fix: preserve site properties over cell transform (#4123)

Make sure site properties are properly transferred from the original cell to the primitive or refined one. Co-authored-by: Shyue Ping Ong <[email protected]>
materialsproject · Oct 21, 2024 · 7b7e61b · 7b7e61b
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commit 7b7e61b
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Showing 2 changed files with 22 additions and 2 deletions.
diff --git a/src/pymatgen/symmetry/analyzer.py b/src/pymatgen/symmetry/analyzer.py
@@ -369,7 +369,7 @@ def get_refined_structure(self, keep_site_properties: bool = False) -> Structure
         if keep_site_properties:
             site_properties = {}
             for k, v in self._site_props.items():
-                site_properties[k] = [v[i - 1] for i in numbers]
+                site_properties[k] = [v[self._numbers.index(i)] for i in numbers]
         else:
             site_properties = None
         struct = Structure(lattice, species, scaled_positions, site_properties=site_properties)
@@ -398,7 +398,7 @@ def find_primitive(self, keep_site_properties: bool = False) -> Structure:
         if keep_site_properties:
             site_properties = {}
             for key, val in self._site_props.items():
-                site_properties[key] = [val[i - 1] for i in numbers]
+                site_properties[key] = [val[self._numbers.index(i)] for i in numbers]
         else:
             site_properties = None
 

diff --git a/tests/symmetry/test_analyzer.py b/tests/symmetry/test_analyzer.py
@@ -201,6 +201,15 @@ def test_get_refined_structure(self):
         refined_struct = sg.get_refined_structure(keep_site_properties=False)
         assert refined_struct.site_properties.get("magmom") is None
 
+        structure = Structure.from_file(f"{TEST_FILES_DIR}/cif/bcc_1927.cif")
+        for site in structure:
+            site.properties["magmom"] = 1.0 if site.specie.name == "Dy" else -1.0
+        sg = SpacegroupAnalyzer(structure, symprec=1e-2)
+        refined_struct = sg.get_refined_structure(keep_site_properties=True)
+        assert len(refined_struct) != len(structure), "this test is only interesting if the number of sites changes"
+        for site in refined_struct:
+            assert (1.0 if site.specie.name == "Dy" else -1.0) == site.properties["magmom"]
+
     def test_symmetrized_structure(self):
         symm_struct = self.sg.get_symmetrized_structure()
         assert symm_struct.lattice.angles == (90, 90, 90)
@@ -246,6 +255,17 @@ def test_find_primitive(self):
         primitive_structure = spga.find_primitive(keep_site_properties=False)
         assert primitive_structure.site_properties.get("magmom") is None
 
+        structure = Structure.from_spacegroup("Fm-3m", np.eye(3) * 5.6, ["Na", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
+        for site in structure:
+            site.properties["magmom"] = 1.0 if site.specie.name == "Na" else -1.0
+        sg = SpacegroupAnalyzer(structure, symprec=1e-2)
+        primitive_structure = sg.find_primitive(keep_site_properties=True)
+        assert len(primitive_structure) != len(
+            structure
+        ), "this test is only interesting if the number of sites changes"
+        for site in primitive_structure:
+            assert (1.0 if site.specie.name == "Na" else -1.0) == site.properties["magmom"]
+
     def test_get_ir_reciprocal_mesh(self):
         grid = self.sg.get_ir_reciprocal_mesh()
         assert len(grid) == 216