update: add use cartesian to point defects and used functions

src/py/mat3ra/made/tools/analyze.py

@@ -77,25 +77,34 @@ def get_chemical_formula(atoms: ASEAtoms):
     return atoms.get_chemical_formula()
 
 
-def get_closest_site_id_from_coordinate(material: Material, coordinate: List[float]) -> int:
+def get_closest_site_id_from_coordinate(
+    material: Material, coordinate: List[float], use_cartesian_coordinates: bool = False
+) -> int:
     """
     Get the site ID of the closest site to a given coordinate in the crystal.
 
     Args:
         material (Material): The material object to find the closest site in.
         coordinate (List[float]): The coordinate to find the closest site to.
+        use_cartesian_coordinates (bool): Whether to use Cartesian coordinates for the calculation.
 
     Returns:
         int: The site ID of the closest site.
     """
-    coordinates = np.array(material.coordinates_array)
+    new_material = material.clone()
+    if use_cartesian_coordinates:
+        new_material.to_cartesian()
+    coordinates = np.array(new_material.coordinates_array)
     coordinate = np.array(coordinate)  # type: ignore
     distances = np.linalg.norm(coordinates - coordinate, axis=1)
     return int(np.argmin(distances))
 
 
 def get_closest_site_id_from_coordinate_and_element(
-    material: Material, coordinate: List[float], chemical_element: Optional[str] = None
+    material: Material,
+    coordinate: List[float],
+    chemical_element: Optional[str] = None,
+    use_cartesian_coordinates: bool = False,
 ) -> int:
     """
     Get the site ID of the closest site with a given element to a given coordinate in the crystal.
@@ -104,16 +113,20 @@ def get_closest_site_id_from_coordinate_and_element(
         material (Material): The material object to find the closest site in.
         coordinate (List[float]): The coordinate to find the closest site to.
         chemical_element (str): The element of the site to find.
+        use_cartesian_coordinates (bool): Whether to use Cartesian coordinates for the calculation.
 
     Returns:
         int: The site ID of the closest site with the given element.
     """
-    coordinates = np.array(material.basis.coordinates.values)
+    new_material = material.clone()
+    if use_cartesian_coordinates:
+        new_material.to_cartesian()
+    coordinates = np.array(new_material.basis.coordinates.values)
     coordinate = np.array(coordinate)  # type: ignore
     distances = np.linalg.norm(coordinates - coordinate, axis=1)
 
     if chemical_element is not None:
-        elements = np.array(material.basis.elements.values)
+        elements = np.array(new_material.basis.elements.values)
         element_indices = np.where(elements == chemical_element)[0]
         distances = distances[element_indices]
         return int(element_indices[np.argmin(distances)])

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

@@ -76,6 +76,7 @@ def _generate(self, configuration: BaseBuilder._ConfigurationType) -> List[_Gene
         pymatgen_periodic_site = PymatgenPeriodicSite(
             species=self._get_species(configuration),
             coords=configuration.coordinate,
+            coords_are_cartesian=configuration.use_cartesian_coordinates,
             lattice=pymatgen_structure.lattice,
         )
         # oxi_state set to 0 to allow for 2D materials, otherwise oxi_state search takes infinite loop in pymatgen

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

@@ -41,8 +41,9 @@ class PointDefectConfiguration(BaseDefectConfiguration, InMemoryEntity):
     """
 
     defect_type: PointDefectTypeEnum
-    coordinate: List[float] = [0, 0, 0]  # crystal coordinates
+    coordinate: List[float] = [0, 0, 0]
     chemical_element: Optional[str] = None
+    use_cartesian_coordinates: bool = False
 
     @classmethod
     def from_site_id(
@@ -60,10 +61,15 @@ def from_approximate_position(
         defect_type: PointDefectTypeEnum,
         approximate_coordinate: List[float],
         chemical_element: Optional[str] = None,
+        use_cartesian_coordinates: bool = False,
     ):
         if not crystal:
             raise RuntimeError("Crystal is not defined")
-        closest_site_id = get_closest_site_id_from_coordinate(crystal, approximate_coordinate)
+        closest_site_id = get_closest_site_id_from_coordinate(
+            material=crystal,
+            coordinate=approximate_coordinate,
+            use_cartesian_coordinates=use_cartesian_coordinates,
+        )
         return cls.from_site_id(
             crystal=crystal, defect_type=defect_type, site_id=closest_site_id, chemical_element=chemical_element
         )