(Structure|Molecule).alphabetical_formula (#3478)

* fix AssertionError assert structure  # for mypy

        if temperature and not structure:
            raise ValueError("If using temperature input, you must also include structure")

* Add alphabetical_formula property to
SiteCollection class

* add TestIStructure.test_alphabetical_formula

* Update PBE64Base.yaml hash in test_sets.py

pymatgen/analysis/elasticity/elastic.py

@@ -599,7 +599,6 @@ def get_tgt(self, temperature: float | None = None, structure: Structure = None,
         """
         if temperature and not structure:
             raise ValueError("If using temperature input, you must also include structure")
-        assert structure  # for mypy
 
         quad = quad or DEFAULT_QUAD
         points = quad["points"]
@@ -611,7 +610,7 @@ def get_tgt(self, temperature: float | None = None, structure: Structure = None,
             us = [u / np.linalg.norm(u) for u in np.transpose(us)]
             for u in us:
                 # TODO: this should be benchmarked
-                if temperature:
+                if temperature and structure:
                     c = self.get_heat_capacity(temperature, structure, p, u)
                 num += c * self.get_ggt(p, u) * w
                 denom += c * w

pymatgen/core/structure.py

@@ -357,6 +357,11 @@ def formula(self) -> str:
         """Returns the formula as a string."""
         return self.composition.formula
 
+    @property
+    def alphabetical_formula(self) -> str:
+        """Returns the formula as a string."""
+        return self.composition.alphabetical_formula
+
     @property
     def elements(self) -> list[Element | Species | DummySpecies]:
         """Returns the elements in the structure as a list of Element objects."""

pymatgen/core/units.py

@@ -207,10 +207,10 @@ def __pow__(self, i):
     def __iter__(self):
         return iter(self._unit)
 
-    def __getitem__(self, i):
+    def __getitem__(self, i) -> int:
         return self._unit[i]
 
-    def __len__(self):
+    def __len__(self) -> int:
         return len(self._unit)
 
     def __repr__(self):
@@ -254,16 +254,16 @@ def get_conversion_factor(self, new_unit):
         Args:
             new_unit: The new unit.
         """
-        uo_base, ofactor = self.as_base_units
-        un_base, nfactor = Unit(new_unit).as_base_units
-        units_new = sorted(un_base.items(), key=lambda d: _UNAME2UTYPE[d[0]])
-        units_old = sorted(uo_base.items(), key=lambda d: _UNAME2UTYPE[d[0]])
-        factor = ofactor / nfactor
-        for uo, un in zip(units_old, units_new):
-            if uo[1] != un[1]:
-                raise UnitError(f"Units {uo} and {un} are not compatible!")
-            c = ALL_UNITS[_UNAME2UTYPE[uo[0]]]
-            factor *= (c[uo[0]] / c[un[0]]) ** uo[1]
+        old_base, old_factor = self.as_base_units
+        new_base, new_factor = Unit(new_unit).as_base_units
+        units_new = sorted(new_base.items(), key=lambda d: _UNAME2UTYPE[d[0]])
+        units_old = sorted(old_base.items(), key=lambda d: _UNAME2UTYPE[d[0]])
+        factor = old_factor / new_factor
+        for old, new in zip(units_old, units_new):
+            if old[1] != new[1]:
+                raise UnitError(f"Units {old} and {new} are not compatible!")
+            c = ALL_UNITS[_UNAME2UTYPE[old[0]]]
+            factor *= (c[old[0]] / c[new[0]]) ** old[1]
         return factor
 
 

tests/core/test_structure.py

@@ -84,6 +84,7 @@ def setUp(self):
             [[3.8401979337, 0, 0], [1.9200989668, 3.3257101909, 0], [0, -2.2171384943, 3.1355090603]],
             pbc=(True, True, False),
         )
+        self.V2O3 = IStructure.from_file(f"{TEST_FILES_DIR}/V2O3.cif")
 
     @skipIf(not (mcsqs_cmd and enum_cmd), "enumlib or mcsqs executable not present")
     def test_get_orderings(self):
@@ -145,6 +146,13 @@ def test_formula(self):
         assert self.struct.formula == "Si2"
         assert self.labeled_structure.formula == "Si2"
         assert self.propertied_structure.formula == "Si2"
+        assert self.V2O3.formula == "V4 O6"
+
+    def test_alphabetical_formula(self):
+        assert self.struct.alphabetical_formula == "Si2"
+        assert self.labeled_structure.alphabetical_formula == "Si2"
+        assert self.propertied_structure.alphabetical_formula == "Si2"
+        assert self.V2O3.alphabetical_formula == "O6 V4"
 
     def test_elements(self):
         assert self.struct.elements == [Element("Si")]

tests/io/vasp/test_sets.py

@@ -120,7 +120,7 @@ def test_sets_changed(self):
             "MVLGWSet.yaml": "104ae93c3b3be19a13b0ee46ebdd0f40ceb96597",
             "MVLRelax52Set.yaml": "4cfc6b1bd0548e45da3bde4a9c65b3249da13ecd",
             "PBE54Base.yaml": "ec317781a7f344beb54c17a228db790c0eb49282",
-            "PBE64Base.yaml": "a0d6cd02c6ff8e24b0005e30c56a33b155c2280b",
+            "PBE64Base.yaml": "480c41c2448cb25706181de268090618e282b264",
             "VASPIncarBase.yaml": "19762515f8deefb970f2968fca48a0d67f7964d4",
             "vdW_parameters.yaml": "04bb09bb563d159565bcceac6a11e8bdf0152b79",
         }