Add method to get the Pearson symbol to SpaceGroupAnalyzer (#4281)

* fea: add method to get the pearson symbol

* test: test the pearson symbols

* clean: clean and comment sga tests

* fix: LiPo4 actually FePO4

* fix linting and supress warning.

---------

Signed-off-by: Matthew Horton <[email protected]>
Co-authored-by: Matthew Horton <[email protected]>
Co-authored-by: Shyue Ping Ong <[email protected]>

Author: 3 people

src/pymatgen/analysis/local_env.py

@@ -3745,25 +3745,28 @@ def get_nn_info(self, structure: Structure, n: int):
 
         if self.use_fictive_radius:
             # calculate fictive ionic radii
-            fict_ionic_radii = [_get_fictive_ionic_radius(site, neighbor) for neighbor in neighbors]
+            fictive_ionic_radii = [_get_fictive_ionic_radius(site, neighbor) for neighbor in neighbors]
         else:
             # just use the bond distance
-            fict_ionic_radii = [neighbor.nn_distance for neighbor in neighbors]
+            fictive_ionic_radii = [neighbor.nn_distance for neighbor in neighbors]
 
         # calculate mean fictive ionic radius
-        mefir = _get_mean_fictive_ionic_radius(fict_ionic_radii)
+        mean_fictive_ionic_radius = _get_mean_fictive_ionic_radius(fictive_ionic_radii)
 
         # iteratively solve MEFIR; follows equation 4 in Hoppe's EconN paper
-        prev_mefir = float("inf")
-        while abs(prev_mefir - mefir) > 1e-4:
+        prev_mean_fictive_ionic_radius = float("inf")
+        while abs(prev_mean_fictive_ionic_radius - mean_fictive_ionic_radius) > 1e-4:
             # this is guaranteed to converge
-            prev_mefir = mefir
-            mefir = _get_mean_fictive_ionic_radius(fict_ionic_radii, minimum_fir=mefir)
+            prev_mean_fictive_ionic_radius = mean_fictive_ionic_radius
+            mean_fictive_ionic_radius = _get_mean_fictive_ionic_radius(
+                fictive_ionic_radii,
+                minimum_fir=mean_fictive_ionic_radius,
+            )
 
         siw = []
-        for nn, fir in zip(neighbors, fict_ionic_radii, strict=True):
+        for nn, fictive_ionic_radius in zip(neighbors, fictive_ionic_radii, strict=True):
             if nn.nn_distance < self.cutoff:
-                w = math.exp(1 - (fir / mefir) ** 6)
+                w = math.exp(1 - (fictive_ionic_radius / mean_fictive_ionic_radius) ** 6)
                 if w > self.tol:
                     bonded_site = {
                         "site": nn,

src/pymatgen/symmetry/analyzer.py

@@ -246,6 +246,29 @@ def get_lattice_type(self) -> LatticeType:
             return "rhombohedral"
         return "hexagonal" if system == "trigonal" else system
 
+    def get_pearson_symbol(self) -> str:
+        """Get the Pearson symbol for the structure.
+
+        Returns:
+            str: Pearson symbol for structure.
+        """
+        cry_sys = self.get_crystal_system()
+        spg_sym = self.get_space_group_symbol()
+        centering = "C" if spg_sym[0] in ("A", "B", "C", "S") else spg_sym[0]
+
+        CRYSTAL_FAMILY_SYMBOLS = {
+            "triclinic": "a",
+            "monoclinic": "m",
+            "orthorhombic": "o",
+            "tetragonal": "t",
+            "trigonal": "h",
+            "hexagonal": "h",
+            "cubic": "c",
+        }
+
+        num_sites_conventional = len(self._space_group_data.std_types)
+        return f"{CRYSTAL_FAMILY_SYMBOLS[cry_sys]}{centering}{num_sites_conventional}"
+
     def get_symmetry_dataset(self) -> SpglibDataset:
         """Get the symmetry dataset as a SpglibDataset.
 

tests/symmetry/test_analyzer.py

@@ -26,19 +26,25 @@
 
 class TestSpacegroupAnalyzer(PymatgenTest):
     def setUp(self):
+        # FePO4
         self.structure = Structure.from_file(f"{VASP_IN_DIR}/POSCAR")
         self.sg = SpacegroupAnalyzer(self.structure, 0.001)
+
+        # Li10GeP2S12
         self.disordered_structure = self.get_structure("Li10GeP2S12")
         self.disordered_sg = SpacegroupAnalyzer(self.disordered_structure, 0.001)
+
+        # FePO4 with order of sites changed so the atoms aren't grouped by element.
         struct = self.structure.copy()
         site = struct[0]
         del struct[0]
         struct.append(site.species, site.frac_coords)
         self.sg3 = SpacegroupAnalyzer(struct, 0.001)
-        graphite = self.get_structure("Graphite")
-        graphite.add_site_property("magmom", [0.1] * len(graphite))
-        self.sg4 = SpacegroupAnalyzer(graphite, 0.001)
-        self.structure4 = graphite
+
+        # Graphite
+        self.structure4 = self.get_structure("Graphite")
+        self.structure4.add_site_property("magmom", [0.1] * len(self.structure4))
+        self.sg4 = SpacegroupAnalyzer(self.structure4, 0.001)
 
     def test_primitive(self):
         struct = Structure.from_spacegroup("Fm-3m", np.eye(3) * 3, ["Cu"], [[0, 0, 0]])
@@ -49,9 +55,7 @@ def test_primitive(self):
     def test_is_laue(self):
         struct = Structure.from_spacegroup("Fm-3m", np.eye(3) * 3, ["Cu"], [[0, 0, 0]])
         assert SpacegroupAnalyzer(struct).is_laue()
-
         assert self.sg.is_laue()
-
         assert self.disordered_sg.is_laue()
 
     def test_magnetic(self):
@@ -86,6 +90,12 @@ def test_get_pointgroup(self):
         assert self.sg.get_point_group_symbol() == "mmm"
         assert self.disordered_sg.get_point_group_symbol() == "4/mmm"
 
+    def test_get_pearson_symbol(self):
+        assert self.sg.get_pearson_symbol() == "oP24"
+        assert self.disordered_sg.get_pearson_symbol() == "tP58"
+        assert self.sg3.get_pearson_symbol() == "oP24"
+        assert self.sg4.get_pearson_symbol() == "hP4"
+
     def test_get_point_group_operations(self):
         sg: SpacegroupAnalyzer
         rng = np.random.default_rng()