is_subgroup() modifications in SpaceGroup and PointGroup (#3941)

* Modified SpaceGroup.is_subgroup() following issue #3937, added tests.

* Added crystal_system attribute to PointGroup, modified is_subgroup warning of SymmetryGroup.

* Modified is_subgroup of PointGroup to raise NotImplementedError if group subgroup relationship would be possible (fr. crystal system), but cannot be checked currently due to crystallographic direction issue.

* Enabled PointGroup init from different settings, added test for that, added missing setting differences (trigonal groups), re-enabled SpaceGroup.is_subgroup shortcut with constraint of non-klassengleiche group subgroup relationship

* Removed bug in short Hermann Mauguin symbol of some trigonal groups introduced by myself in #3859

---------

Signed-off-by: Katharina Ueltzen <[email protected]>

dev_scripts/update_spacegroup_data.py

@@ -56,6 +56,8 @@ def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
     if symbol in ("P 1", "C 1", "P 1 "):
         return symbol
     blickrichtungen = symbol.split(" ")
+    if blickrichtungen[1].startswith("3"):
+        return symbol
     blickrichtungen_new = []
     for br in blickrichtungen:
         if br != "1":
@@ -76,6 +78,11 @@ def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
 
 SYMM_DATA["space_group_encoding"] = new_symm_data
 
+for sg_symbol in SYMM_DATA["space_group_encoding"]:
+    SYMM_DATA["space_group_encoding"][sg_symbol]["point_group"] = PointGroup.from_space_group(
+        sg_symbol=sg_symbol
+    ).symbol
+
 for spg in SYMM_OPS:
     if "(" in spg["hermann_mauguin"]:
         spg["hermann_mauguin"] = spg["hermann_mauguin"].split("(")[0]

src/pymatgen/symmetry/groups.py

@@ -44,6 +44,24 @@
 
 SYMM_DATA = loadfn(os.path.join(os.path.dirname(__file__), "symm_data.json"))
 
+PG_ABBREV_MAP = {
+    "2/m2/m2/m": "mmm",
+    "4/m2/m2/m": "4/mmm",
+    "-32/m": "-3m",
+    "6/m2/m2/m": "6/mmm",
+    "2/m-3": "m-3",
+    "4/m-32/m": "m-3m",
+}
+PG_SETTINGS_MAP = {  # only one setting per crystal class in SYMM_DATA database available right now
+    "m2m": "mm2",
+    "2mm": "mm2",
+    "-4m2": "-42m",
+    "-62m": "-6m2",
+    "312": "32",
+    "31m": "3m",
+    "-31m": "-3m",
+}
+
 
 class SymmetryGroup(Sequence, Stringify, ABC):
     """Abstract class representing a symmetry group."""
@@ -86,7 +104,10 @@ def is_subgroup(self, supergroup: SymmetryGroup) -> bool:
         Returns:
             bool: True if this group is a subgroup of the supplied group.
         """
-        warnings.warn("This is not fully functional. Only trivial subsets are tested right now. ")
+        warnings.warn(
+            "This is not fully functional. Only trivial subsets are tested right now. "
+            "This will not work if the crystallographic directions of the two groups are different."
+        )
         return set(self.symmetry_ops).issubset(supergroup.symmetry_ops)
 
     def is_supergroup(self, subgroup: SymmetryGroup) -> bool:
@@ -98,7 +119,10 @@ def is_supergroup(self, subgroup: SymmetryGroup) -> bool:
         Returns:
             bool: True if this group is a supergroup of the supplied group.
         """
-        warnings.warn("This is not fully functional. Only trivial subsets are tested right now. ")
+        warnings.warn(
+            "This is not fully functional. Only trivial subsets are tested right now. "
+            "This will not work if the crystallographic directions of the two groups are different."
+        )
         return set(subgroup.symmetry_ops).issubset(self.symmetry_ops)
 
     def to_latex_string(self) -> str:
@@ -125,16 +149,23 @@ def __init__(self, int_symbol: str) -> None:
         Please note that only the 32 crystal classes are supported right now.
 
         Args:
-            int_symbol (str): International or Hermann-Mauguin Symbol.
+            int_symbol (str): International or Hermann-Mauguin Symbol. Please note that the PointGroup object
+            may have a different setting than specified in the int_symbol as only one setting per point group
+            is available right now.
         """
         from pymatgen.core.operations import SymmOp
 
+        int_symbol = int_symbol.replace(" ", "")
+        int_symbol = PG_ABBREV_MAP.get(int_symbol, int_symbol)
+        int_symbol = PG_SETTINGS_MAP.get(int_symbol, int_symbol)
+
         self.symbol = int_symbol
         self.generators = [
             SYMM_DATA["generator_matrices"][enc] for enc in SYMM_DATA["point_group_encoding"][int_symbol]
         ]
         self._symmetry_ops = {SymmOp.from_rotation_and_translation(m) for m in self._generate_full_symmetry_ops()}
         self.order = len(self._symmetry_ops)
+        self.crystal_system = SYMM_DATA["point_group_crystal_system_map"][int_symbol]
 
     @property
     def symmetry_ops(self) -> set[SymmOp]:
@@ -176,10 +207,49 @@ def get_orbit(self, p: ArrayLike, tol: float = 1e-5) -> list[np.ndarray]:
                 orbit.append(pp)
         return orbit
 
+    def is_subgroup(self, supergroup: PointGroup) -> bool:
+        """True if this group is a subgroup of the supplied group.
+            Modification of SymmetryGroup method with a few more constraints.
+
+        Args:
+            supergroup (pointGroup): Supergroup to test.
+
+        Returns:
+            bool: True if this group is a subgroup of the supplied group.
+        """
+        possible_but_direction_differences = (
+            ["trigonal", "cubic"],
+            ["monoclinic", "tetragonal"],
+            ["monoclinic", "hexagonal"],
+            ["monoclinic", "trigonal"],
+            ["orthorhombic", "hexagonal"],
+            ["orthorhombic", "tetragonal"],
+        )
+        if [self.crystal_system, supergroup.crystal_system] in possible_but_direction_differences:
+            raise NotImplementedError
+        warnings.warn(
+            "This is not fully functional. Only trivial subsets are tested right now. "
+            "This will not work if the crystallographic directions of the two groups are different."
+        )
+        return set(self.symmetry_ops).issubset(supergroup.symmetry_ops)
+
+    def is_supergroup(self, subgroup: PointGroup) -> bool:
+        """True if this group is a subgroup of the supplied group.
+            Modification of SymmetryGroup method with a few more constraints.
+
+        Args:
+            subgroup (PointGroup): Subgroup to test.
+
+        Returns:
+            bool: True if this group is a supergroup of the supplied group.
+        """
+        return subgroup.is_subgroup(self)
+
     @classmethod
     def from_space_group(cls, sg_symbol: str) -> PointGroup:
         """Instantiate one of the 32 crystal classes from a space group symbol in
         Hermann Mauguin notation (int symbol or full symbol).
+        Please note that the axes of space group and crystal class may be different.
 
         Args:
             sg_symbol: space group symbol in Hermann Mauguin notation.
@@ -190,20 +260,6 @@ def from_space_group(cls, sg_symbol: str) -> PointGroup:
         Returns:
             crystal class in Hermann-Mauguin notation.
         """
-        abbrev_map = {
-            "2/m2/m2/m": "mmm",
-            "4/m2/m2/m": "4/mmm",
-            "-32/m": "-3m",
-            "6/m2/m2/m": "6/mmm",
-            "2/m-3": "m-3",
-            "4/m-32/m": "m-3m",
-        }
-        non_standard_map = {
-            "m2m": "mm2",
-            "2mm": "mm2",
-            "-4m2": "-42m",  # technically not non-standard
-            "-62m": "-6m2",  # technically not non-standard
-        }
         symbol = re.sub(r" ", "", sg_symbol)
 
         symm_ops = loadfn(os.path.join(os.path.dirname(__file__), "symm_ops.json"))  # get short symbol if possible
@@ -223,8 +279,8 @@ def from_space_group(cls, sg_symbol: str) -> PointGroup:
         symbol = symbol[1:]  # Remove centering
         symbol = symbol.translate(str.maketrans("abcden", "mmmmmm"))  # Remove translation from glide planes
         symbol = re.sub(r"_.", "", symbol)  # Remove translation from screw axes
-        symbol = abbrev_map.get(symbol, symbol)
-        symbol = non_standard_map.get(symbol, symbol)
+        symbol = PG_ABBREV_MAP.get(symbol, symbol)
+        symbol = PG_SETTINGS_MAP.get(symbol, symbol)
 
         if symbol not in SYMM_DATA["point_group_encoding"]:
             raise ValueError(f"Could not create a valid crystal class ({symbol}) from {sg_symbol=}")
@@ -565,7 +621,7 @@ def is_subgroup(self, supergroup: SymmetryGroup) -> bool:
         if not isinstance(supergroup, SpaceGroup):
             return NotImplemented
 
-        if len(supergroup.symmetry_ops) < len(self.symmetry_ops):
+        if len(supergroup.symmetry_ops) < len(self.symmetry_ops) and supergroup.point_group != self.point_group:
             return False
 
         groups = [{supergroup.int_number}]
@@ -574,7 +630,10 @@ def is_subgroup(self, supergroup: SymmetryGroup) -> bool:
         while True:
             new_sub_groups = set()
             for i in groups[-1]:
-                new_sub_groups.update([j for j in max_subgroups[i] if j not in all_groups])
+                if len(groups) == 1:
+                    new_sub_groups.update(list(max_subgroups[i]))
+                else:
+                    new_sub_groups.update([j for j in max_subgroups[i] if j not in all_groups])
             if self.int_number in new_sub_groups:
                 return True
 

tests/symmetry/test_groups.py

@@ -56,11 +56,16 @@ def test_is_sub_super_group(self):
         pg_m3m = PointGroup("m-3m")
         pg_6mmm = PointGroup("6/mmm")
         pg_3m = PointGroup("-3m")
-        # TODO: Fix the test below.
+        # TODO: Fix the tests below.
         # assert pg3m.is_subgroup(pgm3m)
+        # assert PointGroup("32").is_subgroup(PointGroup("-6m2"))
         assert pg_3m.is_subgroup(pg_6mmm)
         assert not pg_m3m.is_supergroup(pg_6mmm)
 
+    def test_init_different_settings_and_full_notation(self):
+        PointGroup("2/m 2/m 2/m")
+        PointGroup("31m")
+
     def test_from_space_group(self):
         assert PointGroup.from_space_group("P 2_1/n2_1/m2_1/a").symbol == "mmm"
         assert PointGroup.from_space_group("F d d d").symbol == "mmm"
@@ -227,6 +232,8 @@ def test_other_settings(self):
     def test_subgroup_supergroup(self):
         assert SpaceGroup("Pma2").is_subgroup(SpaceGroup("Pccm"))
         assert not SpaceGroup.from_int_number(229).is_subgroup(SpaceGroup.from_int_number(230))
+        assert SpaceGroup("P3").is_subgroup(SpaceGroup("P3"))  # Added after #3937
+        assert SpaceGroup("Fm-3m").is_subgroup(SpaceGroup("Pm-3m"))  # Added after #3937
 
     def test_hexagonal(self):
         for num in (146, 148, 155, 160, 161, 166, 167):