From 34ff05aca8f59309c86d6339fe910e47d8849382 Mon Sep 17 00:00:00 2001
From: Ryan Kingsbury <rkingsbury@users.noreply.github.com>
Date: Sat, 20 Jul 2024 09:33:31 -0400
Subject: [PATCH] Ion: special handling of CH4, NH4, N3-, SCN-, formate,
 oxalate

---
 src/pymatgen/core/ion.py | 32 ++++++++++++++++++++++++++++++--
 tests/core/test_ion.py   |  9 ++++++++-
 2 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/src/pymatgen/core/ion.py b/src/pymatgen/core/ion.py
index 7ba9ceabaff..439617fdfcb 100644
--- a/src/pymatgen/core/ion.py
+++ b/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
diff --git a/tests/core/test_ion.py b/tests/core/test_ion.py
index 52aaa199b05..3b59a461664 100644
--- a/tests/core/test_ion.py
+++ b/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)"),