Merge pull request #1229 from RoberTnf/fix-1228

Use TypeError as oxi_state is set to None, not unset
materialsproject · Aug 4, 2018 · 0c989ca · 0c989ca
2 parents 10d92e0 + a7ee771
commit 0c989ca
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Showing 3 changed files with 52 additions and 7 deletions.
diff --git a/pymatgen/command_line/tests/test_enumlib_caller.py b/pymatgen/command_line/tests/test_enumlib_caller.py
@@ -135,7 +135,7 @@ def test_timeout(self):
         a = SpacegroupAnalyzer(s, 0.1)
         s["Al3+"] = {"Al3+": 0.5, "Ga3+": 0.5}
         adaptor = EnumlibAdaptor(s, 1, 1, enum_precision_parameter=0.01,
-                                 timeout=0.0000001)
+                                 timeout=0.0000000000001)
         self.assertRaises(TimeoutError, adaptor._run_multienum)
 
 

diff --git a/pymatgen/io/cif.py b/pymatgen/io/cif.py
@@ -1208,20 +1208,17 @@ def __init__(self, struct, symprec=None, write_magmoms=False):
         loops.append(["_symmetry_equiv_pos_site_id",
                       "_symmetry_equiv_pos_as_xyz"])
 
-        contains_oxidation = True
         try:
             symbol_to_oxinum = OrderedDict([
                 (el.__str__(),
                  float(el.oxi_state))
                 for el in sorted(comp.elements)])
-        except AttributeError:
-            symbol_to_oxinum = OrderedDict([(el.symbol, 0) for el in
-                                            sorted(comp.elements)])
-            contains_oxidation = False
-        if contains_oxidation:
             block["_atom_type_symbol"] = symbol_to_oxinum.keys()
             block["_atom_type_oxidation_number"] = symbol_to_oxinum.values()
             loops.append(["_atom_type_symbol", "_atom_type_oxidation_number"])
+        except (TypeError, AttributeError):
+            symbol_to_oxinum = OrderedDict([(el.symbol, 0) for el in
+                                            sorted(comp.elements)])
 
         atom_site_type_symbol = []
         atom_site_symmetry_multiplicity = []

diff --git a/pymatgen/io/tests/test_cif.py b/pymatgen/io/tests/test_cif.py
@@ -1288,6 +1288,54 @@ def test_write(self):
         self.assertAlmostEqual(list_magmoms[1][0], -5.1234749999999991)
         self.assertAlmostEqual(list_magmoms[1][1], 2.9580396704363183)
 
+        # test creating an structure without oxidation state doesn't raise errors
+        s_manual = Structure(Lattice.cubic(4.2), ["Cs", "Cl"],[[0, 0, 0], [0.5, 0.5, 0.5]])
+        s_manual.add_spin_by_site([1, -1])
+        cw = CifWriter(s_manual, write_magmoms=True)
+
+        # check oxidation state
+        cw_manual_oxi_string = """# generated using pymatgen
+data_CsCl
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.20000000
+_cell_length_b   4.20000000
+_cell_length_c   4.20000000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   CsCl
+_chemical_formula_sum   'Cs1 Cl1'
+_cell_volume   74.08800000
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Cs+  1.0
+  Cl+  1.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cs+  Cs1  1  0.000000  0.000000  0.000000  1
+  Cl+  Cl2  1  0.500000  0.500000  0.500000  1
+loop_
+ _atom_site_moment_label
+ _atom_site_moment_crystalaxis_x
+ _atom_site_moment_crystalaxis_y
+ _atom_site_moment_crystalaxis_z
+"""
+        s_manual.add_oxidation_state_by_site([1,1])
+        cw = CifWriter(s_manual, write_magmoms=True)
+        self.assertEqual(cw.__str__(), cw_manual_oxi_string)
 
     @unittest.skipIf(pybtex is None, "pybtex not present")
     def test_bibtex(self):