Preprocess Structure Reduction Before Bulk Match (#4137)

The `AflowPrototypeMatcher` matches a structure against predefined AFLOW
prototype structures using `StructureMatcher`. `StructureMatcher` requires
preprocessing via lattice reduction and primitive-cell conversion. This commit
optimizes performance by preprocessing AFLOW prototype structures during the
initialization of `AflowPrototypeMatcher`. This change eliminates redundant
processing when `AflowPrototypeMatcher.get_prototypes` is called multiple times.

Co-authored-by: Shyue Ping Ong <[email protected]>

src/pymatgen/analysis/prototypes.py

@@ -22,7 +22,7 @@
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
-    from pymatgen.core import Structure
+    from pymatgen.core.structure import Structure
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{MODULE_DIR}/aflow_prototypes.json")
@@ -62,12 +62,24 @@ def __init__(self, initial_ltol=0.2, initial_stol=0.3, initial_angle_tol=5):
         self.initial_stol = initial_stol
         self.initial_angle_tol = initial_angle_tol
 
+        # Preprocess AFLOW prototypes
+        self._aflow_prototype_library = []
+        for dct in AFLOW_PROTOTYPE_LIBRARY:
+            structure: Structure = dct["snl"].structure
+            reduced_structure = self._preprocess_structure(structure)
+            self._aflow_prototype_library.append((reduced_structure, dct))
+
     @staticmethod
-    def _match_prototype(structure_matcher, structure):
+    def _preprocess_structure(structure: Structure) -> Structure:
+        return structure.get_reduced_structure(reduction_algo="niggli").get_primitive_structure()
+
+    def _match_prototype(self, structure_matcher: StructureMatcher, reduced_structure: Structure):
         tags = []
-        for dct in AFLOW_PROTOTYPE_LIBRARY:
-            struct = dct["snl"].structure
-            match = structure_matcher.fit_anonymous(struct, structure)
+        for aflow_reduced_structure, dct in self._aflow_prototype_library:
+            # Since both structures are already reduced, we can skip the structure reduction step
+            match = structure_matcher.fit_anonymous(
+                aflow_reduced_structure, reduced_structure, skip_structure_reduction=True
+            )
             if match:
                 tags.append(dct)
         return tags
@@ -77,13 +89,15 @@ def _match_single_prototype(self, structure: Structure):
             ltol=self.initial_ltol,
             stol=self.initial_stol,
             angle_tol=self.initial_angle_tol,
+            primitive_cell=True,
         )
-        tags = self._match_prototype(sm, structure)
+        reduced_structure = self._preprocess_structure(structure)
+        tags = self._match_prototype(sm, reduced_structure)
         while len(tags) > 1:
             sm.ltol *= 0.8
             sm.stol *= 0.8
             sm.angle_tol *= 0.8
-            tags = self._match_prototype(sm, structure)
+            tags = self._match_prototype(sm, reduced_structure)
             if sm.ltol < 0.01:
                 break
         return tags