Fix apply_operation(fractional=True) (#4057)

* Fix `apply_operation(fractional=True)` * Add tests for `apply_operation` * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
materialsproject · Sep 9, 2024 · ed4de1d · ed4de1d
1 parent dc6a292
commit ed4de1d
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Showing 2 changed files with 24 additions and 2 deletions.
diff --git a/src/pymatgen/core/structure.py b/src/pymatgen/core/structure.py
@@ -4297,8 +4297,9 @@ def apply_operation(self, symm_op: SymmOp, fractional: bool = False) -> Self:
             def operate_site(site):
                 return PeriodicSite(
                     site.species,
-                    symm_op.operate(site.frac_coords),
+                    site.lattice.get_cartesian_coords(symm_op.operate(site.frac_coords)),
                     self._lattice,
+                    coords_are_cartesian=True,
                     properties=site.properties,
                     skip_checks=True,
                     label=site.label,

diff --git a/tests/core/test_structure.py b/tests/core/test_structure.py
@@ -1237,19 +1237,40 @@ def test_add_remove_spin_states(self):
     def test_apply_operation(self):
         op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
         struct = self.struct.copy()
+        spg_info = struct.get_space_group_info()
         returned = struct.apply_operation(op)
         assert returned is struct
         assert_allclose(
             struct.lattice.matrix,
             [[0, 3.840198, 0], [-3.325710, 1.920099, 0], [2.217138, -0, 3.135509]],
             atol=1e-6,
         )
+        assert returned.get_space_group_info() == spg_info
 
-        op = SymmOp([[1, 1, 0, 0.5], [1, 0, 0, 0.5], [0, 0, 1, 0.5], [0, 0, 0, 1]])
+        op = SymmOp([[1, 1, 0, 0.5], [1, 0, 0, 0.5], [0, 0, 1, 0.5], [0, 0, 0, 1]])  # not a SymmOp of this struct
         struct = self.struct.copy()
         struct.apply_operation(op, fractional=True)
         assert_allclose(struct.lattice.matrix, [[5.760297, 3.325710, 0], [3.840198, 0, 0], [0, -2.217138, 3.135509]], 5)
 
+        struct = self.struct.copy()
+        # actual SymmOp of this struct: (SpacegroupAnalyzer(struct).get_symmetry_operations()[-2])
+        op = SymmOp([[0.0, 0.0, -1.0, 0.75], [-1.0, -1.0, 1.0, 0.5], [0.0, -1.0, 1.0, 0.75], [0.0, 0.0, 0.0, 1.0]])
+        struct.apply_operation(op, fractional=True)
+        assert struct.get_space_group_info() == spg_info
+
+        # same SymmOp in Cartesian coordinates:
+        op = SymmOp(
+            [
+                [-0.5, -0.288675028, -0.816496280, 3.84019793],
+                [-0.866025723, 0.166666176, 0.471404694, 0],
+                [0, -0.942808868, 0.333333824, 2.35163180],
+                [0, 0, 0, 1.0],
+            ]
+        )
+        struct = self.struct.copy()
+        struct.apply_operation(op, fractional=False)
+        assert struct.get_space_group_info() == spg_info
+
     def test_apply_strain(self):
         struct = self.struct
         initial_coord = struct[1].coords