def fromHDF5(cls, store, dataset):
from CDTK.SpaceGroups import space_groups
from CDTK.Crystal import UnitCell
space_group = space_groups[dataset.attrs['space_group']]
cell = UnitCell(dataset.attrs['a'],
dataset.attrs['b'],
dataset.attrs['c'],
dataset.attrs['alpha'],
dataset.attrs['beta'],
dataset.attrs['gamma'])
self = cls(ReflectionSet(cell, space_group))
self._reflections = dataset[...]
try:
self._absences = dataset.attrs['systematic_absences']
except KeyError:
self._absences = np.zeros((0,), dtype=self._dtype)
r1, r2, r3 = cell.reciprocalBasisVectors()
sv = self._reflections['h'][:, np.newaxis]*r1.array + \
self._reflections['k'][:, np.newaxis]*r2.array + \
self._reflections['l'][:, np.newaxis]*r3.array
sva = self._absences['h'][:, np.newaxis]*r1.array + \
self._absences['k'][:, np.newaxis]*r2.array + \
self._absences['l'][:, np.newaxis]*r3.array
s = np.concatenate([np.sqrt(np.sum(sv**2, axis=1)),
np.sqrt(np.sum(sva**2, axis=1))])
self.s_min = s.min()
self.s_max = s.max()
return self
def test_geometry(self):
for params, rb, sg in datasets:
cell1 = UnitCell(*params)
basis = cell1.basisVectors()
reciprocal_basis = cell1.reciprocalBasisVectors()
for i in range(3):
self.assert_((reciprocal_basis[i]-rb[i]).length()
< 1.e-6)
for i in range(3):
for j in range(3):
p = basis[i]*reciprocal_basis[j]
if i == j:
self.assertAlmostEqual(p, 1., 10)
else:
self.assertAlmostEqual(p, 0., 10)
cell2 = UnitCell(*tuple(basis))
self.assertAlmostEqual(cell1.a, cell2.a, 5)
self.assertAlmostEqual(cell1.b, cell2.b, 5)
self.assertAlmostEqual(cell1.c, cell2.c, 5)
self.assertAlmostEqual(cell1.alpha, cell2.alpha, 5)
self.assertAlmostEqual(cell1.beta, cell2.beta, 5)
self.assertAlmostEqual(cell1.gamma, cell2.gamma, 5)