Ion: special handling of CH4, NH4, N3-, SCN-, formate, oxalate

src/pymatgen/core/ion.py

@@ -7,6 +7,7 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
+
 from pymatgen.core.composition import Composition, reduce_formula
 from pymatgen.util.string import Stringify, charge_string, formula_double_format
 
@@ -173,8 +174,9 @@ 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)
 
- # 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")):
+ # 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:
@@ -213,6 +215,32 @@ def get_reduced_formula_and_factor(
  elif formula == "O" and factor % 3 == 0:
  formula = "O3"
  factor /= 3
+ # ammonia
+ elif formula == "H4N[+1]":
+ formula = "NH4[+1]"
+ elif formula == "H3N(aq)":
+ formula = "NH3(aq)"
+ # methane
+ elif formula == "H4C(aq)":
+ formula = "CH4(aq)"
+ # thiocyanate
+ elif formula == "CSN[-1]":
+ formula = "SCN[-1]"
+ # triiodide, nitride, an phosphide
+ elif formula == "I[-0.33333333]":
+ formula = "I3[-1]"
+ elif formula == "N[-0.33333333]":
+ formula = "N3[-1]"
+ elif formula == "P[-0.33333333]":
+ formula = "P[-1]"
+ # formate # codespell:ignore
+ elif formula == "HCOO[-1]":
+ formula = "HCO2[-1]"
+ # oxalate
+ elif formula == "CO2[-1]":
+ formula = "C2O4[-2]"
+
+ # diatomic gases
  elif formula in {"O", "N", "F", "Cl", "H"} and factor % 2 == 0:
  formula += "2"
  factor /= 2

tests/core/test_ion.py

@@ -4,7 +4,9 @@
 from unittest import TestCase
 
 import pytest
-from pymatgen.core import Composition, Element
+
+from pymatgen.core.composition import Composition
+from pymatgen.core.element import Element
 from pymatgen.core.ion import Ion
 
 
@@ -66,6 +68,11 @@ def test_special_formulas(self):
  ("CH3COOH", "CH3COOH(aq)"),
  ("CH3OH", "CH3OH(aq)"),
  ("H4CO", "CH3OH(aq)"),
+ ("CH4", "CH4(aq)"),
+ ("NH4", "NH4[+1]"),
+ ("NH3", "NH3(aq)"),
+ ("N3-", "N3[-1]"),
+ ("HCOO-", "HCOO[-1]"),
  ("C2H6O", "C2H5OH(aq)"),
  ("C3H8O", "C3H7OH(aq)"),
  ("C4H10O", "C4H9OH(aq)"),