def test_getAtoms_aniso_u_orthogonal(self):
uElements = {
'11': [u'0.01', u'0.02'],
'12': [u'0.0', u'0.0'],
'13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'],
'33': [u'0.04', u'0.05']
}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value)
for key, value in iteritems(uElements)])
uDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
# u_equiv should be (0.01 + 0.01 + 0.04)/3 = 0.02 and (0.2 + 0.2 + 0.5)/3 = 0.03
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.02;Al 0.34 0.56 0.23 1.0 0.03')
def test_find_bases_with_non_orthogonal_cell(self):
cell = UnitCell(1, 1, 1, 90, 95, 103)
cart_cell = cell.getB()
qs = np.array([
[.5, 0, 0],
[0, .5, 0],
[0, 0, .5],
[0, 0, .25],
])
qs = np.dot(qs, cart_cell)
ndim, bases = indexing.find_bases(qs, 1e-5)
self.assertEqual(ndim, 3, "Number of dimensions must be 3")
expected_bases = np.array([
[0., 0., 0.25],
[0., .5, 0.],
[0.51521732, 0.11589868, 0.04490415]
])
npt.assert_almost_equal(bases, expected_bases, err_msg="Basis vectors do not match")
def test_find_indexing_with_non_orthogonal_cell(self):
cell = UnitCell(1, 1, 1, 90, 95, 103)
cart_cell = cell.getB()
qs = np.array([
[.5, 0, 0],
[0, .5, 0],
[0, 0, .5],
[0, 0, .25],
])
qs = np.dot(qs, cart_cell)
indices = indexing.index_q_vectors(qs)
expected_indexing = np.array([
[0, 0, 1],
[0, 1, 0],
[2, 0, 0],
[1, 0, 0]
])
npt.assert_equal(indices, expected_indexing, err_msg="Indexing does not match expected.")
def test_getAtoms_iso_preferred(self):
uElements = {
'11': [u'0.01', u'0.02'],
'12': [u'0.0', u'0.0'],
'13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'],
'33': [u'0.04', u'0.05']
}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value)
for key, value in uElements.items()])
uDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_aniso_b_orthogonal(self):
bElements = {
'11': [u'1.0', u'2.0'],
'12': [u'0.0', u'0.0'],
'13': [u'0.0', u'0.0'],
'22': [u'1.0', u'2.0'],
'23': [u'0.0', u'0.0'],
'33': [u'4.0', u'5.0']
}
bDict = dict([(u'_atom_site_aniso_b_{0}'.format(key), value)
for key, value in bElements.items()])
bDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])]))
data = self._getData(bDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(
self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.02533;Al 0.34 0.56 0.23 1.0 0.038')
def test_setMaxOrder_accepts_int(self):
unit = UnitCell(3, 3, 3)
unit.setMaxOrder(2)
self.assertEquals(2, unit.getMaxOrder())
def test_getMaxOrder_returns_int(self):
unit = UnitCell(3, 3, 3)
self.assertTrue(isinstance(unit.getMaxOrder(), int))
def test_getModVec_returns_v3d(self):
unit = UnitCell(3, 3, 3)
self.assertTrue(isinstance(unit.getModVec(0), V3D))
self.assertTrue(isinstance(unit.getModVec(1), V3D))
self.assertTrue(isinstance(unit.getModVec(2), V3D))
