From a6e62c4e561002536689ae7697a887318ceea8e9 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 18 Oct 2024 18:24:58 -0700
Subject: [PATCH 1/9] update: add vacuum to slab defect gen

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

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 0ab99396..d66646dc 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -137,6 +137,7 @@ def merge_slab_and_defect(self, material: Material, isolated_defect: Material) -
             material_name=material.name,
             merge_dangerously=True,
         )
+        new_material = add_vacuum(new_material, self.build_parameters.vacuum_thickness)
         return new_material
 
 

From 02394380312f7c3f97506169e3f15a11392b0cf7 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 21 Oct 2024 20:07:05 -0700
Subject: [PATCH 2/9] update: add fractional layers support to slab defects

---
 .../made/tools/build/defect/builders.py       | 96 ++++++++++++++++++-
 .../made/tools/build/defect/configuration.py  |  4 +-
 2 files changed, 93 insertions(+), 7 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index d66646dc..6fb41abc 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -115,18 +115,104 @@ class SlabDefectBuilder(DefectBuilder):
     _BuildParametersType = SlabDefectBuilderParameters
     _DefaultBuildParameters = SlabDefectBuilderParameters()
 
-    def create_material_with_additional_layers(self, material: Material, added_thickness: int = 1) -> Material:
+    def create_material_with_additional_layers(
+        self, material: Material, added_thickness: Union[int, float] = 1
+    ) -> Material:
+        """
+        Adds a number of layers to the material.
+
+        Args:
+            material: The original material.
+            added_thickness: The thickness to add.
+
+        Returns:
+            A new Material instance with the added layers.
+        """
+        if isinstance(added_thickness, int):
+            return self.create_material_with_additional_layers_int(material, added_thickness)
+        elif isinstance(added_thickness, float):
+            return self.create_material_with_additional_layers_float(material, added_thickness)
+        else:
+            raise TypeError("added_thickness must be an integer or float for this method.")
+
+    def create_material_with_additional_layers_int(self, material: Material, added_thickness: int = 1) -> Material:
+        """
+        Adds an integer number of layers to the material.
+
+        Args:
+            material: The original material.
+            added_thickness: The number of whole layers to add.
+
+        Returns:
+            A new Material instance with the added layers.
+        """
+        if not isinstance(added_thickness, int):
+            raise TypeError("added_thickness must be an integer for this method.")
+
         new_material = material.clone()
         termination = Termination.from_string(new_material.metadata.get("build").get("termination"))
-        build_config = new_material.metadata.get("build").get("configuration")
+        build_config = new_material.metadata.get("build").get("configuration").copy()
+
         if build_config["type"] != "SlabConfiguration":
             raise ValueError("Material is not a slab.")
         build_config.pop("type")
-        build_config["thickness"] = build_config["thickness"] + added_thickness
+        build_config["thickness"] += added_thickness
+
         new_slab_config = SlabConfiguration(**build_config)
-        material_with_additional_layer = create_slab(new_slab_config, termination)
+        material_with_additional_layers = create_slab(new_slab_config, termination)
+
+        return material_with_additional_layers
+
+    def create_material_with_additional_layers_float(
+        self, material: Material, added_thickness: float = 1.0
+    ) -> Material:
+        """
+        Adds a fractional number of layers to the material.
 
-        return material_with_additional_layer
+        Args:
+            material: The original material.
+            added_thickness: The fractional thickness to add.
+
+        Returns:
+            A new Material instance with the fractional layer added.
+        """
+        if not isinstance(added_thickness, float):
+            raise TypeError("added_thickness must be a float for this method.")
+
+        whole_layers = int(added_thickness)
+        fractional_part = added_thickness - whole_layers
+
+        if whole_layers > 0:
+            material_with_additional_layers = self.create_material_with_additional_layers_int(material, whole_layers)
+        else:
+            material_with_additional_layers = material.clone()
+
+            if fractional_part > 0.0:
+                material_with_additional_layers = self.create_material_with_additional_layers_int(
+                    material_with_additional_layers, 1
+                )
+
+                original_c = material.lattice.c
+                new_c = material_with_additional_layers.lattice.c
+                added_layers = whole_layers + 1
+                layer_height = (new_c - original_c) / added_layers
+
+                added_fractional_thickness = fractional_part * layer_height
+
+                original_max_z = get_atomic_coordinates_extremum(material, "max", "z", use_cartesian_coordinates=True)
+                added_layers_min_z = original_max_z + whole_layers * layer_height
+                added_layers_max_z = added_layers_min_z + added_fractional_thickness
+
+                added_layers_max_z_crystal = material_with_additional_layers.basis.cell.convert_point_to_crystal(
+                    [0, 0, added_layers_max_z]
+                )[2]
+
+                material_with_additional_layers = filter_by_box(
+                    material=material_with_additional_layers,
+                    min_coordinate=[0, 0, added_layers_min_z],
+                    max_coordinate=[1, 1, added_layers_max_z_crystal],
+                )
+        return material_with_additional_layers
 
     def merge_slab_and_defect(self, material: Material, isolated_defect: Material) -> Material:
         new_vacuum = isolated_defect.lattice.c - material.lattice.c
diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index 33d62081..13c035b4 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -109,10 +109,10 @@ class SlabDefectConfiguration(BaseDefectConfiguration, InMemoryEntity):
 
     Args:
         crystal (Material): The Material object.
-        number_of_added_layers (int): The number of added layers.
+        number_of_added_layers (Union[int, float]): The number of added layers to the slab.
     """
 
-    number_of_added_layers: int = 1
+    number_of_added_layers: Union[int, float] = 1
 
     @property
     def _json(self):

From 0fa6b7dc8a99088b72c5b06608d521d7ee5b6cd9 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 21 Oct 2024 20:08:55 -0700
Subject: [PATCH 3/9] update: fix a mistake

---
 .../made/tools/build/defect/builders.py       | 50 +++++++++----------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 6fb41abc..1dd44ee1 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -187,31 +187,31 @@ def create_material_with_additional_layers_float(
         else:
             material_with_additional_layers = material.clone()
 
-            if fractional_part > 0.0:
-                material_with_additional_layers = self.create_material_with_additional_layers_int(
-                    material_with_additional_layers, 1
-                )
-
-                original_c = material.lattice.c
-                new_c = material_with_additional_layers.lattice.c
-                added_layers = whole_layers + 1
-                layer_height = (new_c - original_c) / added_layers
-
-                added_fractional_thickness = fractional_part * layer_height
-
-                original_max_z = get_atomic_coordinates_extremum(material, "max", "z", use_cartesian_coordinates=True)
-                added_layers_min_z = original_max_z + whole_layers * layer_height
-                added_layers_max_z = added_layers_min_z + added_fractional_thickness
-
-                added_layers_max_z_crystal = material_with_additional_layers.basis.cell.convert_point_to_crystal(
-                    [0, 0, added_layers_max_z]
-                )[2]
-
-                material_with_additional_layers = filter_by_box(
-                    material=material_with_additional_layers,
-                    min_coordinate=[0, 0, added_layers_min_z],
-                    max_coordinate=[1, 1, added_layers_max_z_crystal],
-                )
+        if fractional_part > 0.0:
+            material_with_additional_layers = self.create_material_with_additional_layers_int(
+                material_with_additional_layers, 1
+            )
+
+            original_c = material.lattice.c
+            new_c = material_with_additional_layers.lattice.c
+            added_layers = whole_layers + 1
+            layer_height = (new_c - original_c) / added_layers
+
+            added_fractional_thickness = fractional_part * layer_height
+
+            original_max_z = get_atomic_coordinates_extremum(material, "max", "z", use_cartesian_coordinates=True)
+            added_layers_min_z = original_max_z + whole_layers * layer_height
+            added_layers_max_z = added_layers_min_z + added_fractional_thickness
+
+            added_layers_max_z_crystal = material_with_additional_layers.basis.cell.convert_point_to_crystal(
+                [0, 0, added_layers_max_z]
+            )[2]
+
+            material_with_additional_layers = filter_by_box(
+                material=material_with_additional_layers,
+                min_coordinate=[0, 0, added_layers_min_z],
+                max_coordinate=[1, 1, added_layers_max_z_crystal],
+            )
         return material_with_additional_layers
 
     def merge_slab_and_defect(self, material: Material, isolated_defect: Material) -> Material:

From d0d4655c9440a445828926aefef6ac6c962d493c Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 21 Oct 2024 20:54:51 -0700
Subject: [PATCH 4/9] chore: shorten function

---
 .../mat3ra/made/tools/build/defect/builders.py | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index 1dd44ee1..ad04182e 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -146,8 +146,6 @@ def create_material_with_additional_layers_int(self, material: Material, added_t
         Returns:
             A new Material instance with the added layers.
         """
-        if not isinstance(added_thickness, int):
-            raise TypeError("added_thickness must be an integer for this method.")
 
         new_material = material.clone()
         termination = Termination.from_string(new_material.metadata.get("build").get("termination"))
@@ -176,9 +174,6 @@ def create_material_with_additional_layers_float(
         Returns:
             A new Material instance with the fractional layer added.
         """
-        if not isinstance(added_thickness, float):
-            raise TypeError("added_thickness must be a float for this method.")
-
         whole_layers = int(added_thickness)
         fractional_part = added_thickness - whole_layers
 
@@ -191,25 +186,16 @@ def create_material_with_additional_layers_float(
             material_with_additional_layers = self.create_material_with_additional_layers_int(
                 material_with_additional_layers, 1
             )
-
-            original_c = material.lattice.c
             new_c = material_with_additional_layers.lattice.c
-            added_layers = whole_layers + 1
-            layer_height = (new_c - original_c) / added_layers
-
-            added_fractional_thickness = fractional_part * layer_height
-
+            layer_height = (new_c - material.lattice.c) / (whole_layers + 1)
             original_max_z = get_atomic_coordinates_extremum(material, "max", "z", use_cartesian_coordinates=True)
-            added_layers_min_z = original_max_z + whole_layers * layer_height
-            added_layers_max_z = added_layers_min_z + added_fractional_thickness
-
+            added_layers_max_z = original_max_z + added_thickness * layer_height
             added_layers_max_z_crystal = material_with_additional_layers.basis.cell.convert_point_to_crystal(
                 [0, 0, added_layers_max_z]
             )[2]
 
             material_with_additional_layers = filter_by_box(
                 material=material_with_additional_layers,
-                min_coordinate=[0, 0, added_layers_min_z],
                 max_coordinate=[1, 1, added_layers_max_z_crystal],
             )
         return material_with_additional_layers

From 2554ce8fe0b560a82fa1447cdd1d3a56eeefdd5a Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Mon, 21 Oct 2024 21:07:46 -0700
Subject: [PATCH 5/9] chore: revert some lines

---
 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 ad04182e..d430724c 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -149,12 +149,12 @@ def create_material_with_additional_layers_int(self, material: Material, added_t
 
         new_material = material.clone()
         termination = Termination.from_string(new_material.metadata.get("build").get("termination"))
-        build_config = new_material.metadata.get("build").get("configuration").copy()
+        build_config = new_material.metadata.get("build").get("configuration")
 
         if build_config["type"] != "SlabConfiguration":
             raise ValueError("Material is not a slab.")
         build_config.pop("type")
-        build_config["thickness"] += added_thickness
+        build_config["thickness"] = build_config["thickness"] + added_thickness
 
         new_slab_config = SlabConfiguration(**build_config)
         material_with_additional_layers = create_slab(new_slab_config, termination)

From f54b37c1bc763006d7edc91bbf4040de925c90d4 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 23 Oct 2024 13:30:55 -0700
Subject: [PATCH 6/9] update: add from dict to allow for condtons

---
 .../made/tools/build/defect/configuration.py  | 48 +++++++++++++++++--
 .../mat3ra/made/tools/build/defect/enums.py   |  6 +++
 2 files changed, 51 insertions(+), 3 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index 13c035b4..609caf84 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -1,4 +1,4 @@
-from typing import Optional, List, Union
+from typing import Optional, List, Union, Generic, TypeVar
 from pydantic import BaseModel
 
 from mat3ra.code.entity import InMemoryEntity
@@ -10,9 +10,10 @@
     SphereCoordinateCondition,
     BoxCoordinateCondition,
     TriangularPrismCoordinateCondition,
-    PlaneCoordinateCondition,
+    PlaneCoordinateCondition, CoordinateCondition,
 )
-from .enums import PointDefectTypeEnum, SlabDefectTypeEnum, AtomPlacementMethodEnum, ComplexDefectTypeEnum
+from .enums import PointDefectTypeEnum, SlabDefectTypeEnum, AtomPlacementMethodEnum, ComplexDefectTypeEnum, \
+    CoordinatesShapeEnum
 
 
 class BaseDefectConfiguration(BaseModel):
@@ -188,6 +189,9 @@ def _json(self):
         }
 
 
+CoordinateConditionType = TypeVar('CoordinateConditionType', bound=CoordinateCondition)
+
+
 class IslandSlabDefectConfiguration(SlabDefectConfiguration):
     """
     Configuration for an island slab defect.
@@ -207,8 +211,46 @@ class IslandSlabDefectConfiguration(SlabDefectConfiguration):
         BoxCoordinateCondition,
         TriangularPrismCoordinateCondition,
         PlaneCoordinateCondition,
+        CoordinateConditionType
     ] = CylinderCoordinateCondition()
 
+    @classmethod
+    def from_dict(cls, crystal: Material, data: dict):
+        if "condition" in data:
+            condition = cls.get_coordinate_condition(data["condition"]["shape"], data["condition"]["params"])
+            return cls(crystal=crystal, condition=condition, **data)
+        else:
+            return cls(crystal=crystal, **data)
+
+    def get_coordinate_condition(self, shape: CoordinatesShapeEnum, dict_params: dict):
+        if shape == CoordinatesShapeEnum.CYLINDER:
+            return CylinderCoordinateCondition(
+                center_position=dict_params['center_position'],
+                radius=dict_params['radius'],
+                min_z=dict_params['min_z'],
+                max_z=dict_params['max_z']
+            )
+        elif shape == 'sphere':
+            return SphereCoordinateCondition(
+                center_position=dict_params['center_position'],
+                radius=dict_params['radius']
+            )
+        elif shape == 'box':
+            return BoxCoordinateCondition(
+                min_coordinates=dict_params['min_coordinates'],
+                max_coordinates=dict_params['max_coordinates']
+            )
+        elif shape == 'triangular_prism':
+            return TriangularPrismCoordinateCondition(
+                position_on_surface_1=dict_params['position_on_surface_1'],
+                position_on_surface_2=dict_params['position_on_surface_2'],
+                position_on_surface_3=dict_params['position_on_surface_3'],
+                min_z=dict_params['min_z'],
+                max_z=dict_params['max_z']
+            )
+        else:
+            raise ValueError(f"Unsupported island shape: {shape}")
+
     @property
     def _json(self):
         return {
diff --git a/src/py/mat3ra/made/tools/build/defect/enums.py b/src/py/mat3ra/made/tools/build/defect/enums.py
index a169ad69..0b28080f 100644
--- a/src/py/mat3ra/made/tools/build/defect/enums.py
+++ b/src/py/mat3ra/made/tools/build/defect/enums.py
@@ -26,3 +26,9 @@ class AtomPlacementMethodEnum(str, Enum):
     EQUIDISTANT = "equidistant"
     # Places the atom at the existing or extrapolated crystal site closest to the given coordinate.
     CRYSTAL_SITE = "crystal_site"
+
+class CoordinatesShapeEnum(str, Enum):
+    SPHERE = "sphere"
+    CYLINDER = "cylinder"
+    BOX = "rectangle"
+    TRIANGULAR_PRISM = "triangular_prism"

From 6a9eeb56c43b307cd65057421033aba597ed1327 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 23 Oct 2024 14:02:39 -0700
Subject: [PATCH 7/9] update: fix signatures and types

---
 .../made/tools/build/defect/configuration.py  | 82 ++++++++++++-------
 .../mat3ra/made/tools/build/defect/enums.py   |  1 +
 2 files changed, 52 insertions(+), 31 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/configuration.py b/src/py/mat3ra/made/tools/build/defect/configuration.py
index 609caf84..7eda27cd 100644
--- a/src/py/mat3ra/made/tools/build/defect/configuration.py
+++ b/src/py/mat3ra/made/tools/build/defect/configuration.py
@@ -10,10 +10,16 @@
     SphereCoordinateCondition,
     BoxCoordinateCondition,
     TriangularPrismCoordinateCondition,
-    PlaneCoordinateCondition, CoordinateCondition,
+    PlaneCoordinateCondition,
+    CoordinateCondition,
+)
+from .enums import (
+    PointDefectTypeEnum,
+    SlabDefectTypeEnum,
+    AtomPlacementMethodEnum,
+    ComplexDefectTypeEnum,
+    CoordinatesShapeEnum,
 )
-from .enums import PointDefectTypeEnum, SlabDefectTypeEnum, AtomPlacementMethodEnum, ComplexDefectTypeEnum, \
-    CoordinatesShapeEnum
 
 
 class BaseDefectConfiguration(BaseModel):
@@ -189,10 +195,10 @@ def _json(self):
         }
 
 
-CoordinateConditionType = TypeVar('CoordinateConditionType', bound=CoordinateCondition)
+CoordinateConditionType = TypeVar("CoordinateConditionType", bound=CoordinateCondition)
 
 
-class IslandSlabDefectConfiguration(SlabDefectConfiguration):
+class IslandSlabDefectConfiguration(SlabDefectConfiguration, Generic[CoordinateConditionType]):
     """
     Configuration for an island slab defect.
 
@@ -211,42 +217,56 @@ class IslandSlabDefectConfiguration(SlabDefectConfiguration):
         BoxCoordinateCondition,
         TriangularPrismCoordinateCondition,
         PlaneCoordinateCondition,
-        CoordinateConditionType
+        CoordinateConditionType,
     ] = CylinderCoordinateCondition()
 
     @classmethod
-    def from_dict(cls, crystal: Material, data: dict):
-        if "condition" in data:
-            condition = cls.get_coordinate_condition(data["condition"]["shape"], data["condition"]["params"])
-            return cls(crystal=crystal, condition=condition, **data)
-        else:
-            return cls(crystal=crystal, **data)
-
-    def get_coordinate_condition(self, shape: CoordinatesShapeEnum, dict_params: dict):
-        if shape == CoordinatesShapeEnum.CYLINDER:
+    def from_dict(cls, crystal: Material, condition: dict, **kwargs):
+        """
+        Creates an IslandSlabDefectConfiguration instance from a dictionary.
+
+        Args:
+            crystal (Material): The material object.
+            condition (dict): The dictionary with shape and other parameters for the condition.
+            kwargs: Other configuration parameters (like number_of_added_layers).
+        """
+        condition_obj = cls.get_coordinate_condition(shape=condition["shape"], dict_params=condition)
+        return cls(crystal=crystal, condition=condition_obj, **kwargs)
+
+    @staticmethod
+    def get_coordinate_condition(shape: CoordinatesShapeEnum, dict_params: dict):
+        """
+        Returns the appropriate coordinate condition based on the shape provided.
+
+        Args:
+            shape (CoordinatesShapeEnum): Shape of the island (e.g., cylinder, box, etc.).
+            dict_params (dict): Parameters for the shape condition.
+
+        Returns:
+            CoordinateCondition: The appropriate condition object.
+        """
+        if shape == "cylinder":
             return CylinderCoordinateCondition(
-                center_position=dict_params['center_position'],
-                radius=dict_params['radius'],
-                min_z=dict_params['min_z'],
-                max_z=dict_params['max_z']
+                center_position=dict_params.get("center_position", [0.5, 0.5]),
+                radius=dict_params["radius"],
+                min_z=dict_params["min_z"],
+                max_z=dict_params["max_z"],
             )
-        elif shape == 'sphere':
+        elif shape == "sphere":
             return SphereCoordinateCondition(
-                center_position=dict_params['center_position'],
-                radius=dict_params['radius']
+                center_position=dict_params.get("center_position", [0.5, 0.5]), radius=dict_params["radius"]
             )
-        elif shape == 'box':
+        elif shape == "box":
             return BoxCoordinateCondition(
-                min_coordinates=dict_params['min_coordinates'],
-                max_coordinates=dict_params['max_coordinates']
+                min_coordinate=dict_params["min_coordinate"], max_coordinate=dict_params["max_coordinate"]
             )
-        elif shape == 'triangular_prism':
+        elif shape == "triangular_prism":
             return TriangularPrismCoordinateCondition(
-                position_on_surface_1=dict_params['position_on_surface_1'],
-                position_on_surface_2=dict_params['position_on_surface_2'],
-                position_on_surface_3=dict_params['position_on_surface_3'],
-                min_z=dict_params['min_z'],
-                max_z=dict_params['max_z']
+                position_on_surface_1=dict_params["position_on_surface_1"],
+                position_on_surface_2=dict_params["position_on_surface_2"],
+                position_on_surface_3=dict_params["position_on_surface_3"],
+                min_z=dict_params["min_z"],
+                max_z=dict_params["max_z"],
             )
         else:
             raise ValueError(f"Unsupported island shape: {shape}")
diff --git a/src/py/mat3ra/made/tools/build/defect/enums.py b/src/py/mat3ra/made/tools/build/defect/enums.py
index 0b28080f..bdc22279 100644
--- a/src/py/mat3ra/made/tools/build/defect/enums.py
+++ b/src/py/mat3ra/made/tools/build/defect/enums.py
@@ -27,6 +27,7 @@ class AtomPlacementMethodEnum(str, Enum):
     # Places the atom at the existing or extrapolated crystal site closest to the given coordinate.
     CRYSTAL_SITE = "crystal_site"
 
+
 class CoordinatesShapeEnum(str, Enum):
     SPHERE = "sphere"
     CYLINDER = "cylinder"

From dff5a05517dcb9f0485349fa4d7e197f22202e24 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 23 Oct 2024 18:58:16 -0700
Subject: [PATCH 8/9] update: move fractional layer logic to a function

---
 .../made/tools/build/defect/builders.py       | 54 +++++++++++++------
 1 file changed, 38 insertions(+), 16 deletions(-)

diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
index d430724c..07a735a1 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -183,21 +183,42 @@ def create_material_with_additional_layers_float(
             material_with_additional_layers = material.clone()
 
         if fractional_part > 0.0:
-            material_with_additional_layers = self.create_material_with_additional_layers_int(
-                material_with_additional_layers, 1
-            )
-            new_c = material_with_additional_layers.lattice.c
-            layer_height = (new_c - material.lattice.c) / (whole_layers + 1)
-            original_max_z = get_atomic_coordinates_extremum(material, "max", "z", use_cartesian_coordinates=True)
-            added_layers_max_z = original_max_z + added_thickness * layer_height
-            added_layers_max_z_crystal = material_with_additional_layers.basis.cell.convert_point_to_crystal(
-                [0, 0, added_layers_max_z]
-            )[2]
-
-            material_with_additional_layers = filter_by_box(
-                material=material_with_additional_layers,
-                max_coordinate=[1, 1, added_layers_max_z_crystal],
+            material_with_additional_layers = self.add_fractional_layer(
+                material_with_additional_layers, whole_layers, fractional_part
             )
+
+        return material_with_additional_layers
+
+    def add_fractional_layer(
+        self,
+        material: Material,
+        whole_layers: int,
+        fractional_thickness: float,
+    ) -> Material:
+        """
+        Adds a fractional layer to the material.
+
+        Args:
+            material: The original material.
+            fractional_thickness: The fractional thickness to add.
+
+        Returns:
+            A new Material instance with the fractional layer added.
+        """
+        material_with_additional_layers = self.create_material_with_additional_layers_int(material, 1)
+        new_c = material_with_additional_layers.lattice.c
+        layer_height = (new_c - material.lattice.c) / (whole_layers + 1)
+        original_max_z = get_atomic_coordinates_extremum(material, "max", "z", use_cartesian_coordinates=True)
+        added_layers_max_z = original_max_z + (whole_layers + fractional_thickness) * layer_height
+        added_layers_max_z_crystal = material_with_additional_layers.basis.cell.convert_point_to_crystal(
+            [0, 0, added_layers_max_z]
+        )[2]
+
+        material_with_additional_layers = filter_by_box(
+            material=material_with_additional_layers,
+            max_coordinate=[1, 1, added_layers_max_z_crystal],
+        )
+
         return material_with_additional_layers
 
     def merge_slab_and_defect(self, material: Material, isolated_defect: Material) -> Material:
@@ -209,8 +230,9 @@ def merge_slab_and_defect(self, material: Material, isolated_defect: Material) -
             material_name=material.name,
             merge_dangerously=True,
         )
-        new_material = add_vacuum(new_material, self.build_parameters.vacuum_thickness)
-        return new_material
+        new_material.to_crystal()
+        new_material_with_vacuum = add_vacuum(new_material, self.build_parameters.vacuum_thickness)
+        return new_material_with_vacuum
 
 
 class AdatomSlabDefectBuilder(SlabDefectBuilder):

From 9853b80c2a7e841d06c64ed55c520e684607ed97 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 23 Oct 2024 19:04:44 -0700
Subject: [PATCH 9/9] update: add vacuum when needed only

---
 src/py/mat3ra/made/tools/build/defect/builders.py | 5 +++--
 1 file changed, 3 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 07a735a1..95f7f9a5 100644
--- a/src/py/mat3ra/made/tools/build/defect/builders.py
+++ b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -231,8 +231,9 @@ def merge_slab_and_defect(self, material: Material, isolated_defect: Material) -
             merge_dangerously=True,
         )
         new_material.to_crystal()
-        new_material_with_vacuum = add_vacuum(new_material, self.build_parameters.vacuum_thickness)
-        return new_material_with_vacuum
+        if self.build_parameters.auto_add_vacuum and get_atomic_coordinates_extremum(new_material, "max", "z") > 1:
+            new_material = add_vacuum(new_material, self.build_parameters.vacuum_thickness)
+        return new_material
 
 
 class AdatomSlabDefectBuilder(SlabDefectBuilder):