Merge a53744e into 9953bbe

materialsproject · May 14, 2021 · 6e3fd1f · 6e3fd1f
2 parents 9953bbe + a53744e
commit 6e3fd1f
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Showing 3 changed files with 21 additions and 15 deletions.
diff --git a/pymatgen/analysis/tests/test_pourbaix_diagram.py b/pymatgen/analysis/tests/test_pourbaix_diagram.py
@@ -206,6 +206,17 @@ def test_get_decomposition(self):
         ph, v = np.meshgrid(np.linspace(0, 14), np.linspace(-3, 3))
         self.pbx.get_decomposition_energy(entry, ph, v)
 
+        # Test custom ions
+        entries = self.test_data["C-Na-Sn"]
+        ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
+        custom_ion_entry = PourbaixEntry(ion, entry_id="my_ion")
+        pbx = PourbaixDiagram(
+            entries + [custom_ion_entry],
+            filter_solids=True,
+            comp_dict={"Na": 1, "Sn": 12, "C": 24},
+        )
+        self.assertAlmostEqual(pbx.get_decomposition_energy(custom_ion_entry, 5, 2), 2.1209002582, 1)
+
     def test_get_stable_entry(self):
         entry = self.pbx.get_stable_entry(0, 0)
         self.assertEqual(entry.entry_id, "ion-0")
@@ -284,18 +295,7 @@ def test_mpr_pipeline(self):
         pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Ag": 1e-8, "Te": 1e-8})
         self.assertEqual(len(pbx.stable_entries), 29)
         test_entry = pbx.find_stable_entry(8, 2)
-        self.assertAlmostEqual(test_entry.energy, 2.3894017960000009, 1)
-
-        # Test custom ions
-        entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
-        ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
-        custom_ion_entry = PourbaixEntry(ion, entry_id="my_ion")
-        pbx = PourbaixDiagram(
-            entries + [custom_ion_entry],
-            filter_solids=True,
-            comp_dict={"Na": 1, "Sn": 12, "C": 24},
-        )
-        self.assertAlmostEqual(pbx.get_decomposition_energy(custom_ion_entry, 5, 2), 2.1209002582, 1)
+        self.assertEqual(sorted(test_entry.entry_id), ["ion-10", "mp-499"])
 
         # Test against ion sets with multiple equivalent ions (Bi-V regression)
         entries = mpr.get_pourbaix_entries(["Bi", "V"])

diff --git a/pymatgen/ext/matproj.py b/pymatgen/ext/matproj.py
@@ -564,7 +564,10 @@ def get_entries(
         if compatible_only:
             from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
 
-            entries = MaterialsProject2020Compatibility().process_entries(entries)
+            # suppress the warning about missing oxidation states
+            with warnings.catch_warnings():
+                warnings.filterwarnings("ignore", message="Failed to guess oxidation states.*")
+                entries = MaterialsProject2020Compatibility().process_entries(entries, clean=True)
         if sort_by_e_above_hull:
             entries = sorted(entries, key=lambda entry: entry.data["e_above_hull"])
         return entries
@@ -629,7 +632,10 @@ def get_pourbaix_entries(self, chemsys, solid_compat="MaterialsProject2020Compat
                 message="You did not provide the required O2 and H2O energies.",
             )
             compat = MaterialsProjectAqueousCompatibility(solid_compat=self.solid_compat)
-        ion_ref_entries = compat.process_entries(ion_ref_entries)
+        # suppress the warning about missing oxidation states
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", message="Failed to guess oxidation states.*")
+            ion_ref_entries = compat.process_entries(ion_ref_entries)
         ion_ref_pd = PhaseDiagram(ion_ref_entries)
 
         # position the ion energies relative to most stable reference state

diff --git a/test_files/pourbaix_test_data.json b/test_files/pourbaix_test_data.json