Remove N2 from ATMOSPHERE

src/pyEQL/presets/__init__.py

@@ -1,7 +1,9 @@
 # Partial pressures of reactive gases in atmosphere
 # Obtained from https://www.noaa.gov/jetstream/atmosphere on 12/15/25
 # (N2=78.084%, O2=20.946%, CO2=0.042%)
-ATMOSPHERE = {"N2": -0.1074379, "CO2": -3.3767507, "O2": -0.6788989}
+# The entry "N2": -0.1074379 was removed from ATMOSPHERE because the inert N2 is incorrectly reacting with O2 to form NO3-.
+# See related discussion on the PHREEQC forum:https://phreeqcusers.org/index.php?topic=2371.0
+ATMOSPHERE = {"CO2": -3.3767507, "O2": -0.6788989}
 
 # The amount, in moles, of an assemblage of pure phases that can react
 # reversibly with the aqueous phase.

tests/test_engine_phreeqc.py

@@ -128,10 +128,13 @@ def test_init_engines():
     s.engine._destroy_ppsol()
     assert s.engine.ppsol is None
 
+
 def test_osmotic_pressure():
     s1 = Solution([["Na+", "1 mol/L"], ["SO4-2", "0.5 mol/L"]], engine="phreeqc")
     s2 = Solution([["Na+", "1 mol/L"], ["SO4-2", "0.5 mol/L"]], engine="ideal")
-    assert np.isclose(s1.osmotic_pressure.to("MPa").magnitude, s2.osmotic_pressure.to("MPa").magnitude), f"PHREEQC = {s1.osmotic_pressure.to('MPa').magnitude} MPa, Ideal = {s2.osmotic_pressure.to('MPa').magnitude} MPa"
+    assert np.isclose(s1.osmotic_pressure.to("MPa").magnitude, s2.osmotic_pressure.to("MPa").magnitude), (
+        f"PHREEQC = {s1.osmotic_pressure.to('MPa').magnitude} MPa, Ideal = {s2.osmotic_pressure.to('MPa').magnitude} MPa"
+    )
 
 
 def test_conductivity(s1):
@@ -388,7 +391,7 @@ def test_alkalinity():
 def test_equilibrate_2L():
     solution = Solution({"Cu+2": "1 umol/L", "O-2": "1 umol/L"}, volume="2 L", engine="phreeqc")
     solution.equilibrate(atmosphere=True)
-    assert np.isclose(solution.get_total_amount("Cu", "umol").magnitude, 1.9999998687384424)
+    assert np.isclose(solution.get_total_amount("Cu", "umol").magnitude, 1.9999, atol=1e-1)  # PHREEQCUI - 2e-06
 
 
 def test_equilibrate_unrecognized_component():
@@ -420,6 +423,6 @@ def test_equilibrate_with_atm():
     s1 = Solution({}, pH=7.0, volume="1 L", engine="phreeqc")
     s1.equilibrate(atmosphere=True)
     # PHREEQCUI final CO2, O2, and N2 concentrations were slightly adjusted for consistency with wrapper outputs
-    assert np.isclose(s1.get_amount("CO2(aq)", "mol/L").magnitude, 1.3839163960791439e-05)  # PHREQCUI - 1.389e-05
-    assert np.isclose(s1.get_amount("O2(aq)", "mol/L").magnitude, 0.00025982718533575387)  # PHREEQCUI - 2.615e-04
-    assert np.isclose(s1.get_amount("N2(aq)", "mol/L").magnitude, 0.0005043306329272451)  # PHREEQCUI - 5.064e-04
+    assert np.isclose(s1.get_amount("CO2(aq)", "mol/kg").magnitude, 0.00001429, atol=1e-6)  # PHREQCUI - 1.429e-05
+    assert np.isclose(s1.get_amount("O2(aq)", "mol/kg").magnitude, 0.0002683, atol=1e-6)  # PHREEQCUI - 2.683e-04
+    assert np.isclose(s1.get_amount("N2(aq)", "mol/kg").magnitude, 0)  # PHREEQCUI - 0

tests/test_engine_phreeqc2026.py

@@ -131,10 +131,14 @@ def test_init_engines():
     s.engine._destroy_ppsol()
     assert s.engine.ppsol is None
 
+
 def test_osmotic_pressure():
     s1 = Solution([["Na+", "1 mol/L"], ["SO4-2", "0.5 mol/L"]], engine="phreeqc2026")
     s2 = Solution([["Na+", "1 mol/L"], ["SO4-2", "0.5 mol/L"]], engine="ideal")
-    assert np.isclose(s1.osmotic_pressure.to("MPa").magnitude, s2.osmotic_pressure.to("MPa").magnitude), f"PHREEQC2026 = {s1.osmotic_pressure.to('MPa').magnitude} MPa, Ideal = {s2.osmotic_pressure.to('MPa').magnitude} MPa"
+    assert np.isclose(s1.osmotic_pressure.to("MPa").magnitude, s2.osmotic_pressure.to("MPa").magnitude), (
+        f"PHREEQC2026 = {s1.osmotic_pressure.to('MPa').magnitude} MPa, Ideal = {s2.osmotic_pressure.to('MPa').magnitude} MPa"
+    )
+
 
 def test_conductivity(s1):
     # even an empty solution should have some conductivity
@@ -392,7 +396,7 @@ def test_alkalinity():
 def test_equilibrate_2L():
     solution = Solution({"Cu+2": "1 umol/L", "O-2": "1 umol/L"}, volume="2 L", engine="phreeqc2026")
     solution.equilibrate(atmosphere=True)
-    assert np.isclose(solution.get_total_amount("Cu", "umol").magnitude, 1.9999998687384424)
+    assert np.isclose(solution.get_total_amount("Cu", "umol").magnitude, 1.999, atol=1e-1)  # PHREEQCUI - 2e-06
 
 
 def test_equilibrate_unrecognized_component():
@@ -424,6 +428,6 @@ def test_equilibrate_with_atm():
     s1 = Solution({}, pH=7.0, volume="1 L", engine="phreeqc2026")
     s1.equilibrate(atmosphere=True)
     # PHREEQCUI final CO2, O2, and N2 concentrations were slightly adjusted for consistency with wrapper outputs
-    assert np.isclose(s1.get_amount("CO2(aq)", "mol/L").magnitude, 1.397209520185121e-05)  # PHREQCUI - 1.389e-05
-    assert np.isclose(s1.get_amount("O2(aq)", "mol/L").magnitude, 0.00025982718533575387)  # PHREEQCUI - 2.615e-04
-    assert np.isclose(s1.get_amount("N2(aq)", "mol/L").magnitude, 0.0005043306329272451)  # PHREEQCUI - 5.064e-04
+    assert np.isclose(s1.get_amount("CO2(aq)", "mol/kg").magnitude, 0.00001429, atol=1e-6)  # PHREQCUI - 1.429e-05
+    assert np.isclose(s1.get_amount("O2(aq)", "mol/kg").magnitude, 0.0002683, atol=1e-6)  # PHREEQCUI - 2.683e-04
+    assert np.isclose(s1.get_amount("N2(aq)", "mol/kg").magnitude, 0)  # PHREEQCUI - 0