Merge branch 'materialsproject:master' into master

gmatteo · Jul 31, 2024 · 1d315a5 · 1d315a5
2 parents 35260ee + 660ba7a
commit 1d315a5
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Showing 17 changed files with 21,055 additions and 6 deletions.
diff --git a/src/pymatgen/core/ion.py b/src/pymatgen/core/ion.py
@@ -173,9 +173,10 @@ def get_reduced_formula_and_factor(
         el_amt_dict = {k: int(round(v)) for k, v in comp.get_el_amt_dict().items()}
         formula, factor = reduce_formula(el_amt_dict, iupac_ordering=iupac_ordering)
 
-        if (self.composition.get("H") and self.composition.get("O")) is not None:
+        # This line checks specifically that the contains an equal amount of O and H. When that is the case,
+        # they should be displayed as "OH" rather than "HO".
+        if self.composition.get("H") == self.composition.get("O"):
             formula = formula.replace("HO", "OH")
-
         if nH2O > 0:
             formula += f".{nH2O}H2O"
 
@@ -187,6 +188,13 @@ def get_reduced_formula_and_factor(
         elif formula == "H2CO":
             formula = "CH3COOH"
             factor /= 2
+        # phosphoric acid system
+        elif formula == "PH3O4":
+            formula = "H3PO4"
+        elif formula == "PHO4":
+            formula = "HPO4"
+        elif formula == "P(HO2)2":
+            formula = "H2PO4"
         # acetate
         elif formula == "H3(CO)2":
             formula = "CH3COO"
@@ -205,6 +213,29 @@ def get_reduced_formula_and_factor(
         elif formula == "O" and factor % 3 == 0:
             formula = "O3"
             factor /= 3
+        # ammonia
+        elif formula == "H4N":
+            formula = "NH4"
+        elif formula == "H3N":
+            formula = "NH3"
+        # methane
+        elif formula == "H4C":
+            formula = "CH4"
+        # thiocyanate
+        elif formula == "CSN":
+            formula = "SCN"
+        # triiodide, nitride, an phosphide
+        elif formula in ["I", "N", "P"] and self.charge == -1:
+            formula += "3"
+            factor /= 3
+        # formate # codespell:ignore
+        elif formula == "HCOO":
+            formula = "HCO2"
+        # oxalate
+        elif formula == "CO2":
+            formula = "C2O4"
+            factor *= 2
+        # diatomic gases
         elif formula in {"O", "N", "F", "Cl", "H"} and factor % 2 == 0:
             formula += "2"
             factor /= 2

diff --git a/src/pymatgen/core/structure.py b/src/pymatgen/core/structure.py
@@ -1874,7 +1874,7 @@ def get_symmetric_neighbor_list(
                         redundant.append(jdx)
 
             # Delete the redundant neighbors
-            m = ~np.in1d(np.arange(len(bonds[0])), redundant)
+            m = ~np.isin(np.arange(len(bonds[0])), redundant)
             idcs_dist = np.argsort(bonds[3][m])
             bonds = (bonds[0][m][idcs_dist], bonds[1][m][idcs_dist], bonds[2][m][idcs_dist], bonds[3][m][idcs_dist])