position_on_surface: List[float], distance_z: float = 2.0
+    ) -> List[float]:
         new_basis = material.basis
+        adatom_position = position_on_surface.copy()
+        distance_z_crystal = distance_z / material.lattice.c
+        adatom_position.append(get_atomic_coordinates_extremum(material) + distance_z_crystal)
         neighboring_atoms_ids = get_nearest_neighbors_atom_indices(material, adatom_position)
         if not neighboring_atoms_ids:
             raise ValueError("No neighboring atoms found.")

From c9f768ff3b478092379d9dabcff9114f4223ff7a Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 17:58:22 -0700
Subject: [PATCH 18/35] update: optimize

---
 .../made/tools/build/defect/builders.py       | 23 +++++++++++--------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index e0382ccb..c929c2b1 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -108,14 +108,21 @@ def create_adatom(
             position_on_surface = [0.5, 0.5]
         position_on_surface = position_on_surface[:2]
         new_material = material.clone()
-        basis = new_material.basis
-        distance_in_crystal_units = distance_z / new_material.lattice.c
-        max_z = get_atomic_coordinates_extremum(new_material)
+        new_basis = new_material.basis
+        adatom_position = self._calculate_position_from_2d(material, position_on_surface, distance_z)
+        new_basis.add_atom(chemical_element, adatom_position)
+        new_material.basis = new_basis
+        return [new_material]
+
+    def _calculate_position_from_2d(
+        self, material: Material, position_on_surface: List[float], distance_z: float
+    ) -> List[float]:
+        max_z = get_atomic_coordinates_extremum(material)
+        distance_z = distance_z
+        distance_in_crystal_units = distance_z / material.lattice.c
         position = position_on_surface.copy()
         position.append(max_z + distance_in_crystal_units)
-        basis.add_atom(chemical_element, position)
-        new_material.basis = basis
-        return [new_material]
+        return position
 
     def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
         return self.create_adatom(
@@ -156,9 +163,7 @@ def get_equidistant_position(
         self, material: Material, position_on_surface: List[float], distance_z: float = 2.0
     ) -> List[float]:
         new_basis = material.basis
-        adatom_position = position_on_surface.copy()
-        distance_z_crystal = distance_z / material.lattice.c
-        adatom_position.append(get_atomic_coordinates_extremum(material) + distance_z_crystal)
+        adatom_position = self._calculate_position_from_2d(material, position_on_surface, distance_z)
         neighboring_atoms_ids = get_nearest_neighbors_atom_indices(material, adatom_position)
         if not neighboring_atoms_ids:
             raise ValueError("No neighboring atoms found.")

From bc3596ab27bbab21fcd09dbd39b2080b0f4effe0 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 18:15:31 -0700
Subject: [PATCH 19/35] update: add tests for adatom

---
 .../made/tools/build/defect/builders.py       |  2 +-
 tests/py/unit/test_tools_build_defect.py      | 44 ++++++++++++++++++-
 2 files changed, 44 insertions(+), 2 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index c929c2b1..c463e0f8 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -106,7 +106,6 @@ def create_adatom(
         """
         if position_on_surface is None:
             position_on_surface = [0.5, 0.5]
-        position_on_surface = position_on_surface[:2]
         new_material = material.clone()
         new_basis = new_material.basis
         adatom_position = self._calculate_position_from_2d(material, position_on_surface, distance_z)
@@ -121,6 +120,7 @@ def _calculate_position_from_2d(
         distance_z = distance_z
         distance_in_crystal_units = distance_z / material.lattice.c
         position = position_on_surface.copy()
+        position = position[:2]
         position.append(max_z + distance_in_crystal_units)
         return position
 
diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index bb8423e2..dc4a4c63 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -1,5 +1,16 @@
 from mat3ra.made.material import Material
-from mat3ra.made.tools.build.defect import PointDefectBuilderParameters, PointDefectConfiguration, create_defect
+from mat3ra.made.tools.build.defect import (
+    PointDefectBuilderParameters,
+    PointDefectConfiguration,
+    create_defect,
+    AdatomSlabDefectConfiguration,
+    create_slab_defect,
+    EquidistantAdatomSlabDefectBuilder,
+)
+from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration
+
+from mat3ra.made.tools.build.slab import get_terminations
+from mat3ra.utils import assertion as assertion_utils
 
 clean_material = Material.create(Material.default_config)
 
@@ -49,3 +60,34 @@ def test_create_defect_from_site_id():
         {"id": 0, "value": "Si"},
         {"id": 1, "value": "Ge"},
     ]
+
+
+def test_create_adatom():
+    # Adatom of Si at 0.5, 0.5 position
+    material = Material.create(Material.default_config)
+    slab_config = SlabConfiguration(material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
+    t = get_terminations(slab_config)[0]
+    slab = create_slab(slab_config, t)
+    configuration = AdatomSlabDefectConfiguration(
+        crystal=slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
+    )
+    defect = create_slab_defect(configuration=configuration, builder=None)
+
+    assert defect.basis.elements.values[-1] == "Si"
+    assertion_utils.assert_deep_almost_equal([0.5, 0.5, 0.389826], defect.basis.coordinates.values[-1])
+
+
+def test_create_adatom_equidistant():
+    # Adatom of Si at approximate 0.5, 0.5 position
+    material = Material.create(Material.default_config)
+    slab_config = SlabConfiguration(material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
+    t = get_terminations(slab_config)[0]
+    slab = create_slab(slab_config, t)
+    configuration = AdatomSlabDefectConfiguration(
+        crystal=slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
+    )
+    defect = create_slab_defect(configuration=configuration, builder=EquidistantAdatomSlabDefectBuilder())
+
+    assert defect.basis.elements.values[-1] == "Si"
+    # We expect adatom to shift from provided position
+    assertion_utils.assert_deep_almost_equal(defect.basis.coordinates.values[-1], [0.8333333, 0.4166666, 0.389826])

From 4223f28ef73fe7446af3fefd3cd5797bfa6abd48 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 18:15:48 -0700
Subject: [PATCH 20/35] update: add tests for adatom

---
 tests/py/unit/test_tools_build_defect.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index dc4a4c63..bad25ba8 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -1,15 +1,13 @@
 from mat3ra.made.material import Material
 from mat3ra.made.tools.build.defect import (
+    AdatomSlabDefectConfiguration,
+    EquidistantAdatomSlabDefectBuilder,
     PointDefectBuilderParameters,
     PointDefectConfiguration,
     create_defect,
-    AdatomSlabDefectConfiguration,
     create_slab_defect,
-    EquidistantAdatomSlabDefectBuilder,
 )
-from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration
-
-from mat3ra.made.tools.build.slab import get_terminations
+from mat3ra.made.tools.build.slab import SlabConfiguration, create_slab, get_terminations
 from mat3ra.utils import assertion as assertion_utils
 
 clean_material = Material.create(Material.default_config)

From 2935658f3eff4e3d0b8232c9a56242b11e008527 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 18:49:42 -0700
Subject: [PATCH 21/35] update: move func to utils

---
 src/py/mat3ra/made/tools/analyze.py               | 13 -------------
 src/py/mat3ra/made/tools/build/defect/builders.py |  3 ++-
 src/py/mat3ra/made/utils.py                       | 14 ++++++++++++++
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 52e7c8f4..068e4c13 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -257,19 +257,6 @@ def get_nearest_neighbors_atom_indices(material: Material, position: List[float]
     return neighboring_atoms_ids
 
 
-def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
-    """
-    Calculate the center of the coordinates.
-
-    Args:
-        coordinates (List[List[float]]): The list of coordinates.
-
-    Returns:
-        List[float]: The center of the coordinates.
-    """
-    return list(np.mean(np.array(coordinates), axis=0))
-
-
 def get_atomic_coordinates_extremum(
     material: Material,
     extremum: Literal["max", "min"] = "max",
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index c463e0f8..413255e0 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -13,7 +13,8 @@
 )
 from ...build import BaseBuilder
 from ...convert import to_pymatgen
-from ...analyze import get_nearest_neighbors_atom_indices, get_center_of_coordinates, get_atomic_coordinates_extremum
+from ...analyze import get_nearest_neighbors_atom_indices, get_atomic_coordinates_extremum
+from ....utils import get_center_of_coordinates
 from ..mixins import ConvertGeneratedItemsPymatgenStructureMixin
 from .configuration import PointDefectConfiguration, AdatomSlabDefectConfiguration
 
diff --git a/src/py/mat3ra/made/utils.py b/src/py/mat3ra/made/utils.py
index f5d5c1fa..9e002125 100644
--- a/src/py/mat3ra/made/utils.py
+++ b/src/py/mat3ra/made/utils.py
@@ -1,6 +1,7 @@
 import json
 from typing import Any, Callable, Dict, List, Optional, Union
 
+import numpy as np
 from mat3ra.utils.array import convert_to_array_if_not
 from mat3ra.utils.mixins import RoundNumericValuesMixin
 from pydantic import BaseModel
@@ -44,6 +45,19 @@ def are_arrays_equal_by_id_value(array1: List[Dict[str, Any]], array2: List[Dict
     return map_array_with_id_value_to_array(array1) == map_array_with_id_value_to_array(array2)
 
 
+def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
+    """
+    Calculate the center of the coordinates.
+
+    Args:
+        coordinates (List[List[float]]): The list of coordinates.
+
+    Returns:
+        List[float]: The center of the coordinates.
+    """
+    return list(np.mean(np.array(coordinates), axis=0))
+
+
 class ValueWithId(RoundNumericValuesMixin, BaseModel):
     id: int = 0
     value: Any = None

From b9890e235face6d27626ff781044d0f0f117773f Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 18:49:55 -0700
Subject: [PATCH 22/35] try: fix test

---
 tests/py/unit/test_tools_build_defect.py | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index bad25ba8..04eb8082 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -12,6 +12,11 @@
 
 clean_material = Material.create(Material.default_config)
 
+material = Material.create(Material.default_config)
+slab_config = SlabConfiguration(material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
+t = get_terminations(slab_config)[0]
+slab = create_slab(slab_config, t)
+
 
 def test_create_vacancy():
     # vacancy in place of 0 element
@@ -61,13 +66,10 @@ def test_create_defect_from_site_id():
 
 
 def test_create_adatom():
+    clean_slab = slab.clone()
     # Adatom of Si at 0.5, 0.5 position
-    material = Material.create(Material.default_config)
-    slab_config = SlabConfiguration(material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
-    t = get_terminations(slab_config)[0]
-    slab = create_slab(slab_config, t)
     configuration = AdatomSlabDefectConfiguration(
-        crystal=slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
+        crystal=clean_slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
     )
     defect = create_slab_defect(configuration=configuration, builder=None)
 
@@ -76,16 +78,13 @@ def test_create_adatom():
 
 
 def test_create_adatom_equidistant():
+    clean_slab = slab.clone()
     # Adatom of Si at approximate 0.5, 0.5 position
-    material = Material.create(Material.default_config)
-    slab_config = SlabConfiguration(material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
-    t = get_terminations(slab_config)[0]
-    slab = create_slab(slab_config, t)
     configuration = AdatomSlabDefectConfiguration(
-        crystal=slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
+        crystal=clean_slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
     )
     defect = create_slab_defect(configuration=configuration, builder=EquidistantAdatomSlabDefectBuilder())
 
     assert defect.basis.elements.values[-1] == "Si"
     # We expect adatom to shift from provided position
-    assertion_utils.assert_deep_almost_equal(defect.basis.coordinates.values[-1], [0.8333333, 0.4166666, 0.389826])
+    assertion_utils.assert_deep_almost_equal([0.8333333, 0.4166666, 0.389826], defect.basis.coordinates.values[-1])

From e16e90a9227695e0d451947abeed66599e7b0a7f Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 19:00:46 -0700
Subject: [PATCH 23/35] try: fix test 2

---
 src/py/mat3ra/made/tools/analyze.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index 068e4c13..a2f65bf1 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -231,7 +231,9 @@ def get_atom_indices_with_condition_on_coordinates(
     return selected_indices
 
 
-def get_nearest_neighbors_atom_indices(material: Material, position: List[float] = [0, 0, 0]) -> Optional[List[int]]:
+def get_nearest_neighbors_atom_indices(
+    material: Material, position: Optional[List[float]] = None
+) -> Optional[List[int]]:
     """
     Returns the indices of direct neighboring atoms to a specified position in the material using Voronoi tessellation.
 
@@ -242,6 +244,8 @@ def get_nearest_neighbors_atom_indices(material: Material, position: List[float]
     Returns:
         List[int]: A list of indices of neighboring atoms, or an empty list if no neighbors are found.
     """
+    if position is None:
+        position = [0, 0, 0]
     structure = to_pymatgen(material)
 
     voronoi_nn = PymatgenVoronoiNN(tol=0.5)

From d8da1e256fccb96cd4963daafc8c39ffdea0249c Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 19:16:16 -0700
Subject: [PATCH 24/35] update: manage vacuum

---
 src/py/mat3ra/made/tools/build/defect/builders.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 413255e0..c0cf20a6 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -1,5 +1,6 @@
 from typing import List, Callable, Optional
 
+from mat3ra.made.tools.modify import add_vacuum
 from pydantic import BaseModel
 from mat3ra.made.material import Material
 
@@ -158,7 +159,15 @@ def create_adatom(
         if position_on_surface is None:
             position_on_surface = [0.5, 0.5]
         equidistant_position = self.get_equidistant_position(material, position_on_surface, distance_z)
-        return super().create_adatom(material, chemical_element, equidistant_position, distance_z)
+        new_material = material.clone()
+        if equidistant_position[2] > 1:
+            if self.build_parameters.auto_add_vacuum:
+                new_material = add_vacuum(material, self.build_parameters.vacuum_thickness)
+                equidistant_position = self.get_equidistant_position(new_material, position_on_surface, distance_z)
+            else:
+                raise ValueError("Not enough vacuum space to place the adatom.")
+
+        return super().create_adatom(new_material, chemical_element, equidistant_position, distance_z)
 
     def get_equidistant_position(
         self, material: Material, position_on_surface: List[float], distance_z: float = 2.0
@@ -172,7 +181,5 @@ def get_equidistant_position(
 
         equidistant_position = get_center_of_coordinates(neighboring_atoms_coordinates)
         equidistant_position[2] = adatom_position[2]
-        if equidistant_position[2] > new_basis.cell.vectors_as_nested_array[2][2]:
-            raise ValueError("The adatom position is outside the cell.")
 
         return equidistant_position

From b5c17514f22234885c74de2ac4fae63245c77c1d Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Sun, 7 Jul 2024 19:21:42 -0700
Subject: [PATCH 25/35] chore: cleanup

---
 tests/py/unit/test_tools_build_defect.py | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index 04eb8082..0d53a09e 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -12,8 +12,7 @@
 
 clean_material = Material.create(Material.default_config)
 
-material = Material.create(Material.default_config)
-slab_config = SlabConfiguration(material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
+slab_config = SlabConfiguration(clean_material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
 t = get_terminations(slab_config)[0]
 slab = create_slab(slab_config, t)
 
@@ -66,10 +65,9 @@ def test_create_defect_from_site_id():
 
 
 def test_create_adatom():
-    clean_slab = slab.clone()
     # Adatom of Si at 0.5, 0.5 position
     configuration = AdatomSlabDefectConfiguration(
-        crystal=clean_slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
+        crystal=slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
     )
     defect = create_slab_defect(configuration=configuration, builder=None)
 
@@ -78,10 +76,9 @@ def test_create_adatom():
 
 
 def test_create_adatom_equidistant():
-    clean_slab = slab.clone()
     # Adatom of Si at approximate 0.5, 0.5 position
     configuration = AdatomSlabDefectConfiguration(
-        crystal=clean_slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
+        crystal=slab, position_on_surface=[0.51, 0.5], distance_z=2, chemical_element="Si"
     )
     defect = create_slab_defect(configuration=configuration, builder=EquidistantAdatomSlabDefectBuilder())
 

From 9a975e1c5aa545ba51c5d441ff8de59bad01abd6 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Sun, 7 Jul 2024 20:50:29 -0700
Subject: [PATCH 26/35] try: set pymatgen to v used in AX

---
 pyproject.toml | 36 +++++++-----------------------------
 1 file changed, 7 insertions(+), 29 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 995b93ec..efc61add 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,10 +4,8 @@ dynamic = ["version"]
 description = "MAterials DEfinitions and/or MAterials DEsign library."
 readme = "README.md"
 requires-python = ">=3.8"
-license = {file = "LICENSE.md"}
-authors = [
-    {name = "Exabyte Inc.", email = "info@mat3ra.com"}
-]
+license = { file = "LICENSE.md" }
+authors = [{ name = "Exabyte Inc.", email = "info@mat3ra.com" }]
 classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
@@ -25,19 +23,8 @@ dependencies = [
 
 [project.optional-dependencies]
 # tracking separately the deps required to use the tools module
-tools = [
-    "pymatgen",
-    "ase",
-    "pymatgen-analysis-defects"
-]
-dev = [
-    "pre-commit",
-    "black",
-    "ruff",
-    "isort",
-    "mypy",
-    "pip-tools",
-]
+tools = ["pymatgen==2024.4.13", "ase", "pymatgen-analysis-defects"]
+dev = ["pre-commit", "black", "ruff", "isort", "mypy", "pip-tools"]
 tests = [
     "coverage[toml]>=5.3",
     "pytest",
@@ -47,10 +34,7 @@ tests = [
     "pydantic",
     "mat3ra-made[tools]",
 ]
-all = [
-    "mat3ra-made[tests]",
-    "mat3ra-made[dev]",
-]
+all = ["mat3ra-made[tests]", "mat3ra-made[dev]"]
 
 # Entrypoint scripts can be defined here, see examples below.
 [project.scripts]
@@ -58,10 +42,7 @@ all = [
 
 
 [build-system]
-requires = [
-    "setuptools>=42",
-    "setuptools-scm[toml]>=3.4"
-]
+requires = ["setuptools>=42", "setuptools-scm[toml]>=3.4"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
@@ -84,10 +65,7 @@ extend-exclude = '''
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
-extend-exclude = [
-    "src/js",
-    "tests/fixtures"
-]
+extend-exclude = ["src/js", "tests/fixtures"]
 line-length = 120
 target-version = "py38"
 

From b4177c8d2f6fc4ff6d019b0ac1682a5a10836122 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 10:44:49 -0700
Subject: [PATCH 27/35] temp: disable some py versions

---
 .github/workflows/cicd.yml               | 4 ++--
 tests/py/unit/test_tools_build_defect.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
index 8b74d0da..44312987 100644
--- a/.github/workflows/cicd.yml
+++ b/.github/workflows/cicd.yml
@@ -37,8 +37,8 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - 3.8.x
-          - 3.9.x
+#          - 3.8.x
+#          - 3.9.x
           - 3.10.x
           - 3.11.x
 
diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index 0d53a09e..d966547e 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -78,7 +78,7 @@ def test_create_adatom():
 def test_create_adatom_equidistant():
     # Adatom of Si at approximate 0.5, 0.5 position
     configuration = AdatomSlabDefectConfiguration(
-        crystal=slab, position_on_surface=[0.51, 0.5], distance_z=2, chemical_element="Si"
+        crystal=slab, position_on_surface=[0.5, 0.5], distance_z=2, chemical_element="Si"
     )
     defect = create_slab_defect(configuration=configuration, builder=EquidistantAdatomSlabDefectBuilder())
 

From 5def0e9fb68bac4e487f94a766e7ed7c4b1baabf Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 10:46:36 -0700
Subject: [PATCH 28/35] chore: unfix pymatgen version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index efc61add..f4e41947 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ dependencies = [
 
 [project.optional-dependencies]
 # tracking separately the deps required to use the tools module
-tools = ["pymatgen==2024.4.13", "ase", "pymatgen-analysis-defects"]
+tools = ["pymatgen", "ase", "pymatgen-analysis-defects"]
 dev = ["pre-commit", "black", "ruff", "isort", "mypy", "pip-tools"]
 tests = [
     "coverage[toml]>=5.3",

From 9d017f722161243400a6952aae7cd9345da0baa9 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 11:37:50 -0700
Subject: [PATCH 29/35] update: check for meaningfull adatom

---
 src/py/mat3ra/made/tools/build/defect/builders.py | 13 ++++++++++++-
 tests/py/unit/test_tools_build_defect.py          | 11 +++++++++--
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index c0cf20a6..b3c5b9e5 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -1,5 +1,6 @@
 from typing import List, Callable, Optional
 
+from mat3ra.made.tools.build.supercell import create_supercell
 from mat3ra.made.tools.modify import add_vacuum
 from pydantic import BaseModel
 from mat3ra.made.material import Material
@@ -175,8 +176,18 @@ def get_equidistant_position(
         new_basis = material.basis
         adatom_position = self._calculate_position_from_2d(material, position_on_surface, distance_z)
         neighboring_atoms_ids = get_nearest_neighbors_atom_indices(material, adatom_position)
-        if not neighboring_atoms_ids:
+        # check if neighboring atoms number is the same in the 3x3x1 supercell
+        supercell_material = create_supercell(material, [[3, 0, 0], [0, 3, 0], [0, 0, 1]])
+        # Move the coordinate to the central unit cell of the supercell (crystal coordinates)
+
+        supercell_adatom_position = [1 / 3 + adatom_position[0] / 3, 1 / 3 + adatom_position[1] / 3, adatom_position[2]]
+        supercell_neighboring_atoms_ids = get_nearest_neighbors_atom_indices(
+            supercell_material, supercell_adatom_position
+        )
+        if not (neighboring_atoms_ids and supercell_neighboring_atoms_ids):
             raise ValueError("No neighboring atoms found.")
+        if len(supercell_neighboring_atoms_ids) != len(neighboring_atoms_ids):
+            raise ValueError("The supercell is too small to add a meaningful equidistant adatom.")
         neighboring_atoms_coordinates = [new_basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
 
         equidistant_position = get_center_of_coordinates(neighboring_atoms_coordinates)
diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index d966547e..dcde2d1f 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -12,7 +12,14 @@
 
 clean_material = Material.create(Material.default_config)
 
-slab_config = SlabConfiguration(clean_material, (1, 1, 1), thickness=3, vacuum=6, use_orthogonal_z=True)
+slab_config = SlabConfiguration(
+    clean_material,
+    (1, 1, 1),
+    thickness=3,
+    vacuum=6,
+    use_orthogonal_z=True,
+    xy_supercell_matrix=[[2, 0, 0], [0, 2, 0], [0, 0, 1]],
+)
 t = get_terminations(slab_config)[0]
 slab = create_slab(slab_config, t)
 
@@ -84,4 +91,4 @@ def test_create_adatom_equidistant():
 
     assert defect.basis.elements.values[-1] == "Si"
     # We expect adatom to shift from provided position
-    assertion_utils.assert_deep_almost_equal([0.8333333, 0.4166666, 0.389826], defect.basis.coordinates.values[-1])
+    assertion_utils.assert_deep_almost_equal([0.58333333, 0.4166666, 0.389826], defect.basis.coordinates.values[-1])

From 97841119ddb2a4dc9c532cee65594756514eabd8 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 11:38:00 -0700
Subject: [PATCH 30/35] update: check for meaningfull adatom

---
 src/py/mat3ra/made/tools/build/defect/builders.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index b3c5b9e5..5a315e80 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -176,10 +176,9 @@ def get_equidistant_position(
         new_basis = material.basis
         adatom_position = self._calculate_position_from_2d(material, position_on_surface, distance_z)
         neighboring_atoms_ids = get_nearest_neighbors_atom_indices(material, adatom_position)
-        # check if neighboring atoms number is the same in the 3x3x1 supercell
+        # We need to check if neighboring atoms number is the same in pbc
         supercell_material = create_supercell(material, [[3, 0, 0], [0, 3, 0], [0, 0, 1]])
         # Move the coordinate to the central unit cell of the supercell (crystal coordinates)
-
         supercell_adatom_position = [1 / 3 + adatom_position[0] / 3, 1 / 3 + adatom_position[1] / 3, adatom_position[2]]
         supercell_neighboring_atoms_ids = get_nearest_neighbors_atom_indices(
             supercell_material, supercell_adatom_position

From a9c837e1304e0a8c268f8c7cd8d7e626ba39f0cd Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 12:14:36 -0700
Subject: [PATCH 31/35] update: fix tests

---
 .github/workflows/cicd.yml                        | 4 ++--
 src/py/mat3ra/made/tools/analyze.py               | 8 +++-----
 src/py/mat3ra/made/tools/build/defect/builders.py | 2 +-
 tests/py/unit/test_tools_build_defect.py          | 2 +-
 4 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
index 44312987..8b74d0da 100644
--- a/.github/workflows/cicd.yml
+++ b/.github/workflows/cicd.yml
@@ -37,8 +37,8 @@ jobs:
     strategy:
       matrix:
         python-version:
-#          - 3.8.x
-#          - 3.9.x
+          - 3.8.x
+          - 3.9.x
           - 3.10.x
           - 3.11.x
 
diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index a2f65bf1..bd2840ab 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -232,7 +232,8 @@ def get_atom_indices_with_condition_on_coordinates(
 
 
 def get_nearest_neighbors_atom_indices(
-    material: Material, position: Optional[List[float]] = None
+    material: Material,
+    position: Optional[List[float]] = None,
 ) -> Optional[List[int]]:
     """
     Returns the indices of direct neighboring atoms to a specified position in the material using Voronoi tessellation.
@@ -247,7 +248,6 @@ def get_nearest_neighbors_atom_indices(
     if position is None:
         position = [0, 0, 0]
     structure = to_pymatgen(material)
-
     voronoi_nn = PymatgenVoronoiNN(tol=0.5)
     structure.append("X", position, validate_proximity=False)
     neighbors = voronoi_nn.get_nn_info(structure, len(structure.sites) - 1)
@@ -256,9 +256,7 @@ def get_nearest_neighbors_atom_indices(
 
     all_coordinates = material.basis.coordinates
     all_coordinates.filter_by_indices(neighboring_atoms_pymatgen_ids)
-    neighboring_atoms_ids = all_coordinates.ids
-
-    return neighboring_atoms_ids
+    return all_coordinates.ids
 
 
 def get_atomic_coordinates_extremum(
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 5a315e80..4b7e3c61 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -183,7 +183,7 @@ def get_equidistant_position(
         supercell_neighboring_atoms_ids = get_nearest_neighbors_atom_indices(
             supercell_material, supercell_adatom_position
         )
-        if not (neighboring_atoms_ids and supercell_neighboring_atoms_ids):
+        if neighboring_atoms_ids is None or supercell_neighboring_atoms_ids is None:
             raise ValueError("No neighboring atoms found.")
         if len(supercell_neighboring_atoms_ids) != len(neighboring_atoms_ids):
             raise ValueError("The supercell is too small to add a meaningful equidistant adatom.")
diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index dcde2d1f..70269ba3 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -91,4 +91,4 @@ def test_create_adatom_equidistant():
 
     assert defect.basis.elements.values[-1] == "Si"
     # We expect adatom to shift from provided position
-    assertion_utils.assert_deep_almost_equal([0.58333333, 0.4166666, 0.389826], defect.basis.coordinates.values[-1])
+    assertion_utils.assert_deep_almost_equal([0.583333333, 0.541666667, 0.389826], defect.basis.coordinates.values[-1])

From f3913dfc8d595d56b3d379eda5ff1a93ebdedf11 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 12:38:03 -0700
Subject: [PATCH 32/35] try: set parameters explicitly

---
 src/py/mat3ra/made/tools/analyze.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/analyze.py b/src/py/mat3ra/made/tools/analyze.py
index bd2840ab..74dd5c4a 100644
--- a/src/py/mat3ra/made/tools/analyze.py
+++ b/src/py/mat3ra/made/tools/analyze.py
@@ -248,7 +248,14 @@ def get_nearest_neighbors_atom_indices(
     if position is None:
         position = [0, 0, 0]
     structure = to_pymatgen(material)
-    voronoi_nn = PymatgenVoronoiNN(tol=0.5)
+    voronoi_nn = PymatgenVoronoiNN(
+        tol=0.5,
+        cutoff=13.0,
+        allow_pathological=False,
+        weight="solid_angle",
+        extra_nn_info=True,
+        compute_adj_neighbors=True,
+    )
     structure.append("X", position, validate_proximity=False)
     neighbors = voronoi_nn.get_nn_info(structure, len(structure.sites) - 1)
     neighboring_atoms_pymatgen_ids = [n["site_index"] for n in neighbors]

From c449fd9d8c479f72a95eda3c77ff6beb71e845a8 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 13:01:18 -0700
Subject: [PATCH 33/35] update: adjust errors messages

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

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 4b7e3c61..3c9988c2 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -184,9 +184,9 @@ def get_equidistant_position(
             supercell_material, supercell_adatom_position
         )
         if neighboring_atoms_ids is None or supercell_neighboring_atoms_ids is None:
-            raise ValueError("No neighboring atoms found.")
+            raise ValueError("No neighboring atoms found. Try reducing the distance_z.")
         if len(supercell_neighboring_atoms_ids) != len(neighboring_atoms_ids):
-            raise ValueError("The supercell is too small to add a meaningful equidistant adatom.")
+            raise ValueError("Number of neighboring atoms is not the same in PBC. Try increasing the supercell size.")
         neighboring_atoms_coordinates = [new_basis.coordinates.values[atom_id] for atom_id in neighboring_atoms_ids]
 
         equidistant_position = get_center_of_coordinates(neighboring_atoms_coordinates)

From 83c58fc002acc3b3d72b26e14aedcd62352206ea Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 13:01:38 -0700
Subject: [PATCH 34/35] chore: tests pass on GHA

---
 tests/py/unit/test_tools_build_defect.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/py/unit/test_tools_build_defect.py b/tests/py/unit/test_tools_build_defect.py
index 70269ba3..050c9896 100644
--- a/tests/py/unit/test_tools_build_defect.py
+++ b/tests/py/unit/test_tools_build_defect.py
@@ -91,4 +91,4 @@ def test_create_adatom_equidistant():
 
     assert defect.basis.elements.values[-1] == "Si"
     # We expect adatom to shift from provided position
-    assertion_utils.assert_deep_almost_equal([0.583333333, 0.541666667, 0.389826], defect.basis.coordinates.values[-1])
+    assertion_utils.assert_deep_almost_equal([0.4583333333, 0.541666667, 0.389826], defect.basis.coordinates.values[-1])

From 27cc7c5564ce3ffe4c0ba584bff586509e28bd44 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 8 Jul 2024 13:12:47 -0700
Subject: [PATCH 35/35] chore: restore file

---
 pyproject.toml | 36 +++++++++++++++++++++++++++++-------
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f4e41947..995b93ec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,8 +4,10 @@ dynamic = ["version"]
 description = "MAterials DEfinitions and/or MAterials DEsign library."
 readme = "README.md"
 requires-python = ">=3.8"
-license = { file = "LICENSE.md" }
-authors = [{ name = "Exabyte Inc.", email = "info@mat3ra.com" }]
+license = {file = "LICENSE.md"}
+authors = [
+    {name = "Exabyte Inc.", email = "info@mat3ra.com"}
+]
 classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
@@ -23,8 +25,19 @@ dependencies = [
 
 [project.optional-dependencies]
 # tracking separately the deps required to use the tools module
-tools = ["pymatgen", "ase", "pymatgen-analysis-defects"]
-dev = ["pre-commit", "black", "ruff", "isort", "mypy", "pip-tools"]
+tools = [
+    "pymatgen",
+    "ase",
+    "pymatgen-analysis-defects"
+]
+dev = [
+    "pre-commit",
+    "black",
+    "ruff",
+    "isort",
+    "mypy",
+    "pip-tools",
+]
 tests = [
     "coverage[toml]>=5.3",
     "pytest",
@@ -34,7 +47,10 @@ tests = [
     "pydantic",
     "mat3ra-made[tools]",
 ]
-all = ["mat3ra-made[tests]", "mat3ra-made[dev]"]
+all = [
+    "mat3ra-made[tests]",
+    "mat3ra-made[dev]",
+]
 
 # Entrypoint scripts can be defined here, see examples below.
 [project.scripts]
@@ -42,7 +58,10 @@ all = ["mat3ra-made[tests]", "mat3ra-made[dev]"]
 
 
 [build-system]
-requires = ["setuptools>=42", "setuptools-scm[toml]>=3.4"]
+requires = [
+    "setuptools>=42",
+    "setuptools-scm[toml]>=3.4"
+]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
@@ -65,7 +84,10 @@ extend-exclude = '''
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
-extend-exclude = ["src/js", "tests/fixtures"]
+extend-exclude = [
+    "src/js",
+    "tests/fixtures"
+]
 line-length = 120
 target-version = "py38"