Fix PhonopyAtoms for yaml text output in case of mass undefined.

phonopy/structure/atoms.py

@@ -260,12 +260,17 @@ class PhonopyAtoms(Atoms):
             lines.append("- [ %21.15f, %21.15f, %21.15f ] # %s" %
                          (v[0], v[1], v[2], a))
         lines.append("points:")
+        if self.masses is None:
+            masses = [None] * len(self.symbols)
+        else:
+            masses = self.masses
         for i, (s, v, m) in enumerate(
-                zip(self.symbols, self.scaled_positions, self.masses)):
+                zip(self.symbols, self.scaled_positions, masses)):
             lines.append("- symbol: %-2s # %d" % (s, i + 1))
             lines.append("  coordinates: [ %18.15f, %18.15f, %18.15f ]" %
                          tuple(v))
-            lines.append("  mass: %f" % m)
+            if m is not None:
+                lines.append("  mass: %f" % m)
         return lines
 
     def __str__(self):

test/phonopy/structure/test_atoms.py

@@ -15,22 +15,31 @@ class TestCell(unittest.TestCase):
                   [0.7, 0.7, 0.0],
                   [0.2, 0.8, 0.5],
                   [0.8, 0.2, 0.5]]
-        
-        self._cell = Atoms(cell=lattice,
-                           scaled_positions=points,
-                           symbols=symbols)
+
+        self._cells = []
+        self._cells.append(Atoms(cell=lattice,
+                                 scaled_positions=points,
+                                 symbols=symbols))
+
+        # The element for which mass is not defined.
+        symbols = ['Ac'] * 2 + ['O'] * 4
+        self._cells.append(Atoms(cell=lattice,
+                                 scaled_positions=points,
+                                 symbols=symbols))
     
     def tearDown(self):
         pass
     
     def test_atoms(self):
-        print(self._cell.get_cell())
-        for s, p in zip(self._cell.get_chemical_symbols(),
-                        self._cell.get_scaled_positions()):
-            print("%s %s" % (s, p))
+        for cell in self._cells:
+            print(cell.get_cell())
+            for s, p in zip(cell.get_chemical_symbols(),
+                            cell.get_scaled_positions()):
+                print("%s %s" % (s, p))
 
     def test_phonopy_atoms(self):
-        print(PhonopyAtoms(atoms=self._cell))
+        for cell in self._cells:
+            print(PhonopyAtoms(atoms=cell))
 
 if __name__ == '__main__':
     unittest.main()