def compute_dHKL(self, inplace=False):
"""
Compute the real space lattice plane spacing, d, associated with
the HKL indices in the object.
Parameters
----------
inplace : bool
Whether to add the column in place or return a copy
"""
dHKL = compute_dHKL(self.get_hkls(), self.cell)
self['dHKL'] = rs.DataSeries(dHKL, dtype='R', index=self.index)
return self
def test_generate_reciprocal_cell(cell, dtype):
"""Test rs.utils.generate_reciprocal_cell"""
dmin = 5.0
hkl = generate_reciprocal_cell(cell, dmin, dtype)
assert hkl.dtype == dtype
# Check that reflection 0,0,0 is omitted
assert np.all(np.any(hkl != 0, axis=1))
assert len(hkl) > 0
assert len(np.unique(hkl, axis=0)) == len(hkl)
assert compute_dHKL(hkl, cell).min() >= dmin
assert cell.calculate_d_array(hkl).min() >= dmin
def test_compute_dHKL(dataset_hkl, cell):
"""Test rs.utils.compute_dHKL()"""
hmax = 10
H = np.mgrid[-hmax:hmax + 1:1, -hmax:hmax + 1:1, -hmax:hmax + 1:1].reshape(
(3, -1)).T
H = H[~np.all(H == 0, axis=1)] #Remove 0,0,0
result = compute_dHKL(H, cell)
# Compare to gemmi result
expected = np.zeros(len(result), dtype=np.float32)
for i, h in enumerate(H):
expected[i] = cell.calculate_d(h)
assert np.allclose(result, expected)
assert np.all(np.isfinite(result))