update: add first implementation of hollow sites

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

@@ -44,6 +44,7 @@
     PointDefectPairConfiguration,
 )
 from .factories import DefectBuilderFactory
+from pymatgen.analysis.adsorption import AdsorbateSiteFinder
 
 
 class PointDefectBuilderParameters(BaseModel):
@@ -434,6 +435,36 @@ def create_adatom(
         return self.merge_slab_and_defect(new_material, only_adatom_material)
 
 
+class HollowSiteAdatomSlabDefectBuilder(AdatomSlabDefectBuilder):
+    """
+    Builder class for generating adatoms at hollow sites.
+
+    The adatom is placed at the hollow site closest to the specified position on the surface of the material.
+
+    """
+
+    def _calculate_coordinate_from_position_and_distance(
+        self, material: Material, position_on_surface: List[float], distance_z: float
+    ) -> List[float]:
+        coordinate = super()._calculate_coordinate_from_position_and_distance(material, position_on_surface, distance_z)
+        pymatgen_structure = to_pymatgen(material)
+        asf = AdsorbateSiteFinder(pymatgen_structure)
+
+        sites = asf.find_adsorption_sites(
+            positions=[
+                "hollow",
+            ],
+            no_obtuse_hollow=False,
+        )
+        hollow_coordinates = [array.tolist() for array in sites["hollow"]]
+        print(hollow_coordinates)
+        closest_hollow_site_coordinate = min(
+            hollow_coordinates, key=lambda x: np.linalg.norm(np.array(x) - np.array(coordinate))
+        )
+        print(closest_hollow_site_coordinate[0:2] + [coordinate[2]])
+        return closest_hollow_site_coordinate[0:2] + [coordinate[2]]
+
+
 class DefectPairBuilder(DefectBuilder):
     def create_defect_pair(
         self,

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

@@ -26,6 +26,12 @@ 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"
+    # Places the atom at the hollow site of the surface (for HEX)
+    HOLLOW_SITE = "hollow"
+    # Places the atom at the bridge site of the surface (for HEX)
+    BRIDGE_SITE = "bridge"
+    # Places the atom at the on-top site of the surface (for HEX)
+    ON_TOP_SITE = "on_top"
 
 
 class CoordinatesShapeEnum(str, Enum):