Fix isotropicunit initialization.

Assign isotropicunit when Lattice is initialized from base vectors.

Author: pavoljuhas

diffpy/Structure/lattice.py

@@ -202,11 +202,7 @@ def setLatPar(self, a=None, b=None, c=None,
         # bases normalized to unit reciprocal vectors
         self.normbase = self.base * [[ar], [br], [cr]]
         self.recnormbase = self.recbase / [ar, br, cr]
-        self.isotropicunit = numpy.dot(self.recnormbase.T, self.recnormbase)
-        # ensure there are no round-off deviations on the diagonal
-        self.isotropicunit[0, 0] = 1
-        self.isotropicunit[1, 1] = 1
-        self.isotropicunit[2, 2] = 1
+        self.isotropicunit = _isotropicunit(self.recnormbase)
         return
 
 
@@ -263,6 +259,7 @@ def setLatBase(self, base):
         # bases normalized to unit reciprocal vectors
         self.normbase = self.base * [[ar], [br], [cr]]
         self.recnormbase = self.recbase / [ar, br, cr]
+        self.isotropicunit = _isotropicunit(self.recnormbase)
         # update metrics tensor
         self.metrics = numpy.array([
                 [ a*a,     a*b*cg,  a*c*cb ],
@@ -482,6 +479,22 @@ def unitvolume(self):
 
 # End of class Lattice
 
+# Local Helper Functions -----------------------------------------------------
+
+def _isotropicunit(recnormbase):
+    """Calculate matrix for unit isotropic displacement parameters.
+
+    recnormbase -- inverse of normalized base vectors of the lattice.
+
+    Return numpy array.
+    """
+    isounit = numpy.dot(recnormbase.T, recnormbase)
+    # ensure there are no round-off deviations on the diagonal
+    isounit[0, 0] = 1
+    isounit[1, 1] = 1
+    isounit[2, 2] = 1
+    return isounit
+
 # Module Constants -----------------------------------------------------------
 
 cartesian = Lattice()

diffpy/Structure/tests/TestLattice.py

@@ -57,8 +57,10 @@ def test___init__(self):
         self.assertTrue(numpy.array_equal(L0.base, L1.base))
         L2 = Lattice(base=L0.base)
         self.assertTrue(numpy.array_equal(L0.base, L2.base))
+        self.assertTrue(numpy.array_equal(L0.isotropicunit, L2.isotropicunit))
         L3 = Lattice(*L0.abcABG(), baserot=L0.baserot)
         self.assertTrue(numpy.allclose(L0.base, L3.base))
+        self.assertTrue(numpy.array_equal(L0.isotropicunit, L3.isotropicunit))
         return