Reset label for sites changed by Structure.replace_species() (#3672)

* Reset label in `Structure.replace_species()`

* Add test for partial occupancy

* avoid needless trailing zeros in Site.species_string float formatting

* fix partial occu replacement test

* fix expected Si Site in test_str

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

pymatgen/analysis/phase_diagram.py

@@ -1905,8 +1905,8 @@ def __init__(self, entry1, entry2, all_entries, tol: float = 1e-4, float_fmt="%.
                 number of decimal places in reaction string. Defaults to "%.4f".
         """
         elem_set = set()
-        for ent in [entry1, entry2]:
-            elem_set.update([el.symbol for el in ent.elements])
+        for entry in [entry1, entry2]:
+            elem_set.update([el.symbol for el in entry.elements])
 
         elements = tuple(elem_set)  # Fix elements to ensure order.
 
@@ -1939,8 +1939,8 @@ def fmt(fl):
 
                 try:
                     mat = []
-                    for ent in face_entries:
-                        mat.append([ent.composition.get_atomic_fraction(el) for el in elements])
+                    for entry in face_entries:
+                        mat.append([entry.composition.get_atomic_fraction(el) for el in elements])
                     mat.append(comp_vec2 - comp_vec1)
                     matrix = np.array(mat).T
                     coeffs = np.linalg.solve(matrix, comp_vec2)
@@ -1967,12 +1967,12 @@ def fmt(fl):
 
                         energy = -(x * entry1.energy_per_atom + (1 - x) * entry2.energy_per_atom)
 
-                        for c, ent in zip(coeffs[:-1], face_entries):
+                        for c, entry in zip(coeffs[:-1], face_entries):
                             if c > tol:
-                                r = ent.composition.reduced_composition
+                                r = entry.composition.reduced_composition
                                 products.append(f"{fmt(c / r.num_atoms * factor)} {r.reduced_formula}")
-                                product_entries.append((c, ent))
-                                energy += c * ent.energy_per_atom
+                                product_entries.append((c, entry))
+                                energy += c * entry.energy_per_atom
 
                         rxn_str += " + ".join(products)
                         comp = x * comp_vec1 + (1 - x) * comp_vec2
@@ -1995,9 +1995,9 @@ def fmt(fl):
         self.entry2 = entry2
         self.rxn_entries = rxn_entries
         self.labels = {}
-        for i, ent in enumerate(rxn_entries):
-            self.labels[str(i + 1)] = ent.attribute
-            ent.name = str(i + 1)
+        for idx, entry in enumerate(rxn_entries):
+            self.labels[str(idx + 1)] = entry.attribute
+            entry.name = str(idx + 1)
         self.all_entries = all_entries
         self.pd = pd
 

pymatgen/core/sites.py

@@ -101,7 +101,7 @@ def label(self) -> str:
         return self._label if self._label is not None else self.species_string
 
     @label.setter
-    def label(self, label: str) -> None:
+    def label(self, label: str | None) -> None:
         self._label = label
 
     @property
@@ -158,8 +158,7 @@ def species_string(self) -> str:
         """String representation of species on the site."""
         if self.is_ordered:
             return str(next(iter(self.species)))
-        sorted_species = sorted(self.species)
-        return ", ".join(f"{sp}:{self.species[sp]:.3f}" for sp in sorted_species)
+        return ", ".join(f"{sp}:{self.species[sp]:.3}" for sp in sorted(self.species))
 
     @property
     def specie(self) -> Element | Species | DummySpecies:

pymatgen/core/structure.py

@@ -528,11 +528,13 @@ def replace_species(
     ) -> SiteCollection:
         """Swap species.
 
+        Note that this clears the label of any affected site.
+
         Args:
             species_mapping (dict): Species to swap. Species can be elements too. E.g.,
                 {Element("Li"): Element("Na")} performs a Li for Na substitution. The second species can
                 be a sp_and_occu dict. For example, a site with 0.5 Si that is passed the mapping
-                {Element('Si): {Element('Ge'): 0.75, Element('C'): 0.25} } will have .375 Ge and .125 C.
+                {Element('Si'): {Element('Ge'): 0.75, Element('C'): 0.25} } will have .375 Ge and .125 C.
             in_place (bool): Whether to perform the substitution in place or modify a copy.
                 Defaults to True.
 
@@ -559,6 +561,7 @@ def replace_species(
                     except Exception:
                         comp += {new_sp: amt}
                 site.species = comp
+                site.label = None  # type: ignore
 
         return site_coll
 

tests/core/test_sites.py

@@ -226,7 +226,7 @@ def test_repr(self):
 
     def test_str(self):
         assert str(self.site) == "[2.5 3.5 4.5] Fe"
-        assert str(self.site2) == "[0. 0. 0.] Si:0.500"
+        assert str(self.site2) == "[0. 0. 0.] Si:0.5"
         assert str(self.propertied_site) == "[2.5 3.5 4.5] Fe2+"
         assert str(self.labeled_site) == "[2.5 3.5 4.5] Fe"
 

tests/core/test_structure.py

@@ -977,6 +977,17 @@ def test_replace_species(self):
         assert struct.formula == "K1.5 P0.5"
         assert new_struct.formula == "Li1.5 P0.5"
 
+    def test_replace_species_labels(self):
+        """https://github.com/materialsproject/pymatgen/issues/3658"""
+        struct = self.labeled_structure
+        new1 = struct.replace_species({"Si": "Ge"}, in_place=False)
+        assert new1.labels == ["Ge", "Ge"]
+
+        replacement = {"Si": 0.5, "Ge": 0.5}
+        label = ", ".join(f"{key}:{val:.3}" for key, val in replacement.items())
+        new2 = struct.replace_species({"Si": replacement}, in_place=False)
+        assert new2.labels == [label] * len(struct)
+
     def test_append_insert_remove_replace_substitute(self):
         struct = self.struct
         struct.insert(1, "O", [0.5, 0.5, 0.5])