Merge pull request #251 from simphony/fix-nan-value-for-primitive-cell

ValueError if the angle(s) for rhombohedral/triclinic are too big

simphony/cuds/primitive_cell.py

@@ -189,11 +189,16 @@ def for_rhombohedral_lattice(cls, a, alpha):
 
         cosa = np.cos(alpha)
         sina = np.sin(alpha)
+        delta2 = sina**2 - ((cosa-cosa**2) / sina)**2
+        if delta2 < 0:
+            message = ('Angle is too big (>120 degree). '
+                       'Third vector is imaginary')
+            raise ValueError(message)
 
         p1 = (a, 0, 0)
         p2 = (a*cosa, a*sina, 0)
         p3 = (a*cosa, a*(cosa-cosa**2) / sina,
-              a*np.sqrt(sina**2 - ((cosa-cosa**2) / sina)**2))
+              a*np.sqrt(delta2))
         return cls(p1, p2, p3, BravaisLattice.RHOMBOHEDRAL)
 
     @classmethod
@@ -493,11 +498,15 @@ def for_triclinic_lattice(cls, a, b, c, alpha, beta, gamma):
         sinb = np.sin(beta)
         cosg = np.cos(gamma)
         sing = np.sin(gamma)
+        delta2 = sinb**2 - ((cosa-cosb*cosg) / sing)**2
+        if delta2 < 0:
+            message = "Angles are too big.  Third vector is imaginary"
+            raise ValueError(message)
 
         p1 = (a, 0, 0)
         p2 = (b*cosg, b*sing, 0)
         p3 = (c*cosb, c*(cosa-cosb*cosg) / sing,
-              c*np.sqrt(sinb**2 - ((cosa-cosb*cosg) / sing)**2))
+              c*np.sqrt(delta2))
         return cls(p1, p2, p3, BravaisLattice.TRICLINIC)
 
     @property

simphony/cuds/tests/test_primitive_cell.py

@@ -71,6 +71,10 @@ def test_primitive_cell_for_rhombohedral_lattice(self):
         with self.assertRaises(ValueError):
             PrimitiveCell.for_rhombohedral_lattice(1, np.pi)
 
+        with self.assertRaises(ValueError):
+            # angle too big
+            PrimitiveCell.for_rhombohedral_lattice(1, np.pi*2./3.+0.1)
+
         cosa = np.cos(self.alpha)
         sina = np.sin(self.alpha)
 
@@ -225,6 +229,10 @@ def test_primitive_cell_for_triclinic_lattice(self):
         with self.assertRaises(ValueError):
             PrimitiveCell.for_triclinic_lattice(1, 2, 3, 0.1, 0.2, 0.8)
 
+        with self.assertRaises(ValueError):
+            # angles too big
+            PrimitiveCell.for_triclinic_lattice(1, 2, 3, 2.1, 2.1, 2.1)
+
         cosa = np.cos(self.alpha)
         cosb = np.cos(self.beta)
         sinb = np.sin(self.beta)