feature/SOF-7948-speedup

src/py/mat3ra/made/basis/__init__.py

@@ -175,9 +175,12 @@ def add_atoms_from_another_basis(self, other_basis: "Basis"):
             other_basis (Basis): The other basis to add atoms from.
         """
 
-        self.elements.add_items(other_basis.elements.values)
-        self.coordinates.add_items(other_basis.coordinates.values)
-        self.labels.add_items(other_basis.labels.values)
+        for el in other_basis.elements.values:
+            self.elements.add_item(el)
+        for coord in other_basis.coordinates.values:
+            self.coordinates.add_item(coord)
+        for label in other_basis.labels.values:
+            self.labels.add_item(label)
 
     def remove_atom_by_id(self, id: int):
         self.elements.remove_item(id)

src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/crystal_site/crystal_site.py

@@ -6,13 +6,14 @@
     CrystalSiteSchema,
 )
 from mat3ra.made.material import Material
+from pydantic import Field
 
 
 class CrystalSite(CrystalSiteSchema, InMemoryEntityPydantic):
-    crystal: Optional[Material] = None
+    crystal: Optional[Material] = Field(None, exclude=True)
     # element: str
     coordinate: Optional[List[float]] = None
-    nearest_neighbor_vectors: List[np.ndarray] = []
+    nearest_neighbor_vectors: List[np.ndarray] = Field([], exclude=True)
     # coordination_number: int = 0
     # see https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list for an example
 

src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/point_defect_site/builder.py

@@ -1,3 +1,6 @@
+from mat3ra.code.array_with_ids import ArrayWithIds
+from mat3ra.made.basis import Basis, Coordinates
+
 from ......build_components import MaterialWithBuildMetadata
 from ..... import BaseSingleBuilder
 from .configuration import PointDefectSiteConfiguration
@@ -14,18 +17,16 @@ def _generate(self, configuration: PointDefectSiteConfiguration) -> MaterialWith
         if configuration.crystal is None:
             raise ValueError("Crystal configuration is required for PointDefectSiteBuilder")
 
-        new_material = MaterialWithBuildMetadata.create(
-            {
-                "name": configuration.crystal.name,
-                "lattice": configuration.crystal.lattice.to_dict(),
-                "basis": configuration.crystal.basis.to_dict(),
-            }
+        crystal = configuration.crystal
+        basis = Basis(
+            elements=ArrayWithIds(values=[], ids=[]),
+            coordinates=Coordinates(values=[], ids=[]),
+            units=crystal.basis.units,
+            cell=crystal.basis.cell,
         )
-        elements = configuration.crystal.basis.elements.values
-        new_material.basis.remove_atoms_by_elements(elements)
-        new_material.basis.add_atom(
+        basis.add_atom(
             element=configuration.element.chemical_element,
             coordinate=configuration.coordinate,
             label=configuration.host_atom_label,
         )
-        return new_material
+        return MaterialWithBuildMetadata(name=crystal.name, lattice=crystal.lattice, basis=basis)

src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/builder.py

@@ -79,6 +79,15 @@ def _generate(self, configuration: TypeConfiguration) -> MaterialWithBuildMetada
         if len(materials) == 1:
             return materials[0]
 
+        # Optimization: when there are many materials to merge, combine all non-first
+        # materials into one before merging with the base to avoid N sequential merges.
+        if len(materials) > 2:
+            base = materials[0]
+            combined = materials[1]
+            for m in materials[2:]:
+                combined.basis.add_atoms_from_another_basis(m.basis)
+            materials = [base, combined]
+
         parameters = self.build_parameters or self._DefaultBuildParameters
         merge_method = getattr(configuration, "merge_method", None)
         return self._merge_by_method(materials, parameters, merge_method)